~ubuntu-branches/ubuntu/maverick/cdk/maverick

<xsd:schema targetNamespace="http://www.xml-cml.org/schema" xmlns:h="http://www.w3.org/1999/xhtml" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="http://www.xml-cml.org/schema"><xsd:simpleType id="st.actionOrderType" name="actionOrderType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">Describes whether child elements are sequential or parallel.</h:div>

<h:div class="description">There is no default.</h:div>

</xsd:documentation>

</xsd:annotation>

<xsd:restriction base="xsd:string">

<xsd:enumeration value="sequential"/>

<xsd:enumeration value="parallel"/>

</xsd:restriction>

</xsd:simpleType><xsd:simpleType id="st.alternativeTypeType" name="alternativeTypeType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">The type of an alternative.</h:div>

<h:div class="general">This adds semantics to an _alternative_ and might be used by an RDF or related engine.</h:div>

</xsd:documentation>

</xsd:annotation>

<xsd:union>

<xsd:simpleType>

<xsd:restriction base="xsd:string">

<xsd:enumeration value="synonym"/>

<xsd:enumeration value="quasi-synonym"/>

<xsd:enumeration value="acronym"/>

<xsd:enumeration value="abbreviation"/>

<xsd:enumeration value="homonym"/>

<xsd:enumeration value="identifier"/>

</xsd:restriction>

</xsd:simpleType>

<xsd:simpleType>

<xsd:restriction base="namespaceRefType"/>

</xsd:simpleType>

</xsd:union>

</xsd:simpleType><xsd:simpleType name="angleUnitsType" id="st.angleUnitsType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">An enumeration of allowed angle units.</h:div>

<h:div class="description">May be obsolete.</h:div>

<!--

<h:div class="example">

<h:pre>

</pre.</h:div>

-->

</xsd:documentation>

</xsd:annotation>

<xsd:restriction base="xsd:string">

<xsd:enumeration value="degrees"/>

<xsd:enumeration value="radians"/>

</xsd:restriction>

</xsd:simpleType><xsd:simpleType name="atomIDType" id="st.atomIDType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">An identifier for an atom.</h:div>

<h:div class="description">

<h:p>Of the form prefix:suffix where prefix and suffix

are purely alphanumeric (with _ and -) and prefix

is optional. This is similar to XML IDs (and we promote

this as good practice for atomIDs. Other punctuation and

whitespace is forbidden, so IDs from (say) PDB files are

not satisfactory.</h:p>

<h:p>The prefix is intended to form a pseudo-namespace so that

atom IDs in different molecules may have identical suffixes.

It is also useful if the prefix is the ID for the molecule

(though this clearly has its limitation). Atom IDs should not

be typed as XML IDs since they may not validate.</h:p></h:div>

<h:div class="example" href="atomIDType1.xml"/>

</xsd:documentation>

<xsd:appinfo/>

</xsd:annotation>

<xsd:restriction base="xsd:string">

<xsd:pattern value="[A-Za-z_][A-Za-z0-9_\-]*(:[A-Za-z0-9_\-]+)?"/>

</xsd:restriction>

</xsd:simpleType><xsd:simpleType name="atomRefArrayType" id="st.atomRefArrayType">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">An array of atomRefs.</h:div>

<h:div class="description">The atomRefs

cannot be schema- or schematron-validated. Instances of this type will

be used in array-style representation of bonds and atomParitys.

It can also be used for arrays of atomIDTypes such as in complex stereochemistry,

geometrical definitions, atom groupings, etc.</h:div>

<h:div class="example" href="atomRefArrayType1.xml"/>

</xsd:documentation>

<xsd:appinfo/>

</xsd:annotation>

<xsd:list itemType="atomIDType"/>

</xsd:simpleType><xsd:simpleType name="atomRefs2Type" id="st.atomRefs2Type">

<xsd:annotation>

<xsd:documentation>

<h:div class="summary">A reference to two distinct existing atoms in order.</h:div>

<h:div class="example" href="atomRefs21.xml"/>

</xsd:documentation>

</xsd:annotation>

<xsd:restriction>

<xsd:simpleType>

<xsd:list itemType="atomIDType"/>

</xsd:simpleType>

<xsd:length value="2"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="atomRefs3Type" id="st.atomRefs3Type">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">A reference to three distinct existing atoms in order.</h:div>

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<h:div class="example" href="atomRefs31.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction>

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<xsd:simpleType>

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<xsd:list itemType="atomIDType"/>

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</xsd:simpleType>

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<xsd:length value="3"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="atomRefs4Type" id="st.atomRefs4Type">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">A reference to four distinct existing atoms in order.</h:div>

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<h:div class="example" href="atomRefs41.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction>

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<xsd:simpleType>

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<xsd:list itemType="atomIDType"/>

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</xsd:simpleType>

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<xsd:length value="4"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="atomRefType" id="st.atomRefType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">A reference to an existing atom.</h:div>

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<h:div class="example" href="atomRefType1.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction base="atomIDType"/>

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</xsd:simpleType><xsd:simpleType name="bondRefArrayType" id="st.bondRefArrayType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">An array of references to bonds.</h:div>

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<h:div class="description">The references cannot (yet)

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cannot be schema- or schematron-validated. Instances of this type will

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be used in array-style representation of electron counts, etc.

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It can also be used for arrays of bondIDTypes such as in complex stereochemistry,

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geometrical definitions, bond groupings, etc.</h:div>

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</xsd:documentation>

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<xsd:appinfo/>

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</xsd:annotation>

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<xsd:list itemType="bondRefType"/>

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</xsd:simpleType><xsd:simpleType name="bondRefType" id="st.bondRefType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">A reference to an existing bond.</h:div>

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<h:div class="general">A reference to a bond may be made by atoms (e.g. for multicentre or pi-bonds), electrons (for annotating reactions or describing electronic properties) or possibly other bonds (no examples yet). The semantics are relatively flexible.</h:div>

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<h:div class="example" href="bond1.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction base="xsd:string">

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<xsd:pattern value="[A-Za-z0-9_\-]+(:[A-Za-z0-9_\-]+)?"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="box3Type" id="st.box3Type">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">A box in 3-space.</h:div>

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<h:div class="description">Defined by 6 real numbers

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(x1 y1 z1 x2 y2 z2). By default these are Cartesian coordinates (with units

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specified elsewhere - responsibility of schema creator.) If there is a means

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of specifying oblique axes (e.g. crystallographic cell) the box may be a

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parallelipiped. The components are grouped in threes ans separated by a semicolon

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to avoid problems of guessing the convention.</h:div>

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<h:div class="example" href="box31.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction>

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<xsd:simpleType>

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<xsd:list itemType="xsd:double"/>

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</xsd:simpleType>

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<xsd:length value="6"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="chiralityType" id="st.chiralityType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">The chirality of a system or molecule.</h:div>

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<h:div class="description">This is being actively investigated by a IUPAC committee (2002) so the convention is likely to change. No formal default.</h:div>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction base="xsd:string">

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<xsd:enumeration value="enantiomer"/>

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<xsd:enumeration value="racemate"/>

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<xsd:enumeration value="unknown"/>

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<xsd:enumeration value="other"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="complexType" id="st.complexType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">A pair of floats representing a complex number.</h:div>

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<h:div class="example" href="complex1.xml"/>

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<h:div class="example" href="complex.bad.xml">

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<h:p>This example is schema-invalid as it has three floats</h:p></h:div>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction>

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<xsd:simpleType>

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<xsd:list itemType="xsd:double"/>

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</xsd:simpleType>

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<xsd:length value="2"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="coordinate2Type" id="st.coordinate2Type">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">An x/y coordinate pair.</h:div>

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<h:div class="description">An x/y coordinate pair consisting of

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two real numbers, separated by whitespace or a comma.

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In arrays and matrices, it may be useful to set a separate delimiter</h:div>

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<h:div class="example" href="coordinate2Type1.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction>

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<xsd:simpleType>

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<xsd:list itemType="xsd:double"/>

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</xsd:simpleType>

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<xsd:length value="2"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="coordinate3Type" id="st.coordinate3Type">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">An x/y/z coordinate triple.</h:div>

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<h:div class="description">An x/y/z coordinate triple consisting of three real

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numbers, separated by whitespace or commas. In arrays and matrices, it may be

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useful to set a separate delimiter.</h:div>

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<h:div class="example" href="coordinate3Type1.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction>

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<xsd:simpleType>

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<xsd:list itemType="xsd:double"/>

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</xsd:simpleType>

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<xsd:length value="3"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="coordinateComponentArrayType" id="st.coordinateComponentArrayType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">An array of coordinateComponents for a single coordinate.</h:div>

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<h:div class="description">An array of coordinateComponents for a single coordinate

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where these all refer to an X-coordinate (NOT x,y,z).Instances of this type will be

245

used in array-style representation of 2-D or 3-D coordinates. Currently no machine

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validation. Currently not used in STMML, but re-used by CML (see example).</h:div>

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<h:div class="example" href="coordinateComponentArrayType1.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:list itemType="xsd:double"/>

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</xsd:simpleType><xsd:simpleType name="countArrayType" id="st.countArrayType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">Array of counts.</h:div>

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<h:div class="description">Normally, but not always, integers. can be used with a number of elements</h:div>

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<h:div class="curation">2005-11-01: PMR the combination of dataType and list does not work

257

with JUMBO5.0 - so for the meantime we have removed the restriction</h:div>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:list itemType="xsd:double"/>

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<!-- removed by PMR

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<xsd:restriction base="xsd:double">

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<xsd:minExclusive value="0.0"/>

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<xsd:maxInclusive value="1.0E+99"/>

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</xsd:restriction>

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-->

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</xsd:simpleType><xsd:simpleType name="countType" id="st.countType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">A count multiplier for an object.</h:div>

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<h:div class="description">Many elements represent objects which can occur an arbitrary number of times in a scientific context. Examples are <h:tt>action</h:tt>, <h:tt>object</h:tt> or <h:tt>molecule</h:tt>s.</h:div>

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<h:div class="curation">2005-10-16. Changed to positiveNumerType.</h:div>

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<h:div class="example" href="countType1.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction base="positiveNumberType"/>

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</xsd:simpleType><xsd:simpleType name="dataTypeType" id="st.dataTypeType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">an enumerated type for all dataTypes in STM.</h:div>

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<h:div class="description">

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<h:p>

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<h:tt>dataTypeType</h:tt> represents an enumeration of allowed dataTypes

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(at present identical with those in XML-Schemas (Part2- datatypes).

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This means that implementers should be able to use standard XMLSchema-based

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tools for validation without major implementation problems.

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</h:p>

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<h:p>It will often be used an an attribute on

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<h:a href="el.scalar">scalar</h:a>,

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<h:a href="el.array">array</h:a> or

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<h:a href="el.matrix">matrix</h:a>

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elements.</h:p></h:div>

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<h:div class="description">Note: the attribute xsi:type might be used to enforce the type-checking but I haven't worked this through yet.</h:div>

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<h:div class="example" href="dataTypeType1.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:union>

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<xsd:simpleType>

301

<xsd:restriction base="xsd:string">

302

<xsd:enumeration value="xsd:string"/>

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<xsd:enumeration value="xsd:boolean"/>

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<xsd:enumeration value="xsd:float"/>

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<xsd:enumeration value="xsd:double"/>

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<xsd:enumeration value="xsd:decimal"/>

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<xsd:enumeration value="xsd:duration"/>

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<xsd:enumeration value="xsd:dateTime"/>

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<xsd:enumeration value="xsd:time"/>

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<xsd:enumeration value="xsd:date"/>

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<xsd:enumeration value="xsd:gYearMonth"/>

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<xsd:enumeration value="xsd:gYear"/>

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<xsd:enumeration value="xsd:gMonthDay"/>

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<xsd:enumeration value="xsd:gDay"/>

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<xsd:enumeration value="xsd:gMonth"/>

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<xsd:enumeration value="xsd:hexBinary"/>

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<xsd:enumeration value="xsd:base64Binary"/>

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<xsd:enumeration value="xsd:anyURI"/>

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<xsd:enumeration value="xsd:QName"/>

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<xsd:enumeration value="xsd:NOTATION"/>

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<xsd:enumeration value="xsd:normalizedString"/>

322

<xsd:enumeration value="xsd:token"/>

323

<xsd:enumeration value="xsd:language"/>

324

<xsd:enumeration value="xsd:IDREFS"/>

325

<xsd:enumeration value="xsd:ENTITIES"/>

326

<xsd:enumeration value="xsd:NMTOKEN"/>

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<xsd:enumeration value="xsd:NMTOKENS"/>

328

<xsd:enumeration value="xsd:Name"/>

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<xsd:enumeration value="xsd:NCName"/>

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<xsd:enumeration value="xsd:ID"/>

331

<xsd:enumeration value="xsd:IDREF"/>

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<xsd:enumeration value="xsd:ENTITY"/>

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<xsd:enumeration value="xsd:integer"/>

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<xsd:enumeration value="xsd:nonPositiveInteger"/>

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<xsd:enumeration value="xsd:negativeInteger"/>

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<xsd:enumeration value="xsd:long"/>

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<xsd:enumeration value="xsd:int"/>

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<xsd:enumeration value="xsd:short"/>

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<xsd:enumeration value="xsd:byte"/>

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<xsd:enumeration value="xsd:nonNegativeInteger"/>

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<xsd:enumeration value="xsd:unsignedLong"/>

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<xsd:enumeration value="xsd:unsignedInt"/>

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<xsd:enumeration value="xsd:unsignedShort"/>

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<xsd:enumeration value="xsd:unsignedByte"/>

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<xsd:enumeration value="xsd:positiveInteger"/>

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<xsd:enumeration value="dataTypeType"/>

348

<xsd:enumeration value="namespaceRefType"/>

349

<xsd:enumeration value="unitsType"/>

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</xsd:restriction>

351

</xsd:simpleType>

352

<xsd:simpleType>

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<xsd:restriction base="namespaceRefType"/>

354

</xsd:simpleType>

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</xsd:union>

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</xsd:simpleType><xsd:simpleType name="delimiterType" id="st.delimiterType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">A single non-whitespace character to separate components in arrays.</h:div>

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<h:div class="description">

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<h:p>Some STMML elements (such as <h:a href="el.array">array</h:a>) have

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content representing concatenated values. The default separator is

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whitespace (which can be normalised) and this should be used whenever

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possible. However in some cases the values are empty, or contain whitespace or other

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problematic punctuation, and a delimiter is required.</h:p>

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<h:p>Note that the content string MUST start and end with the delimiter so

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there is no ambiguity as to what the components are. Only printable

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characters from the ASCII character set should be used, and character

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entities should be avoided.</h:p>

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<h:p>When delimiters are used to separate precise whitespace this should always

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consist of spaces and not the other allowed whitespace characters

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(newline, tabs, etc.). If the latter are important it is probably best to redesign

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the application.</h:p>

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<h:p>At present there is a controlled pattern of characters selected so as not to collide with common usage in XML document</h:p></h:div>

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<h:div class="example" href="delimiterType1.xml">

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<h:em>The values in the array are</h:em>

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"A", "B12", "" (empty string) and "D and E"

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<h:em>note the spaces</h:em></h:div>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction base="xsd:string">

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<xsd:pattern value="[!%\^\*@~;#,|/]"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="dictionaryPrefixType" id="st.dictionaryPrefixType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">A dictionaryPrefix</h:div>

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<h:div class="description">

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<h:p>used to identify a dictionary, units, convention or other metadata.

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</h:p>

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</h:div>

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<h:div class="curation">2005-12-12: PMR. Added for use with dictionary</h:div>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction base="xsd:string">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="description">

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<h:p>The dictionary prefix must conform to XSD.</h:p>

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</h:div>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:pattern value="[A-Za-z][A-Za-z0-9_\.\-]*"/>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="dimensionType" id="st.dimensionType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">Allowed values for dimension Types in quantities.</h:div>

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<h:div class="description">

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<h:p>These are the 7 types prescribed by the SI system, together

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with the "dimensionless" type. We intend to be somewhat uncoventional

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and explore enhanced values of "dimensionless", such as "angle".

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This may be heretical, but we find the present system impossible to implement

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in many cases.</h:p>

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<h:p>Used for constructing entries in a dictionary of units</h:p></h:div>

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<h:div class="example" href="dimensionType1.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:restriction base="xsd:string">

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<xsd:enumeration value="mass"/>

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<xsd:enumeration value="length"/>

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<xsd:enumeration value="time"/>

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<xsd:enumeration value="current"/>

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<xsd:enumeration value="amount"/>

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<xsd:enumeration value="luminosity"/>

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<xsd:enumeration value="temperature"/>

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<xsd:enumeration value="dimensionless"/>

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<xsd:enumeration value="angle">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">An angl.</h:div>

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<h:div class="description">(formally dimensionless, but useful to have units).</h:div>

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</xsd:documentation>

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</xsd:annotation>

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</xsd:enumeration>

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</xsd:restriction>

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</xsd:simpleType><xsd:simpleType name="eigenOrientationType" id="st.eigenOrientationType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">Orientation of the eigenvector matrix.</h:div>

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<h:div class="description">

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<h:p>Specifies whether the rows or columns of the (square) matrix

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correspond to the eigenvectors. For example, in molecular orbitals

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the vectors are normally represented as columns, and each column

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would correspond to a different eigenvalue</h:p>

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</h:div>

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<h:div class="curation">2006-01-13: PMR. Created.</h:div>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:union>

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<xsd:simpleType>

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<xsd:restriction base="xsd:string">

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<xsd:enumeration value="columnVectors">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">The columns are the eigenvectors.</h:div>

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</xsd:documentation>

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</xsd:annotation>

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</xsd:enumeration>

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<xsd:enumeration value="rowVectors">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">The columns are the eigenvectors.</h:div>

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</xsd:documentation>

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</xsd:annotation>

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</xsd:enumeration>

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</xsd:restriction>

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</xsd:simpleType>

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<xsd:simpleType>

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<xsd:restriction base="namespaceRefType"/>

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</xsd:simpleType>

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</xsd:union>

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</xsd:simpleType><xsd:simpleType name="elementTypeArrayType" id="st.elementTypeArrayType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">An array of elementTypes.</h:div>

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<h:div class="description">Instances of this type will be used in array-style representation of atoms.</h:div>

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<h:div class="example" href="elementTypeArrayType1.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:list itemType="elementTypeType"/>

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</xsd:simpleType><xsd:simpleType name="elementTypeType" id="st.elementTypeType">

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<xsd:annotation>

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<xsd:documentation>

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<h:div class="summary">Allowed elementType values.</h:div>

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<h:div class="description">

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<h:p>The periodic table (up to

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element number 118. In addition the following strings are allowed:

495

<h:ul>

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<h:li><h:tt>Du</h:tt>. ("dummy") This does not correspond to a "real" atom and can

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support a point in space or within a chemical graph.</h:li>

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<h:li>

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<h:tt>R</h:tt>. ("R-group") This indicates that an atom or group of atoms could be attached at this point. </h:li>

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</h:ul>

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</h:p></h:div>

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<h:div class="example" href="elementTypeType1.xml"/>

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</xsd:documentation>

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</xsd:annotation>

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<xsd:union>

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<xsd:simpleType>

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<xsd:restriction base="xsd:string">

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<xsd:enumeration value="Ac"/>

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<xsd:enumeration value="Al"/>

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<xsd:enumeration value="Ag"/>

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<xsd:enumeration value="Am"/>

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<xsd:enumeration value="Ar"/>

513

<xsd:enumeration value="As"/>

514

<xsd:enumeration value="At"/>

515

<xsd:enumeration value="Au"/>

516

<xsd:enumeration value="B"/>

517

<xsd:enumeration value="Ba"/>

518

<xsd:enumeration value="Bh"/>

519

<xsd:enumeration value="Bi"/>

520

<xsd:enumeration value="Be"/>

521

<xsd:enumeration value="Bk"/>

522

<xsd:enumeration value="Br"/>

523

<xsd:enumeration value="C"/>

524

<xsd:enumeration value="Ca"/>

525

<xsd:enumeration value="Cd"/>

526

<xsd:enumeration value="Ce"/>

527

<xsd:enumeration value="Cf"/>

528

<xsd:enumeration value="Cl"/>

529

<xsd:enumeration value="Cm"/>

530

<xsd:enumeration value="Co"/>

531

<xsd:enumeration value="Cr"/>

532

<xsd:enumeration value="Cs"/>

533

<xsd:enumeration value="Cu"/>

534

<xsd:enumeration value="Db"/>

535

<xsd:enumeration value="Dy"/>

536

<xsd:enumeration value="Er"/>

537

<xsd:enumeration value="Es"/>

538

<xsd:enumeration value="Eu"/>

539

<xsd:enumeration value="F"/>

540

<xsd:enumeration value="Fe"/>

541

<xsd:enumeration value="Fm"/>

542

<xsd:enumeration value="Fr"/>

543

<xsd:enumeration value="Ga"/>

544

<xsd:enumeration value="Gd"/>

545

<xsd:enumeration value="Ge"/>

546

<xsd:enumeration value="H">

547

<xsd:annotation>

548

<xsd:documentation>

549

<h:div class="summary">Any isotope of hydrogen.</h:div>

550

<h:div class="description">

551

<h:p>There are no special element symbols for D and T which should use the <h:tt>isotope</h:tt> attribute. </h:p></h:div>

552

</xsd:documentation>

553

</xsd:annotation>

554

</xsd:enumeration>

555

<xsd:enumeration value="He"/>

556

<xsd:enumeration value="Hf"/>

557

<xsd:enumeration value="Hg"/>

558

<xsd:enumeration value="Ho"/>

559

<xsd:enumeration value="Hs"/>

560

<xsd:enumeration value="I"/>

561

<xsd:enumeration value="In"/>

562

<xsd:enumeration value="Ir"/>

563

<xsd:enumeration value="K"/>

564

<xsd:enumeration value="Kr"/>

565

<xsd:enumeration value="La"/>

566

<xsd:enumeration value="Li"/>

567

<xsd:enumeration value="Lr"/>

568

<xsd:enumeration value="Lu"/>

569

<xsd:enumeration value="Md"/>

570

<xsd:enumeration value="Mg"/>

571

<xsd:enumeration value="Mn"/>

572

<xsd:enumeration value="Mo"/>

573

<xsd:enumeration value="Mt"/>

574

<xsd:enumeration value="N"/>

575

<xsd:enumeration value="Na"/>

576

<xsd:enumeration value="Nb"/>

577

<xsd:enumeration value="Nd"/>

578

<xsd:enumeration value="Ne"/>

579

<xsd:enumeration value="Ni"/>

580

<xsd:enumeration value="No"/>

581

<xsd:enumeration value="Np"/>

582

<xsd:enumeration value="O"/>

583

<xsd:enumeration value="Os"/>

584

<xsd:enumeration value="P"/>

585

<xsd:enumeration value="Pa"/>

586

<xsd:enumeration value="Pb"/>

587

<xsd:enumeration value="Pd"/>

588

<xsd:enumeration value="Pm"/>

589

<xsd:enumeration value="Po"/>

590

<xsd:enumeration value="Pr"/>

591

<xsd:enumeration value="Pt"/>

592

<xsd:enumeration value="Pu"/>

593

<xsd:enumeration value="Ra"/>

594

<xsd:enumeration value="Rb"/>

595

<xsd:enumeration value="Re"/>

596

<xsd:enumeration value="Rf"/>

597

<xsd:enumeration value="Rh"/>

598

<xsd:enumeration value="Rn"/>

599

<xsd:enumeration value="Ru"/>

600

<xsd:enumeration value="S"/>

601

<xsd:enumeration value="Sb"/>

602

<xsd:enumeration value="Sc"/>

603

<xsd:enumeration value="Se"/>

604

<xsd:enumeration value="Sg"/>

605

<xsd:enumeration value="Si"/>

606

<xsd:enumeration value="Sm"/>

607

<xsd:enumeration value="Sn"/>

608

<xsd:enumeration value="Sr"/>

609

<xsd:enumeration value="Ta"/>

610

<xsd:enumeration value="Tb"/>

611

<xsd:enumeration value="Tc"/>

612

<xsd:enumeration value="Te"/>

613

<xsd:enumeration value="Th"/>

614

<xsd:enumeration value="Ti"/>

615

<xsd:enumeration value="Tl"/>

616

<xsd:enumeration value="Tm"/>

617

<xsd:enumeration value="U"/>

618

<xsd:enumeration value="Uun"/>

619

<xsd:enumeration value="Uuu"/>

620

<xsd:enumeration value="Uub"/>

621

<xsd:enumeration value="Uut"/>

622

<xsd:enumeration value="Uuq"/>

623

<xsd:enumeration value="Uup"/>

624

<xsd:enumeration value="Uuh"/>

625

<xsd:enumeration value="Uus"/>

626

<xsd:enumeration value="Uuo"/>

627

<xsd:enumeration value="V"/>

628

<xsd:enumeration value="W"/>

629

<xsd:enumeration value="Xe"/>

630

<xsd:enumeration value="Y"/>

631

<xsd:enumeration value="Yb"/>

632

<xsd:enumeration value="Zn"/>

633

<xsd:enumeration value="Zr"/>

634

635

<xsd:enumeration value="Dummy"/>

636

<xsd:enumeration value="Du">

637

<xsd:annotation>

638

<xsd:documentation>

639

<h:div class="summary">A point or object with no chemical semantics.</h:div>

640

<h:div class="description">

641

<h:p>Examples can be centroids, bond-midpoints, orienting "atoms" in small z-matrices. </h:p>

642

<h:p>Note "Dummy" has the same semantics but is now deprecated.</h:p></h:div>

643

</xsd:documentation>

644

</xsd:annotation>

645

</xsd:enumeration>

646

647

<xsd:enumeration value="R">

648

<xsd:annotation>

649

<xsd:documentation>

650

651

<h:div class="summary">A point at which an atom or group might be attached.</h:div>

652

<h:div class="description">

653

<h:p>Examples are abbreviated organic functional groups, Markush representations, polymers, unknown atoms, etc. Semantics may be determined by the <h:tt>role</h:tt> attribute on the atom. </h:p></h:div>

654

</xsd:documentation>

655

</xsd:annotation>

656

</xsd:enumeration>

657

658

</xsd:restriction>

659

</xsd:simpleType>

660

<xsd:simpleType>

661

<xsd:restriction base="xsd:string">

662

<xsd:pattern value="[A-Za-z]+:[A-Za-z][A-Za-z0-9\-]+"/>

663

</xsd:restriction>

664

</xsd:simpleType>

665

</xsd:union>

666

</xsd:simpleType><xsd:simpleType name="errorBasisType" id="st.errorBasisType">

667

<xsd:annotation>

668

<xsd:documentation>

669

<h:div class="summary">The basis of an error value.</h:div>

670

<h:div class="description">Errors in values can be of several types and this simpleType

671

provides a small controlled vocabulary.</h:div>

672

673

<h:div class="example" href="scalar1.xml"/>

674

</xsd:documentation>

675

</xsd:annotation>

676

<xsd:union>

677

<xsd:simpleType>

678

<xsd:restriction base="xsd:string">

679

<xsd:enumeration value="observedRange"/>

680

<xsd:enumeration value="observedStandardDeviation"/>

681

<xsd:enumeration value="observedStandardError"/>

682

<xsd:enumeration value="estimatedStandardDeviation"/>

683

<xsd:enumeration value="estimatedStandardError"/>

684

</xsd:restriction>

685

</xsd:simpleType>

686

<xsd:simpleType>

687

<xsd:restriction base="namespaceRefType"/>

688

</xsd:simpleType>

689

</xsd:union>

690

</xsd:simpleType><xsd:simpleType name="errorValueArrayType" id="st.errorValueArrayType">

691

<xsd:annotation>

692

<xsd:documentation>

693

<h:div class="summary">Array of error estimate values.</h:div>

694

<h:div class="description">An observed or calculated estimate of the error in the value of a numeric quantity. It should be ignored for dataTypes such as URL, date or string. The statistical basis of the errorValueType is not defined - it could be a range, an estimated standard deviation, an observed standard error, etc. This information can be added through _errorBasisType_.</h:div>

695

<h:div class="example" href="scalar1.xml"/>

696

</xsd:documentation>

697

</xsd:annotation>

698

<xsd:list itemType="errorValueType"/>

699

</xsd:simpleType><xsd:simpleType name="errorValueType" id="st.errorValueType">

700

<xsd:annotation>

701

<xsd:documentation>

702

<h:div class="summary">An estimate of the error in the value of a quantity.</h:div>

703

704

<h:div class="example" href="scalar1.xml"/>

705

</xsd:documentation>

706

</xsd:annotation>

707

<xsd:restriction base="xsd:double"/>

708

</xsd:simpleType><xsd:simpleType name="floatArrayType" id="st.floatArrayType">

709

<xsd:annotation>

710

<xsd:documentation>

711

<h:div class="summary">OBSOLETE An array of floats.</h:div>

712

<h:div class="description">An array of floats or other real numbers.

713

Not used in STM Schema, but re-used by CML and other languages.</h:div>

714

<h:div class="example" href="floatArrayType1.xml"/>

715

</xsd:documentation>

716

</xsd:annotation>

717

<xsd:list itemType="xsd:double"/>

718

</xsd:simpleType><xsd:simpleType name="formalChargeArrayType" id="st.formalChargeArrayType">

719

<xsd:annotation>

720

<xsd:documentation>

721

<h:div class="summary">Array of formalCharges.</h:div>

722

<h:div class="description">Used for electron-bookeeping. This has no relation to its calculated (fractional) charge or oxidation state.</h:div>

723

<h:div class="example" href="formalChargeType1.xml"/>

724

</xsd:documentation>

725

</xsd:annotation>

726

<xsd:list itemType="formalChargeType"/>

727

</xsd:simpleType><xsd:simpleType name="formalChargeType" id="st.formalChargeType">

728

<xsd:annotation>

729

<xsd:documentation>

730

<h:div class="summary">The formal charge on an object.</h:div>

731

<h:div class="description">Used for electron-bookeeping. This has no relation to its calculated (fractional) charge or oxidation state.</h:div>

732

<h:div class="example" href="formalChargeType1.xml"/>

733

</xsd:documentation>

734

</xsd:annotation>

735

<xsd:restriction base="xsd:integer"/>

736

</xsd:simpleType><xsd:simpleType id="st.formatType" name="formatType">

737

<xsd:annotation>

738

<xsd:documentation>

739

<h:div class="summary">Format of a spectrum.</h:div>

740

<h:div class="description">The data structure of the spectrum. (Not the format of the data). This describes how the data structure is to be interpreted.</h:div>

741

</xsd:documentation>

742

</xsd:annotation>

743

<xsd:union>

744

<xsd:simpleType>

745

<xsd:restriction base="xsd:string">

746

<xsd:enumeration value="1D">

747

<xsd:annotation>

748

<xsd:documentation>

749

<h:div class="summary">one dimensional spectru.</h:div>

750

<h:div class="description">

751

Data are represented by two _array_s, one representing the independent variable (e.g. wavelength, mass number) and the other the measured dependent variable (absorption, intensity, etc.). This can normally be plotted directly with the independent variable as the x-axis. The order of the points is not necessarily significant and may be increasing or decreasing.</h:div>

752

</xsd:documentation>

753

</xsd:annotation>

754

</xsd:enumeration>

755

<xsd:enumeration value="2Dsymm">

756

<xsd:annotation>

757

<xsd:documentation>

758

<h:div class="summary">Two dimensional spectru.</h:div>

759

<h:div class="description">

760

Data are represented by a single symmetric _matrix_ with both axes identical (i.e. the same independent variable). A typical example is a "2D 1HNMR spectrum". The dependent variable is represented by the matrix elements. This can normally be plotted as a square symmentric about a diagonal.</h:div>

761

</xsd:documentation>

762

</xsd:annotation>

763

</xsd:enumeration>

764

<xsd:enumeration value="2Dasymm">

765

<xsd:annotation>

766

<xsd:documentation>

767

<h:div class="summary">Two dimensional spectrum with different axe.</h:div>

768

<h:div class="description">Data are represented by non-square _matrix_ with independent axes. A typical example is a "2D 1H 13C NMR spectrum". The dependent variable is represented by the matrix elements. .</h:div>

769

</xsd:documentation>

770

</xsd:annotation>

771

</xsd:enumeration>

772

</xsd:restriction>

773

</xsd:simpleType>

774

<xsd:simpleType>

775

<xsd:restriction base="namespaceRefType"/>

776

</xsd:simpleType>

777

</xsd:union>

778

</xsd:simpleType><xsd:simpleType name="formulaType" id="st.formulaType">

779

<xsd:annotation>

780

<xsd:documentation>

781

<h:div class="summary">A concise representation for a molecular formula.</h:div>

782

<h:div class="description">This MUST adhere to a whitespaced syntax so that it is trivially

783

machine-parsable. Each element is followed by its count (which may be decimal),

784

and the string is optionally ended by a formal charge (of form d or -d, i.e. no '+')

785

NO brackets or other nesting is allowed.</h:div>

786

<h:div class="example" href="formulaType1.xml"/>

787

<h:div class="curation">2005-08-30: allowed decimal points</h:div>

788

</xsd:documentation>

789

<xsd:appinfo/>

790

</xsd:annotation>

791

<xsd:restriction base="xsd:string">

792

<!-- obsoleted

793

<xsd:pattern value="\s*([A-Z][a-z]?\s+([1-9][0-9]*(\.[0-9]*)?\s*))+(\s+[-|+]?[0-9]+)?\s*"/>-->

794

<!-- failed to support charge

795

<xsd:pattern value="\s*([A-Z][a-z]?\s+(([0-9]+(\.[0-9]*)?)|(\.[0-9]*))?\s*)+"/>-->

796

<xsd:pattern value="\s*([A-Z][a-z]?\s+(([0-9]+(\.[0-9]*)?)|(\.[0-9]*))?\s*)+(\s+[-|+]?[0-9]+)?\s*"/>

797

</xsd:restriction>

798

</xsd:simpleType><xsd:simpleType id="st.ftType" name="ftType">

799

<xsd:annotation>

800

<xsd:documentation>

801

<h:div class="summary">Domain of an FT spectrum.</h:div>

802

<h:div class="description">Indicates whether a spectrum is raw FID or has been transforme.</h:div>

803

</xsd:documentation>

804

</xsd:annotation>

805

<xsd:union>

806

<xsd:simpleType>

807

<xsd:restriction base="xsd:string">

808

<xsd:enumeration value="raw">

809

<xsd:annotation>

810

<xsd:documentation>

811

<h:div class="summary">Data are raw, so will normally require transforming.</h:div>

812

</xsd:documentation>

813

</xsd:annotation>

814

</xsd:enumeration>

815

<xsd:enumeration value="transformed">

816

<xsd:annotation>

817

<xsd:documentation>

818

<h:div class="summary">Data have been transformed. This value indicates that an FT experiment and transformation have been performe.</h:div>

819

</xsd:documentation>

820

</xsd:annotation>

821

</xsd:enumeration>

822

<xsd:enumeration value="none">

823

<xsd:annotation>

824

<xsd:documentation>

825

<h:div class="summary">This was not known to be an FT experiment. (It may have been, but the author or abstracter omitted to mention it).</h:div>

826

</xsd:documentation>

827

</xsd:annotation>

828

</xsd:enumeration>

829

</xsd:restriction>

830

</xsd:simpleType>

831

<xsd:simpleType>

832

<xsd:restriction base="namespaceRefType"/>

833

</xsd:simpleType>

834

</xsd:union>

835

</xsd:simpleType><xsd:simpleType name="hydrogenCountArrayType" id="st.hydrogenCountArrayType">

836

<xsd:annotation>

837

<xsd:documentation>

838

<h:div class="summary">Array of hydrogenCounts.</h:div>

839

<h:div class="description">The total number of hydrogen atoms bonded to an atom or contained in a molecule, whether explicitly included as atoms or not. It is an error to have hydrogen count less than the explicit hydrogen count. There is no default value and no assumptions about hydrogen Count can be made if it is not given. If hydrogenCount is given on every atom, then the values can be summed to give the total hydrogenCount for the (sub)molecule. Because of this hydrogenCount should not be used where hydrogen atoms bridge 2 or more atoms.</h:div>

840

<h:div class="example" href="atom1.xml"/>

841

</xsd:documentation>

842

</xsd:annotation>

843

<xsd:list itemType="hydrogenCountType"/>

844

</xsd:simpleType><xsd:simpleType name="hydrogenCountType" id="st.hydrogenCountType">

845

<xsd:annotation>

846

<xsd:documentation>

847

<h:div class="summary">The total number of hydrogen atoms bonded to an object.</h:div>

848

849

<h:div class="example" href="atom1.xml"/>

850

</xsd:documentation>

851

</xsd:annotation>

852

<xsd:restriction base="xsd:nonNegativeInteger"/>

853

</xsd:simpleType><xsd:simpleType name="idArrayType" id="st.idArrayType">

854

<xsd:annotation>

855

<xsd:documentation>

856

<h:div class="summary">An array of ids or idRefs.</h:div>

857

<h:div class="description">See idType.</h:div>

858

</xsd:documentation>

859

</xsd:annotation>

860

<xsd:list itemType="idType"/>

861

</xsd:simpleType><xsd:simpleType name="idType" id="st.idType">

862

<xsd:annotation>

863

<xsd:documentation>

864

<h:div class="summary">A unique ID for an element.</h:div>

865

<h:div class="description">

866

<h:p>This is not formally of type ID (an XML NAME which must start with a letter and contain only letters, digits and <h:tt>.-_:</h:tt>). It is recommended that IDs start with a letter, and contain no punctuation or whitespace. The function in XSLT will generate semantically void unique IDs.</h:p>

867

<h:p>It is difficult to ensure uniqueness when documents are merged. We suggest

868

namespacing IDs, perhaps using the containing elements as the base.

869

Thus <h:tt>mol3:a1</h:tt> could be a useful unique ID.

870

However this is still experimental.</h:p></h:div>

871

</xsd:documentation>

872

</xsd:annotation>

873

874

<xsd:restriction base="xsd:string">

875

<xsd:pattern value="[A-Za-z][A-Za-z0-9\.\-_]*"/>

876

</xsd:restriction>

877

</xsd:simpleType><xsd:simpleType id="st.inheritType" name="inheritType">

878

879

<xsd:annotation>

880

<xsd:documentation>

881

<h:div class="summary">Inheritance mechanism.</h:div>

882

<h:div class="description"><h:p>A reference to an existing element can be used to supplement values such as coordinates. The <h:tt>inheritance</h:tt> attribute determines whether the values are supplemented, overwritten or deleted. In the example:</h:p>

883

<h:pre>

884

885

886

887

</atomArray>

888

</molecule>

889

890

891

892

893

</atomArray>

894

</molecule>

895

896

897

898

899

</atomArray>

900

</molecule>

901

902

903

904

905

</atomArray>

906

</molecule>

907

</h:pre>

908

<h:p>

909

The first <h:tt>molecule/@ref</h:tt> adds complementary information, the second

910

changes the values. Software is allowed to generate two independent copies of the molecule and reference them by different IDs (<h:tt>m1</h:tt> and <h:tt>m2</h:tt>).

911

</h:p>

912

<h:p>This mechanism is necessary to manage the implied inheritance of partial information during minimisations and dynamics. It requires careful software implementation.

913

</h:p></h:div>

914

</xsd:documentation>

915

</xsd:annotation>

916

<xsd:restriction base="xsd:string">

917

<xsd:enumeration value="merge">

918

<xsd:annotation>

919

<xsd:documentation>

920

<h:div class="summary">Values from this element will be merged.</h:div>

921

<h:div class="description">The merging is element-specific with the intention that information from the current element will not conflict with the existing information. It is an error if there is a conflict.</h:div>

922

</xsd:documentation>

923

</xsd:annotation>

924

</xsd:enumeration>

925

<xsd:enumeration value="replace">

926

<xsd:annotation>

927

<xsd:documentation>

928

<h:div class="summary">Values from this element will replace existing information.</h:div>

929

<h:div class="description">The merging is element-specific with the intention that information from the current element will replace the existing information.</h:div>

930

</xsd:documentation>

931

</xsd:annotation>

932

</xsd:enumeration>

933

<xsd:enumeration value="delete">

934

<xsd:annotation>

935

<xsd:documentation>

936

<h:div class="summary">Components of this element will de deleted if they exist.</h:div>

937

</xsd:documentation>

938

</xsd:annotation>

939

</xsd:enumeration>

940

</xsd:restriction>

941

</xsd:simpleType><xsd:simpleType name="integerArrayType" id="st.integerArrayType">

942

<xsd:annotation>

943

<xsd:documentation>

944

<h:div class="summary">An array of integers.</h:div>

945

<h:div class="description">An array of integers; for re-use by other schemas. Not machine-validatable.</h:div>

946

<h:div class="example" href="integerArrayType1.xml"/>

947

</xsd:documentation>

948

</xsd:annotation>

949

<xsd:list itemType="xsd:integer"/>

950

</xsd:simpleType><xsd:simpleType name="isotopeType" id="st.isotopeType">

951

<xsd:annotation>

952

<xsd:documentation>

953

<h:div class="summary">The numeric representation of an isotope.</h:div>

954

<h:div class="description">

955

<h:p>In core CML this represents a single number; either the

956

combined proton/neutron count or a more accurate estimate of the

957

nuclear mass. This is admittedly fuzzy, and requires a more complex

958

object (which can manage conventions, lists of isotopic masses, etc.)

959

See <h:a href="el.isotope">isotope</h:a>.</h:p>

960

<h:p>The default is "natural abundance" - whatever that can be interpreted

961

as.</h:p>

962

<h:p>Delta values (i.e. deviations from the most abundant istopic mass)

963

are never allowed.</h:p></h:div>

964

</xsd:documentation>

965

</xsd:annotation>

966

<xsd:restriction base="xsd:double">

967

<xsd:minInclusive value="0.0"/>

968

<xsd:maxInclusive value="99999999999.0"/>

969

</xsd:restriction>

970

</xsd:simpleType><xsd:simpleType name="isotopicSpinType" id="st.isotopicSpinType">

971

<xsd:annotation>

972

<xsd:documentation>

973

<h:div class="summary">A fractional representation of the spin of the nucleus.</h:div>

974

</xsd:documentation>

975

</xsd:annotation>

976

<xsd:restriction base="xsd:string">

977

<xsd:pattern value="\d{1,}(/\d)?"/>

978

</xsd:restriction>

979

</xsd:simpleType><xsd:simpleType name="latticeType" id="st.latticeType">

980

<xsd:annotation>

981

<xsd:documentation>

982

<h:div class="summary">Allowed lattice types.</h:div>

983

<h:div class="description"/>

984

<h:div class="example" href="lattice3.xml"/>

985

</xsd:documentation>

986

</xsd:annotation>

987

<xsd:union>

988

<xsd:simpleType>

989

<xsd:restriction base="xsd:string">

990

<xsd:enumeration value="primitive"/>

991

<xsd:enumeration value="full"/>

992

<xsd:enumeration value="aCentred">

993

<xsd:annotation>

994

<xsd:documentation>

995

<h:div class="summary">lattice with A centering.</h:div>

996

<h:div class="description">A lattice which uses the translation operator {0, 0.5, 0.5}.</h:div>

997

</xsd:documentation>

998

</xsd:annotation>

999

</xsd:enumeration>

1000

</xsd:restriction>

1001

</xsd:simpleType>

1002

<xsd:simpleType>

1003

<xsd:restriction base="namespaceRefType">

1004

<xsd:annotation>

1005

<xsd:documentation>

1006

<h:div class="summary">User-defined lattice-type.</h:div>

1007

<h:div class="description">This definition must be by reference to a namespaced dictionary entry.</h:div>

1008

</xsd:documentation>

1009

</xsd:annotation>

1010

</xsd:restriction>

1011

</xsd:simpleType>

1012

</xsd:union>

1013

</xsd:simpleType><xsd:simpleType name="line3Type" id="st.line3Type">

1014

<xsd:annotation>

1015

<xsd:documentation>

1016

<h:div class="summary">An unbounded line in 3-space.</h:div>

1017

<h:div class="description">Defined by 6 real numbers, conventionally an arbitrary

1018

point on the line and a vector3. There is no significance to the point

1019

(i.e. it is not the "end of the line") and there are an infinite number of

1020

ways of representing the line. DANGER. Line3 now uses the point3 and vector3 attributes

1021

and the line3Type may be OBSOLETED.</h:div>

1022

<h:div class="example" href="line31.xml"/>

1023

</xsd:documentation>

1024

</xsd:annotation>

1025

<xsd:restriction>

1026

<xsd:simpleType>

1027

<xsd:list itemType="xsd:double"/>

1028

</xsd:simpleType>

1029

<xsd:length value="6"/>

1030

</xsd:restriction>

1031

</xsd:simpleType><xsd:simpleType id="st.linkTypeType" name="linkTypeType">

1032

<xsd:annotation>

1033

<xsd:documentation>

1034

<h:div class="summary">The type of the link.</h:div>

1035

</xsd:documentation>

1036

</xsd:annotation>

1037

<xsd:restriction base="xsd:string">

1038

<xsd:enumeration value="extended">

1039

<xsd:annotation>

1040

<xsd:documentation>

1041

<h:div class="summary">A container for locators.</h:div>

1042

</xsd:documentation>

1043

</xsd:annotation>

1044

</xsd:enumeration>

1045

<xsd:enumeration value="locator">

1046

<xsd:annotation>

1047

<xsd:documentation>

1048

<h:div class="summary">A link to an element.</h:div>

1049

</xsd:documentation>

1050

</xsd:annotation>

1051

</xsd:enumeration>

1052

<xsd:enumeration value="arc">

1053

<xsd:annotation>

1054

<xsd:documentation>

1055

<h:div class="summary">A labelled link.</h:div>

1056

</xsd:documentation>

1057

</xsd:annotation>

1058

</xsd:enumeration>

1059

</xsd:restriction>

1060

</xsd:simpleType><xsd:simpleType id="st.lmType" name="lmType">

1061

<xsd:annotation>

1062

<xsd:documentation>

1063

<h:div class="summary">symbolic represention of l amd m.</h:div>

1064

<h:div class="description">takes avlues of s, p, px, dxy, dx2y2, f, etc.</h:div>

1065

</xsd:documentation>

1066

</xsd:annotation>

1067

<xsd:restriction base="xsd:string">

1068

<xsd:enumeration value="s"/>

1069

<xsd:enumeration value="p"/>

1070

<xsd:enumeration value="px"/>

1071

<xsd:enumeration value="py"/>

1072

<xsd:enumeration value="pz"/>

1073

<xsd:enumeration value="d"/>

1074

<xsd:enumeration value="dxy"/>

1075

<xsd:enumeration value="dyz"/>

1076

<xsd:enumeration value="dxz"/>

1077

<xsd:enumeration value="dx2y2"/>

1078

<xsd:enumeration value="dz2"/>

1079

<xsd:enumeration value="f"/>

1080

<xsd:enumeration value="g"/>

1081

</xsd:restriction>

1082

</xsd:simpleType><xsd:simpleType name="matrix44Type" id="st.matrix44Type">

1083

<xsd:annotation>

1084

<xsd:documentation>

1085

<h:div class="summary">A 4x4 transformation matrix</h:div>

1086

<h:div class="description">This is the base for extending the transform3 element.

1087

</h:div>

1088

</xsd:documentation>

1089

</xsd:annotation>

1090

<xsd:restriction>

1091

<xsd:simpleType>

1092

<xsd:list itemType="xsd:double"/>

1093

</xsd:simpleType>

1094

<xsd:length value="16"/>

1095

</xsd:restriction>

1096

</xsd:simpleType><xsd:simpleType name="matrixType" id="st.matrixType">

1097

<xsd:annotation>

1098

<xsd:documentation>

1099

<h:div class="summary">Allowed matrix types.</h:div>

1100

<h:div class="description">

1101

<h:p>Many are square matrices. By default all elements must be included. For symmetric, antisymmetric and diagonal matrices some compression is possible by not reporting the identical or forced zero elements. These have their own subtypes, usually with UT or LT appended. Use these with caution as there is chance of confusion and you cannot rely on standard software to read these.</h:p>

1102

<h:p>The matrix type fixes the order and semantics of the elements in the XML element but does not mandate any local syntax. Thus an application may insert newline characters after each row or use a <row> element.</h:p></h:div>

1103

<h:div class="example" href="matrix1.xml"/>

1104

</xsd:documentation>

1105

</xsd:annotation>

1106

<xsd:union>

1107

<xsd:simpleType>

1108

<xsd:restriction base="xsd:string">

1109

<xsd:enumeration value="rectangular">

1110

<xsd:annotation>

1111

<xsd:documentation>

1112

<h:div class="description">Rectangular with no semantic constraints and ordered rowwise (i.e. the column index runs fastest).

1113

<h:pre>

1114

1 2 3 4

1115

0 3 5 6

1116

</h:pre></h:div>

1117

</xsd:documentation>

1118

</xsd:annotation>

1119

</xsd:enumeration>

1120

<xsd:enumeration value="square">

1121

<xsd:annotation>

1122

<xsd:documentation>

1123

<h:div class="description">Square with no semantic constraints.

1124

<h:pre>

1125

1 2 78

1126

3 4 -1

1127

-34 2 7

1128

</h:pre></h:div>

1129

</xsd:documentation>

1130

</xsd:annotation>

1131

</xsd:enumeration>

1132

<xsd:enumeration value="squareSymmetric">

1133

<xsd:annotation>

1134

<xsd:documentation>

1135

<h:div class="description">Square symmetric with all elements explicit.

1136

<h:pre>

1137

1 2 3

1138

2 7 1

1139

3 1 9

1140

</h:pre></h:div>

1141

</xsd:documentation>

1142

</xsd:annotation>

1143

</xsd:enumeration>

1144

<xsd:enumeration value="squareSymmetricLT">

1145

<xsd:annotation>

1146

<xsd:documentation>

1147

<h:div class="description">Square symmetric with the diagonal and lower triangle explicit and the upper triangle omitted. Rows are of length 1, 2, 3...

1148

<h:pre>

1149

1150

2 7

1151

3 1 9

1152

</h:pre>

1153

is equivalent to

1154

<h:pre>

1155

1 2 3

1156

2 7 1

1157

3 1 9

1158

</h:pre></h:div>

1159

</xsd:documentation>

1160

</xsd:annotation>

1161

</xsd:enumeration>

1162

<xsd:enumeration value="squareSymmetricUT">

1163

<xsd:annotation>

1164

<xsd:documentation>

1165

<h:div class="description">Square symmetric with the diagonal and upper triangle explicit. Rows are of length n, n-1, ... 2, 1

1166

<h:pre>

1167

1 7 9

1168

2 -1

1169

1170

</h:pre>

1171

is equivalent to

1172

<h:pre>

1173

1 7 9

1174

7 2 -1

1175

9 -1 34

1176

</h:pre></h:div>

1177

</xsd:documentation>

1178

</xsd:annotation>

1179

</xsd:enumeration>

1180

<xsd:enumeration value="squareAntisymmetric">

1181

<xsd:annotation>

1182

<xsd:documentation>

1183

<h:div class="description">Square antisymmetric with all elements explicit. The diagonal is necessarily zero.

1184

<h:pre>

1185

0 -2 3

1186

2 0 1

1187

-3 -1 0

1188

</h:pre></h:div>

1189

</xsd:documentation>

1190

</xsd:annotation>

1191

</xsd:enumeration>

1192

<xsd:enumeration value="squareAntisymmetricLT">

1193

<xsd:annotation>

1194

<xsd:documentation>

1195

<h:div class="description">Square symmetric with the lower triangle explicit and diagonal and upper triangle omitted. Rows are of length 1, 2,... n-1.

1196

<h:pre>

1197

-7

1198

-9 1

1199

</h:pre>

1200

is equivalent to

1201

<h:pre>

1202

0 7 9

1203

-7 0 -1

1204

-9 1 0

1205

</h:pre></h:div>

1206

</xsd:documentation>

1207

</xsd:annotation>

1208

</xsd:enumeration>

1209

<xsd:enumeration value="squareAntisymmetricUT">

1210

<xsd:annotation>

1211

<xsd:documentation>

1212

<h:div class="description">Square symmetric with the upper triangle explicit and diagonal and lower triangle omitted. Rows are of length n-1, n-2,... 2,1.

1213

<h:pre>

1214

7 9

1215

-1

1216

</h:pre>

1217

is equivalent to

1218

<h:pre>

1219

0 7 9

1220

-7 0 -1

1221

-9 1 0

1222

</h:pre></h:div>

1223

</xsd:documentation>

1224

</xsd:annotation>

1225

</xsd:enumeration>

1226

<xsd:enumeration value="diagonal">

1227

<xsd:annotation>

1228

<xsd:documentation>

1229

<h:div class="description">Symmetric. Elements are zero except on the diagonal. No compressed representation available (use <h:tt>array</h:tt> element).</h:div>

1230

<h:pre>

1231

1 0 0

1232

0 3 0

1233

0 0 4

1234

</h:pre>

1235

</xsd:documentation>

1236

</xsd:annotation>

1237

</xsd:enumeration>

1238

<xsd:enumeration value="upperTriangular">

1239

<xsd:annotation>

1240

<xsd:documentation>

1241

<h:div class="description">Square. Elements are zero below the diagonal

1242

<h:pre>

1243

1 2 3 4

1244

0 3 5 6

1245

0 0 4 8

1246

0 0 0 2

1247

</h:pre></h:div>

1248

</xsd:documentation>

1249

</xsd:annotation>

1250

</xsd:enumeration>

1251

<xsd:enumeration value="upperTriangularUT">

1252

<xsd:annotation>

1253

<xsd:documentation>

1254

<h:div class="description">Square. Elements below the diagonal are zero and omitted, and rows are of length n, n-1, ... , 2, 1.

1255

<h:pre>

1256

1 2 3 4

1257

3 5 6

1258

4 8

1259

1260

</h:pre>

1261

is equivalent to

1262

<h:pre>

1263

1 2 3 4

1264

0 3 5 6

1265

0 0 4 8

1266

0 0 0 2

1267

</h:pre></h:div>

1268

</xsd:documentation>

1269

</xsd:annotation>

1270

</xsd:enumeration>

1271

<xsd:enumeration value="lowerTriangular">

1272

<xsd:annotation>

1273

<xsd:documentation>

1274

<h:div class="description">Square. Elements are zero above the diagonal

1275

<h:pre>

1276

1 0 0

1277

7 3 0

1278

9 2 4

1279

</h:pre></h:div>

1280

</xsd:documentation>

1281

</xsd:annotation>

1282

</xsd:enumeration>

1283

<xsd:enumeration value="lowerTriangularLT">

1284

<xsd:annotation>

1285

<xsd:documentation>

1286

<h:div class="description">Square. Elements above the diagonal are zero and omitted, and rows are of length 1, 2, ...n.

1287

<h:pre>

1288

1289

3 7

1290

9 2 3

1291

</h:pre>

1292

is equivalent to

1293

<h:pre>

1294

1 0 0

1295

3 7 0

1296

9 2 3

1297

</h:pre></h:div>

1298

</xsd:documentation>

1299

</xsd:annotation>

1300

</xsd:enumeration>

1301

<xsd:enumeration value="unit">

1302

<xsd:annotation>

1303

<xsd:documentation>

1304

<h:div class="description">Square. Diagonal elements are 1 and off-diagonal are zero.

1305

<h:pre>

1306

1 0 0

1307

0 1 0

1308

0 0 1

1309

</h:pre></h:div>

1310

</xsd:documentation>

1311

</xsd:annotation>

1312

</xsd:enumeration>

1313

<xsd:enumeration value="unitary">

1314

<xsd:annotation>

1315

<xsd:documentation>

1316

<h:div class="description">Square. When multiplied by its transpose gives the unit matrix.

1317

<h:pre>

1318

0 -1 0

1319

1 0 0

1320

0 0 1

1321

</h:pre></h:div>

1322

</xsd:documentation>

1323

</xsd:annotation>

1324

</xsd:enumeration>

1325

<xsd:enumeration value="rowEigenvectors">

1326

<xsd:annotation>

1327

<xsd:documentation>

1328

<h:div class="description">Square. Each row corresponds to an eigenvector of a square matrix. Elements are real. The length of the eigenvectors is undefined, i.e. they are not required to be normalised to 1.

1329

<h:pre>

1330

0 -1 0

1331

1 0 0

1332

0 0 1

1333

</h:pre></h:div>

1334

</xsd:documentation>

1335

</xsd:annotation>

1336

</xsd:enumeration>

1337

<xsd:enumeration value="rotation22">

1338

<xsd:annotation>

1339

<xsd:documentation>

1340

<h:div class="description">The rotation is defined by the matrix premultiplyin a column vector (x, y) .

1341

<h:pre>

1342

0 -1

1343

1 0

1344

</h:pre>

1345

produces (-y, x), i.e. a rotation of -90 degrees.</h:div>

1346

</xsd:documentation>

1347

</xsd:annotation>

1348

</xsd:enumeration>

1349

<xsd:enumeration value="rotationTranslation32">

1350

<xsd:annotation>

1351

<xsd:documentation>

1352

<h:div class="description">A third column defining the translation is added to a rotation22.

1353

<h:pre>

1354

0 -1 22

1355

1 0 33

1356

</h:pre>

1357

produces (-y + 22, x + 33), i.e. a rotation of -90 degrees followed by a translation of (22, 33).</h:div>

1358

</xsd:documentation>

1359

</xsd:annotation>

1360

</xsd:enumeration>

1361

<xsd:enumeration value="homogeneous33"/>

1362

<xsd:enumeration value="rotation33"/>

1363

<xsd:enumeration value="rotationTranslation43"/>

1364

<xsd:enumeration value="homogeneous44"/>

1365

</xsd:restriction>

1366

</xsd:simpleType>

1367

<xsd:simpleType>

1368

<xsd:restriction base="namespaceRefType">

1369

<xsd:annotation>

1370

<xsd:documentation>

1371

<h:div class="summary">User-defined matrix-type.</h:div>

1372

<h:div class="description">This definition must be by reference to a namespaced dictionary entry.</h:div>

1373

</xsd:documentation>

1374

</xsd:annotation>

1375

</xsd:restriction>

1376

</xsd:simpleType>

1377

</xsd:union>

1378

</xsd:simpleType><xsd:simpleType name="maxType" id="st.maxType">

1379

<xsd:annotation>

1380

<xsd:documentation>

1381

<h:div class="summary">The maximum INCLUSIVE value of a quantity.</h:div>

1382

<h:div class="description">

1383

<h:p>The maximum INCLUSIVE value of a sortable quantity such as

1384

numeric, date or string. It should be ignored for dataTypes such as URL.

1385

The use of <h:tt>min</h:tt> and

1386

<h:tt>max</h:tt> attributes can be used to give a range for the quantity.

1387

The statistical basis of this range is not defined. The value of <h:tt>max</h:tt>

1388

is usually an observed

1389

quantity (or calculated from observations). To restrict a value, the <h:tt>

1390

maxExclusive</h:tt> type in a dictionary should be used.</h:p>

1391

<h:p>The type of the maximum is the same as the quantity to which it refers - numeric,

1392

date and string are currently allowed</h:p></h:div>

1393

<h:div class="example" href="maxType1.xml"/>

1394

</xsd:documentation>

1395

</xsd:annotation>

1396

<xsd:restriction base="xsd:string"/>

1397

</xsd:simpleType><xsd:simpleType id="st.measurementType" name="measurementType">

1398

<xsd:annotation>

1399

<xsd:documentation>

1400

<h:div class="summary">Type of spectral measurement.</h:div>

1401

<h:div class="description">The nature of the measured data. This is not an exhaustive list and should only be used if it affects the storage or immediate processing.</h:div>

1402

</xsd:documentation>

1403

</xsd:annotation>

1404

<xsd:union>

1405

<xsd:simpleType>

1406

<xsd:restriction base="xsd:string">

1407

<xsd:enumeration value="transmittance">

1408

<xsd:annotation>

1409

<xsd:documentation>

1410

<h:div class="summary">Data are transmittance, so "peaks" are usually troughs.</h:div>

1411

</xsd:documentation>

1412

</xsd:annotation>

1413

</xsd:enumeration>

1414

<xsd:enumeration value="absorbance">

1415

<xsd:annotation>

1416

<xsd:documentation>

1417

<h:div class="summary">Data are absorbanc.</h:div>

1418

<h:div class="description">so "peaks" are normally peaks.</h:div>

1419

</xsd:documentation>

1420

</xsd:annotation>

1421

</xsd:enumeration>

1422

</xsd:restriction>

1423

</xsd:simpleType>

1424

<xsd:simpleType>

1425

<xsd:restriction base="namespaceRefType"/>

1426

</xsd:simpleType>

1427

</xsd:union>

1428

</xsd:simpleType><xsd:simpleType name="metadataType" id="st.metadataType">

1429

<xsd:annotation>

1430

<xsd:documentation>

1431

<h:div class="summary">The name of the metadata.</h:div>

1432

<h:div class="description">Metadata consists of name-value pairs (value is in the "content" attribute). The names are from a semi-restricted vocabulary, mainly Dublin Core. The content is unrestricted. The order of metadata has no implied semantics at present. Users can create their own metadata names using the namespaced prefix syntax (e.g. foo:institution). Ideally these names should be defined in an STMML dictionary.</h:div>

1433

<h:div class="curation">2003-03-05: Added UNION to manage non-controlled name.</h:div>

1434

</xsd:documentation>

1435

</xsd:annotation>

1436

<xsd:union>

1437

<xsd:simpleType>

1438

<xsd:restriction base="xsd:string">

1439

<xsd:enumeration value="dc:coverage">

1440

<xsd:annotation>

1441

<xsd:documentation>

1442

<h:div class="definition">The extent or scope of the

1443

content of the resource.</h:div>

1444

1445

<h:div class="description">Coverage will typically include

1446

spatial location (a place name or geographic

1447

coordinates), temporal period (a period label, date, or

1448

date range) or jurisdiction (such as a named

1449

administrative entity). Recommended best practice is to

1450

select a value from a controlled vocabulary (for

1451

example, the Thesaurus of Geographic Names [TGN]) and

1452

that, where appropriate, named places or time periods

1453

be used in preference to numeric identifiers such as

1454

sets of coordinates or date ranges.</h:div>

1455

</xsd:documentation>

1456

</xsd:annotation>

1457

</xsd:enumeration>

1458

1459

<xsd:enumeration value="dc:description">

1460

<xsd:annotation>

1461

<xsd:documentation>

1462

<h:div class="definition">An account of the content of the

1463

resource.</h:div>

1464

1465

<h:div class="description">Description may include but is not

1466

limited to: an abstract, table of contents, reference

1467

to a graphical representation of content or a free-text

1468

account of the content.</h:div>

1469

</xsd:documentation>

1470

</xsd:annotation>

1471

</xsd:enumeration>

1472

1473

<xsd:enumeration value="dc:identifier">

1474

<xsd:annotation>

1475

<xsd:documentation>

1476

<h:div class="definition">An unambiguous reference to the

1477

resource within a given context.</h:div>

1478

1479

<h:div class="description">Recommended best practice is to

1480

identify the resource by means of a string or number

1481

conforming to a formal identification system. Example

1482

formal identification systems include the Uniform

1483

Resource Identifier (URI) (including the Uniform

1484

Resource Locator (URL)), the Digital Object Identifier

1485

(DOI) and the International Standard Book Number

1486

(ISBN).</h:div>

1487

</xsd:documentation>

1488

</xsd:annotation>

1489

</xsd:enumeration>

1490

1491

<xsd:enumeration value="dc:format">

1492

<xsd:annotation>

1493

<xsd:documentation>

1494

<h:div class="definition">The physical or digital

1495

manifestation of the resource.</h:div>

1496

1497

<h:div class="description">Typically, Format may include the

1498

media-type or dimensions of the resource. Format may be

1499

used to determine the software, hardware or other

1500

equipment needed to display or operate the resource.

1501

Examples of dimensions include size and duration.

1502

Recommended best practice is to select a value from a

1503

controlled vocabulary (for example, the list of

1504

Internet Media Types [MIME] defining computer media

1505

formats).</h:div>

1506

</xsd:documentation>

1507

</xsd:annotation>

1508

</xsd:enumeration>

1509

1510

<xsd:enumeration value="dc:relation">

1511

<xsd:annotation>

1512

<xsd:documentation>

1513

<h:div class="definition">A reference to a related

1514

resource.</h:div>

1515

1516

<h:div class="description">Recommended best practice is to

1517

reference the resource by means of a string or number

1518

conforming to a formal identification system.</h:div>

1519

</xsd:documentation>

1520

</xsd:annotation>

1521

</xsd:enumeration>

1522

1523

<xsd:enumeration value="dc:rights">

1524

<xsd:annotation>

1525

<xsd:documentation>

1526

<h:div class="definition">Information about rights held in

1527

and over the resource.</h:div>

1528

1529

<h:div class="description">Typically, a Rights element will

1530

contain a rights management statement for the resource,

1531

or reference a service providing such information.

1532

Rights information often encompasses Intellectual

1533

Property Rights (IPR), Copyright, and various Property

1534

Rights. If the Rights element is absent, no assumptions

1535

can be made about the status of these and other rights

1536

with respect to the resource.</h:div>

1537

</xsd:documentation>

1538

</xsd:annotation>

1539

</xsd:enumeration>

1540

1541

<xsd:enumeration value="dc:subject">

1542

<xsd:annotation>

1543

<xsd:documentation>

1544

<h:div class="definition">The topic of the content of the

1545

resource.</h:div>

1546

1547

<h:div class="description">Typically, a Subject will be

1548

expressed as keywords, key phrases or classification

1549

codes that describe a topic of the resource.

1550

Recommended best practice is to select a value from a

1551

controlled vocabulary or formal classification

1552

scheme.</h:div>

1553

</xsd:documentation>

1554

</xsd:annotation>

1555

</xsd:enumeration>

1556

1557

<xsd:enumeration value="dc:title">

1558

<xsd:annotation>

1559

<xsd:documentation>

1560

<h:div class="definition">A name given to the resource.</h:div>

1561

1562

<h:div class="description">Typically, a Title will be a name by

1563

which the resource is formally known.</h:div>

1564

</xsd:documentation>

1565

</xsd:annotation>

1566

</xsd:enumeration>

1567

1568

<xsd:enumeration value="dc:type">

1569

<xsd:annotation>

1570

<xsd:documentation>

1571

<h:div class="definition">The nature or genre of the

1572

content of the resource.</h:div>

1573

1574

<h:div class="description">Type includes terms describing

1575

general categories, functions, genres, or aggregation

1576

levels for content. Recommended best practice is to

1577

select a value from a controlled vocabulary (for

1578

example, the working draft list of Dublin Core Types

1579

[DCT1]). To describe the physical or digital

1580

manifestation of the resource, use the FORMAT

1581

element.</h:div>

1582

</xsd:documentation>

1583

</xsd:annotation>

1584

</xsd:enumeration>

1585

1586

<xsd:enumeration value="dc:contributor">

1587

<xsd:annotation>

1588

<xsd:documentation>

1589

<h:div class="definition">An entity responsible for making

1590

contributions to the content of the resource.</h:div>

1591

1592

<h:div class="description">Examples of a Contributor include a

1593

person, an organisation, or a service. Typically, the

1594

name of a Contributor should be used to indicate the

1595

entity.</h:div>

1596

</xsd:documentation>

1597

</xsd:annotation>

1598

</xsd:enumeration>

1599

1600

<xsd:enumeration value="dc:creator">

1601

<xsd:annotation>

1602

<xsd:documentation>

1603

<h:div class="definition">An entity primarily responsible

1604

for making the content of the resource.</h:div>

1605

1606

<h:div class="description">Examples of a Creator include a

1607

person, an organisation, or a service. Typically, the

1608

name of a Creator should be used to indicate the

1609

entity.</h:div>

1610

</xsd:documentation>

1611

</xsd:annotation>

1612

</xsd:enumeration>

1613

1614

<xsd:enumeration value="dc:publisher">

1615

<xsd:annotation>

1616

<xsd:documentation>

1617

<h:div class="definition">An entity responsible for making

1618

the resource available.</h:div>

1619

1620

<h:div class="description">Examples of a Publisher include a

1621

person, an organisation, or a service. Typically, the

1622

name of a Publisher should be used to indicate the

1623

entity.</h:div>

1624

</xsd:documentation>

1625

</xsd:annotation>

1626

</xsd:enumeration>

1627

1628

<xsd:enumeration value="dc:source">

1629

<xsd:annotation>

1630

<xsd:documentation>

1631

<h:div class="definition">A Reference to a resource from

1632

which the present resource is derived.</h:div>

1633

1634

<h:div class="description">The present resource may be derived

1635

from the Source resource in whole or in part.

1636

Recommended best practice is to reference the resource

1637

by means of a string or number conforming to a formal

1638

identification system.</h:div>

1639

</xsd:documentation>

1640

</xsd:annotation>

1641

</xsd:enumeration>

1642

1643

<xsd:enumeration value="dc:language">

1644

<xsd:annotation>

1645

<xsd:documentation>

1646

<h:div class="definition">A language of the intellectual

1647

content of the resource.</h:div>

1648

1649

<h:div class="description">Recommended best practice for the

1650

values of the Language element is defined by RFC 1766

1651

[RFC1766] which includes a two-letter Language Code

1652

(taken from the ISO 639 standard [ISO639]), followed

1653

optionally, by a two-letter Country Code (taken from

1654

the ISO 3166 standard [ISO3166]). For example, 'en' for

1655

English, 'fr' for French, or 'en-uk' for English used

1656

in the United Kingdom.</h:div>

1657

</xsd:documentation>

1658

</xsd:annotation>

1659

</xsd:enumeration>

1660

1661

<xsd:enumeration value="dc:date">

1662

<xsd:annotation>

1663

<xsd:documentation>

1664

<h:div class="definition">A date associated with an event

1665

in the life cycle of the resource.</h:div>

1666

1667

<h:div class="description">Typically, Date will be associated

1668

with the creation or availability of the resource.

1669

Recommended best practice for encoding the date value

1670

is defined in a profile of ISO 8601 [W3CDTF] and

1671

follows the YYYY-MM-DD format.</h:div>

1672

</xsd:documentation>

1673

</xsd:annotation>

1674

</xsd:enumeration>

1675

1676

<xsd:enumeration value="cmlm:safety">

1677

<xsd:annotation>

1678

<xsd:documentation>

1679

<h:div class="definition">Entry contains information

1680

relating to chemical safety.</h:div>

1681

1682

<h:div class="description">Typically the content will be a

1683

reference to a handbook, MSDS, threshhold or other

1684

human-readable strin.</h:div>

1685

</xsd:documentation>

1686

</xsd:annotation>

1687

</xsd:enumeration>

1688

1689

<xsd:enumeration value="cmlm:insilico">

1690

<xsd:annotation>

1691

<xsd:documentation>

1692

<h:div class="definition">Part or whole of the information

1693

was computer-generated.</h:div>

1694

<h:div class="description">Typically the content will be the

1695

name of a method or a progra.</h:div>

1696

</xsd:documentation>

1697

</xsd:annotation>

1698

</xsd:enumeration>

1699

1700

<xsd:enumeration value="cmlm:structure">

1701

<xsd:annotation>

1702

<xsd:documentation>

1703

<h:div class="definition">3D structure included.</h:div>

1704

<h:div class="description">details include.</h:div>

1705

</xsd:documentation>

1706

</xsd:annotation>

1707

</xsd:enumeration>

1708

1709

<xsd:enumeration value="cmlm:reaction"/>

1710

1711

<xsd:enumeration value="cmlm:identifier"/>

1712

1713

<xsd:enumeration value="other"/>

1714

</xsd:restriction>

1715

</xsd:simpleType>

1716

<xsd:simpleType>

1717

<xsd:restriction base="namespaceRefType"/>

1718

</xsd:simpleType>

1719

</xsd:union>

1720

</xsd:simpleType><xsd:simpleType name="minType" id="st.minType">

1721

<xsd:annotation>

1722

<xsd:documentation>

1723

<h:div class="summary">The minimum INCLUSIVE value of a quantity.</h:div>

1724

<h:div class="description">

1725

<h:p>The minimum INCLUSIVE value of a sortable quantity such as

1726

numeric, date or string. It should be ignored for dataTypes such as URL.

1727

The use of <h:tt>min</h:tt> and

1728

<h:tt>min</h:tt> attributes can be used to give a range for the quantity.

1729

The statistical basis of this range is not defined. The value of <h:tt>min</h:tt>

1730

is usually an observed

1731

quantity (or calculated from observations). To restrict a value, the <h:tt>

1732

minExclusive</h:tt> type in a dictionary should be used.</h:p>

1733

<h:p>The type of the minimum is the same as the quantity to which it refers - numeric,

1734

date and string are currently allowed</h:p></h:div>

1735

<h:div class="example" href="maxType1.xml"/>

1736

</xsd:documentation>

1737

</xsd:annotation>

1738

<xsd:restriction base="xsd:string"/>

1739

</xsd:simpleType><xsd:simpleType name="moleculeRefArrayType" id="st.moleculeRefArrayType">

1740

<xsd:annotation>

1741

<xsd:documentation>

1742

<h:div class="summary">An array of moleculeRefs.</h:div>

1743

<h:div class="description">Typical applications are the annotation of

1744

peaks in chromatograms and mapping reactions. The context of the

1745

id resolution is the childOrSibling concept.</h:div>

1746

1747

</xsd:documentation>

1748

<xsd:appinfo/>

1749

</xsd:annotation>

1750

<xsd:list itemType="moleculeRefType"/>

1751

</xsd:simpleType><xsd:simpleType name="moleculeRefType" id="st.moleculeRefType">

1752

<xsd:annotation>

1753

<xsd:documentation>

1754

<h:div class="summary">A reference to an existing molecule.</h:div>

1755

</xsd:documentation>

1756

</xsd:annotation>

1757

<xsd:restriction base="idType"/>

1758

</xsd:simpleType><xsd:simpleType name="namespaceArrayType" id="st.namespaceArrayType">

1759

<xsd:annotation>

1760

<xsd:documentation>

1761

<h:div class="summary">An array of namespaceURIs with required protocol.</h:div>

1762

<h:div class="description">

1763

<h:p>used to identify dictionaries, units, conventions or other metadata.</h:p>

1764

</h:div>

1765

1766

<h:div class="curation">2005-12-17: PMR. Added for use with unitList</h:div>

1767

</xsd:documentation>

1768

</xsd:annotation>

1769

<xsd:list itemType="namespaceType"/>

1770

</xsd:simpleType><xsd:simpleType name="namespaceRefType" id="st.namespaceRefType">

1771

<xsd:annotation>

1772

<xsd:documentation>

1773

<h:div class="summary">An XML QName with required prefix.</h:div>

1774

<h:div class="description">

1775

<h:p>A string referencing a dictionary, units, convention or other metadata.</h:p>

1776

<h:p>The purpose is to allow authors to extend the vocabulary through

1777

their own namespaces without altering the schema.

1778

The prefix is mandatory. This convention is only used within

1779

CML and related languages; it is NOT a generic URI. </h:p></h:div>

1780

<h:div class="example" href="namespaceRefType1.xml"/>

1781

</xsd:documentation>

1782

</xsd:annotation>

1783

<xsd:restriction base="xsd:string">

1784

<xsd:annotation>

1785

<xsd:documentation>

1786

<h:div class="description">

1787

<h:p>The namespace prefix must start with an alpha character

1788

and can only contain alphanumeric and '_'. The suffix can

1789

have characters from the XML ID specification

1790

(alphanumeric, '_', '.' and '-'</h:p></h:div>

1791

</xsd:documentation>

1792

</xsd:annotation>

1793

<xsd:pattern value="[A-Za-z][A-Za-z0-9_]*:[A-Za-z][A-Za-z0-9_\.\-]*"/>

1794

</xsd:restriction>

1795

</xsd:simpleType><xsd:simpleType name="namespaceType" id="st.namespaceType">

1796

<xsd:annotation>

1797

<xsd:documentation>

1798

<h:div class="summary">A namespaceURI with required protocol.</h:div>

1799

<h:div class="description">

1800

<h:p>used to identify a dictionary, units, convention or other metadata.

1801

Not yet confirmant with XSD</h:p>

1802

</h:div>

1803

<h:div class="example" href="namespaceRefType1.xml"/>

1804

<h:div class="curation">2005-12-10: PMR. Added for use with dictionary</h:div>

1805

</xsd:documentation>

1806

</xsd:annotation>

1807

<xsd:restriction base="xsd:string">

1808

<xsd:annotation>

1809

<xsd:documentation>

1810

<h:div class="description">

1811

<h:p>The namespace prefix must start with a protocol.</h:p>

1812

</h:div>

1813

</xsd:documentation>

1814

</xsd:annotation>

1815

<xsd:pattern value="http://[A-Za-z][A-Za-z0-9_\.\-]*(\/[A-Za-z0-9_\.\-]+)+"/>

1816

</xsd:restriction>

1817

</xsd:simpleType><xsd:simpleType name="nonHydrogenCountType" id="st.nonHydrogenCountType">

1818

<xsd:annotation>

1819

<xsd:documentation>

1820

<h:div class="summary">The number of non-hydrogen atoms attached to an atom.</h:div>

1821

<h:div class="description">Obsolete in core CML. Only useful in CML queries.</h:div>

1822

</xsd:documentation>

1823

</xsd:annotation>

1824

<xsd:restriction base="xsd:nonNegativeInteger"/>

1825

</xsd:simpleType><xsd:simpleType name="nonNegativeAngleType" id="st.nonNegativeAngleType">

1826

<xsd:annotation>

1827

<xsd:documentation>

1828

<h:div class="summary">A non-signed angle.</h:div>

1829

<h:div class="description">Re-used by _angle_. Note that we also provide

1830

positiveAngleType (e.g. for cell angles) and torsionAngleType for _torsion_.</h:div>

1831

<h:div class="example" href="nonNegativeAngleType.xml"/>

1832

</xsd:documentation>

1833

</xsd:annotation>

1834

<xsd:restriction base="xsd:double">

1835

<xsd:minInclusive value="0.0"/>

1836

<xsd:maxInclusive value="180.0"/>

1837

</xsd:restriction>

1838

</xsd:simpleType><xsd:simpleType name="nonNegativeNumberType" id="st.nonNegativeNumberType">

1839

<xsd:annotation>

1840

<xsd:documentation>

1841

<h:div class="description">A nonNegative number.</h:div>

1842

<h:div class="description">Note that we also provide positiveNumber to avoid inclusive zero. The maximum number is 1.0E+999 since 'unbounded' is more difficult to implement. This is greater than Eddington's estimate of the number of particles in the universe so it should work for most people.</h:div>

1843

</xsd:documentation>

1844

</xsd:annotation>

1845

<xsd:restriction base="xsd:double">

1846

<xsd:minInclusive value="0.0"/>

1847

<xsd:maxInclusive value="1.0E+99"/>

1848

</xsd:restriction>

1849

</xsd:simpleType><xsd:simpleType name="occupancyArrayType" id="st.occupancyArrayType">

1850

<xsd:annotation>

1851

<xsd:documentation>

1852

<h:div class="summary">Array of atomic occupancies.</h:div>

1853

<h:div class="description">Primarily for crystallography. Values outside 0-1 are not allowed.</h:div>

1854

<h:div class="example" href="atom1.xml"/>

1855

</xsd:documentation>

1856

</xsd:annotation>

1857

<xsd:list itemType="occupancyType"/>

1858

</xsd:simpleType><xsd:simpleType name="occupancyType" id="st.occupancyType">

1859

<xsd:annotation>

1860

<xsd:documentation>

1861

<h:div class="summary">A floating point number between 0 and 1 inclusive</h:div>

1862

<h:div class="description">Originally for crystallographic occupancy but re-usable

1863

for fractional yield, etc.</h:div>

1864

<h:div class="example" href="atom1.xml"/>

1865

</xsd:documentation>

1866

</xsd:annotation>

1867

<xsd:restriction base="xsd:double">

1868

<xsd:minInclusive value="0"/>

1869

<xsd:maxInclusive value="1"/>

1870

</xsd:restriction>

1871

</xsd:simpleType><xsd:simpleType name="orderArrayType" id="st.orderArrayType">

1872

<xsd:annotation>

1873

<xsd:documentation>

1874

<h:div class="summary">An array of bond orders.</h:div>

1875

<h:div class="description">See order.</h:div>

1876

</xsd:documentation>

1877

</xsd:annotation>

1878

<xsd:list itemType="orderType"/>

1879

</xsd:simpleType><xsd:simpleType name="orderType" id="st.orderType">

1880

<xsd:annotation>

1881

<xsd:documentation>

1882

<h:div class="summary">Bond order.</h:div>

1883

<h:div class="description">

1884

<h:p>This is purely conventional and used

1885

for bond/electron counting. There is no default value.

1886

The emptyString attribute can be used to indicate a bond of

1887

unknown or unspecified type. The interpretation of this is outside

1888

the scope of CML-based algorithms. It may be accompanied by a <h:tt>convention</h:tt>

1889

attribute on the <h:tt>bond</h:tt> which links to a dictionary.

1890

Example: <h:tt><bond convention="ccdc:9" atomRefs2="a1 a2"/></h:tt> could

1891

represent a delocalised bond in the CCDC convention.</h:p></h:div>

1892

</xsd:documentation>

1893

</xsd:annotation>

1894

<xsd:union>

1895

<xsd:simpleType>

1896

<xsd:restriction base="xsd:string">

1897

<xsd:enumeration value="hbond">

1898

<xsd:annotation>

1899

<xsd:documentation>

1900

<h:div class="summary">Hydrogen bond.</h:div>

1901

<h:div class="description">Carries no semantics but will normally be between a hydrogen atom and an element with lone pairs.</h:div>

1902

</xsd:documentation>

1903

</xsd:annotation>

1904

</xsd:enumeration>

1905

<xsd:enumeration value="partial01">

1906

<xsd:annotation>

1907

<xsd:documentation>

1908

<h:div class="summary">Partial bond.</h:div>

1909

<h:div class="description">Can be used for a partial bond in a transition state, intermolecular interaction, etc. There is no numeric value associated and the bond order could be anywhere between 0 and single.</h:div>

1910

</xsd:documentation>

1911

</xsd:annotation>

1912

</xsd:enumeration>

1913

<xsd:enumeration value="S">

1914

<xsd:annotation>

1915

<xsd:documentation>

1916

<h:div class="summary">Single bond.</h:div>

1917

<h:div class="description">synonymous with "1.</h:div>

1918

</xsd:documentation>

1919

</xsd:annotation>

1920

</xsd:enumeration>

1921

<xsd:enumeration value="1">

1922

<xsd:annotation>

1923

<xsd:documentation>

1924

<h:div class="summary">Single bond.</h:div>

1925

</xsd:documentation>

1926

</xsd:annotation>

1927

</xsd:enumeration>

1928

<xsd:enumeration value="partial12">

1929

<xsd:annotation>

1930

<xsd:documentation>

1931

<h:div class="summary">Intermediate between 1 and .</h:div>

1932

<h:div class="description">Could be used for a transition state or a delocalised system.</h:div>

1933

</xsd:documentation>

1934

</xsd:annotation>

1935

</xsd:enumeration>

1936

<xsd:enumeration value="D">

1937

<xsd:annotation>

1938

<xsd:documentation>

1939

<h:div class="summary">Double bond.</h:div>

1940

</xsd:documentation>

1941

</xsd:annotation>

1942

</xsd:enumeration>

1943

<xsd:enumeration value="2">

1944

<xsd:annotation>

1945

<xsd:documentation>

1946

<h:div class="summary">Double bond.</h:div>

1947

</xsd:documentation>

1948

</xsd:annotation>

1949

</xsd:enumeration>

1950

<xsd:enumeration value="partial23">

1951

<xsd:annotation>

1952

<xsd:documentation>

1953

<h:div class="summary">Intermediate between 2 and .</h:div>

1954

<h:div class="description">Could be used for a transition state or a delocalised system.</h:div>

1955

</xsd:documentation>

1956

</xsd:annotation>

1957

</xsd:enumeration>

1958

<xsd:enumeration value="T">

1959

<xsd:annotation>

1960

<xsd:documentation>

1961

<h:div class="summary">Triple bond.</h:div>

1962

</xsd:documentation>

1963

</xsd:annotation>

1964

</xsd:enumeration>

1965

<xsd:enumeration value="3">

1966

<xsd:annotation>

1967

<xsd:documentation>

1968

<h:div class="summary">Triple bond.</h:div>

1969

</xsd:documentation>

1970

</xsd:annotation>

1971

</xsd:enumeration>

1972

<xsd:enumeration value="A">

1973

<xsd:annotation>

1974

<xsd:documentation>

1975

<h:div class="summary">Aromatic bond.</h:div>

1976

</xsd:documentation>

1977

</xsd:annotation>

1978

</xsd:enumeration>

1979

</xsd:restriction>

1980

</xsd:simpleType>

1981

<xsd:simpleType>

1982

<xsd:restriction base="namespaceRefType"/>

1983

</xsd:simpleType>

1984

</xsd:union>

1985

1986

</xsd:simpleType><xsd:simpleType id="st.peakMultiplicityType" name="peakMultiplicityType">

1987

<xsd:annotation>

1988

<xsd:documentation>

1989

<h:div class="summary">Multiplicity of a peak.</h:div>

1990

<h:div class="description">Uses a semi-controlled vocabulary.</h:div>

1991

</xsd:documentation>

1992

</xsd:annotation>

1993

1994

<xsd:union>

1995

<xsd:simpleType>

1996

<xsd:restriction base="xsd:string">

1997

<xsd:enumeration value="singlet">

1998

<xsd:annotation>

1999

<xsd:documentation>

2000

<h:div class="summary">A single maximum within the peak rang.</h:div>

2001

</xsd:documentation>

2002

</xsd:annotation>

2003

</xsd:enumeration>

2004

<xsd:enumeration value="doublet">

2005

<xsd:annotation>

2006

<xsd:documentation>

2007

<h:div class="summary">Two maxima (not necessarily equal) within the peak rang.</h:div>

2008

</xsd:documentation>

2009

</xsd:annotation>

2010

</xsd:enumeration>

2011

<xsd:enumeration value="triplet">

2012

<xsd:annotation>

2013

<xsd:documentation>

2014

<h:div class="summary">Three maxima (not necessarily equal) within the peak rang.</h:div>

2015

</xsd:documentation>

2016

</xsd:annotation>

2017

</xsd:enumeration>

2018

<xsd:enumeration value="quartet">

2019

<xsd:annotation>

2020

<xsd:documentation>

2021

<h:div class="summary">Four maxima (not necessarily equal) within the peak rang.</h:div>

2022

</xsd:documentation>

2023

</xsd:annotation>

2024

</xsd:enumeration>

2025

<xsd:enumeration value="quintet">

2026

<xsd:annotation>

2027

<xsd:documentation>

2028

<h:div class="summary">Five maxima (not necessarily equal) within the peak rang.</h:div>

2029

</xsd:documentation>

2030

</xsd:annotation>

2031

</xsd:enumeration>

2032

<xsd:enumeration value="sextuplet">

2033

<xsd:annotation>

2034

<xsd:documentation>

2035

<h:div class="summary">Six maxima (not necessarily equal) within the peak rang.</h:div>

2036

</xsd:documentation>

2037

</xsd:annotation>

2038

</xsd:enumeration>

2039

<xsd:enumeration value="multiplet">

2040

<xsd:annotation>

2041

<xsd:documentation>

2042

<h:div class="summary">Several maxima (not necessarily equal) within the peak rang.</h:div>

2043

</xsd:documentation>

2044

</xsd:annotation>

2045

</xsd:enumeration>

2046

</xsd:restriction>

2047

</xsd:simpleType>

2048

<xsd:simpleType>

2049

<xsd:restriction base="namespaceRefType">

2050

<xsd:annotation>

2051

<xsd:documentation>

2052

<h:div>User contributed vocabulary of type foo:ba.</h:div>

2053

</xsd:documentation>

2054

</xsd:annotation>

2055

</xsd:restriction>

2056

</xsd:simpleType>

2057

</xsd:union>

2058

</xsd:simpleType><xsd:simpleType id="st.peakShapeType" name="peakShapeType">

2059

<xsd:annotation>

2060

<xsd:documentation>

2061

<h:div class="summary">Shape of a peak.</h:div>

2062

<h:div class="description">Semi-controlled vocabulary such as

2063

broad or sharp.</h:div>

2064

</xsd:documentation>

2065

</xsd:annotation>

2066

<xsd:union>

2067

<xsd:simpleType>

2068

<xsd:restriction base="xsd:string">

2069

<xsd:enumeration value="sharp">

2070

<xsd:annotation>

2071

<xsd:documentation>

2072

<h:div class="summary">A sharp peak.</h:div>

2073

</xsd:documentation>

2074

</xsd:annotation>

2075

</xsd:enumeration>

2076

<xsd:enumeration value="broad">

2077

<xsd:annotation>

2078

<xsd:documentation>

2079

<h:div class="summary">A broad peak.</h:div>

2080

</xsd:documentation>

2081

</xsd:annotation>

2082

</xsd:enumeration>

2083

<xsd:enumeration value="shoulder">

2084

<xsd:annotation>

2085

<xsd:documentation>

2086

<h:div class="summary">A brodening of a peak suggesting the presence of a smaller incompletely resolved component.</h:div>

2087

</xsd:documentation>

2088

</xsd:annotation>

2089

</xsd:enumeration>

2090

</xsd:restriction>

2091

</xsd:simpleType>

2092

<xsd:simpleType>

2093

<xsd:restriction base="namespaceRefType">

2094

<xsd:annotation>

2095

<xsd:documentation>

2096

<h:div class="summary">User contributed vocabulary of type foo:bar.</h:div>

2097

</xsd:documentation>

2098

</xsd:annotation>

2099

</xsd:restriction>

2100

</xsd:simpleType>

2101

</xsd:union>

2102

</xsd:simpleType><xsd:simpleType id="st.peakStructureTypeType" name="peakStructureTypeType">

2103

<xsd:annotation>

2104

<xsd:documentation>

2105

<h:div class="summary">type of a peakStructure.</h:div>

2106

<h:div class="description">Semi-controlled vocabulary such as

2107

coupling or splitting.</h:div>

2108

</xsd:documentation>

2109

</xsd:annotation>

2110

<xsd:union>

2111

<xsd:simpleType>

2112

<xsd:restriction base="xsd:string">

2113

<xsd:enumeration value="coupling">

2114

<xsd:annotation>

2115

<xsd:documentation>

2116

<h:div class="summary">A coupling such as in NMR.</h:div>

2117

</xsd:documentation>

2118

</xsd:annotation>

2119

</xsd:enumeration>

2120

<xsd:enumeration value="splitting">

2121

<xsd:annotation>

2122

<xsd:documentation>

2123

<h:div class="summary">A splitting such as in NMR.</h:div>

2124

</xsd:documentation>

2125

</xsd:annotation>

2126

</xsd:enumeration>

2127

</xsd:restriction>

2128

</xsd:simpleType>

2129

<xsd:simpleType>

2130

<xsd:restriction base="namespaceRefType">

2131

<xsd:annotation>

2132

<xsd:documentation>

2133

<h:div class="summary">User contributed vocabulary.</h:div>

2134

</xsd:documentation>

2135

</xsd:annotation>

2136

</xsd:restriction>

2137

</xsd:simpleType>

2138

</xsd:union>

2139

</xsd:simpleType><xsd:simpleType name="peakWidthType" id="st.peakWidthType">

2140

<xsd:annotation>

2141

<xsd:documentation>

2142

<h:div class="summary">The width of a peak.</h:div>

2143

<h:div class="description">At present we allow a peakWidth to be positive

2144

or exactly zero (to signal that the peak should not be integrated).</h:div>

2145

</xsd:documentation>

2146

</xsd:annotation>

2147

<xsd:restriction base="xsd:double">

2148

<xsd:minInclusive value="0.0"/>

2149

<xsd:maxInclusive value="1.0E+99"/>

2150

</xsd:restriction>

2151

</xsd:simpleType><xsd:simpleType name="plane3Type" id="st.plane3Type">

2152

<xsd:annotation>

2153

<xsd:documentation>

2154

<h:div class="summary">An unbounded plane in 3-space.</h:div>

2155

<h:div class="description">Defined by 4 real numbers, conventionally a vector3

2156

normal to the plane and a signed scalar representing the distance to the origin.

2157

The vector must not be of zero length (and need not be normalized.</h:div>

2158

<h:div class="example" href="plane31.xml">

2159

<h:p>The first three numbers are the vector, followed by the distance</h:p></h:div>

2160

</xsd:documentation>

2161

</xsd:annotation>

2162

<xsd:restriction>

2163

<xsd:simpleType>

2164

<xsd:list itemType="xsd:double"/>

2165

</xsd:simpleType>

2166

<xsd:length value="4"/>

2167

</xsd:restriction>

2168

</xsd:simpleType><xsd:simpleType name="point3Type" id="st.point3Type">

2169

<xsd:annotation>

2170

<xsd:documentation>

2171

<h:div class="summary">A point in 3-space.</h:div>

2172

<h:div class="description">The 3 components can have any signed value.</h:div>

2173

<h:div class="example" href="point31.xml"/>

2174

</xsd:documentation>

2175

</xsd:annotation>

2176

<xsd:restriction>

2177

<xsd:simpleType>

2178

<xsd:list itemType="xsd:double"/>

2179

</xsd:simpleType>

2180

<xsd:length value="3"/>

2181

</xsd:restriction>

2182

</xsd:simpleType><xsd:simpleType name="positiveAngleType" id="st.positiveAngleType">

2183

<xsd:annotation>

2184

<xsd:documentation>

2185

<h:div class="summary">A non-signed angle such as a cell angle.</h:div>

2186

<h:div class="description">Re-used by _crystal_. Note that we also provide

2187

nonNegativeAngleType (e.g. for bond angles).</h:div>

2188

<h:div class="example" href="positiveAngleType.xml"/>

2189

</xsd:documentation>

2190

</xsd:annotation>

2191

<xsd:restriction base="xsd:double">

2192

<xsd:minExclusive value="0.0"/>

2193

<xsd:maxInclusive value="180.0"/>

2194

</xsd:restriction>

2195

</xsd:simpleType><xsd:simpleType name="positiveNumberType" id="st.positiveNumberType" xmlns="http://www.w3.org/1999/xhtml">

2196

<xsd:annotation>

2197

<xsd:documentation>

2198

<h:div class="summary">A positive number.</h:div>

2199

<h:div class="description">Note that we also provide <tt>nonNegativeNumber</tt> with inclusive zero. The maximum number is (quite large) since 'unbounded' is more difficult to implement.</h:div>

2200

</xsd:documentation>

2201

</xsd:annotation>

2202

<xsd:restriction base="xsd:double">

2203

<xsd:minExclusive value="0.0"/>

2204

<xsd:maxInclusive value="1.0E+99"/>

2205

</xsd:restriction>

2206

</xsd:simpleType><xsd:simpleType name="reactionFormatType" id="st.reactionFormatType">

2207

<xsd:annotation>

2208

<xsd:documentation>

2209

<h:div class="summary">The format of the reaction.</h:div>

2210

<h:div>

2211

<h:p>This is provided for machine-understanding of the format of the reaction steps and components.</h:p>

2212

<h:p>Semantics are semi-controlled.</h:p>

2213

</h:div>

2214

</xsd:documentation>

2215

</xsd:annotation>

2216

<xsd:union>

2217

<xsd:simpleType>

2218

<xsd:restriction base="xsd:string">

2219

<xsd:enumeration value="reactantProduct">

2220

<xsd:annotation>

2221

<xsd:documentation>

2222

<h:div>

2223

<h:p>The commonest representation with reactantList and productList.</h:p>

2224

</h:div>

2225

</xsd:documentation>

2226

</xsd:annotation>

2227

</xsd:enumeration>

2228

<xsd:enumeration value="cmlSnap">

2229

<xsd:annotation>

2230

<xsd:documentation>

2231

<h:div>

2232

<h:p>A list of molecules representing snap shots on a reaction pathway.</h:p>

2233

</h:div>

2234

</xsd:documentation>

2235

</xsd:annotation>

2236

</xsd:enumeration>

2237

</xsd:restriction>

2238

</xsd:simpleType>

2239

<xsd:simpleType>

2240

<xsd:restriction base="namespaceRefType"/>

2241

</xsd:simpleType>

2242

</xsd:union>

2243

</xsd:simpleType><xsd:simpleType name="reactionRoleType" id="st.reactionRoleType">

2244

<xsd:annotation>

2245

<xsd:documentation>

2246

<h:div class="summary">The role of the reaction within a reactionList.</h:div>

2247

<h:div class="description">Semantics are semi-controlled.</h:div>

2248

</xsd:documentation>

2249

</xsd:annotation>

2250

<xsd:union>

2251

<xsd:simpleType>

2252

<xsd:restriction base="xsd:string">

2253

<xsd:enumeration value="complete">

2254

<xsd:annotation>

2255

<xsd:documentation>

2256

<h:div>

2257

<h:p>On reactionList signifies that the children are the complete description of the reaction.</h:p></h:div>

2258

</xsd:documentation>

2259

</xsd:annotation>

2260

</xsd:enumeration>

2261

<xsd:enumeration value="overall">

2262

<xsd:annotation>

2263

<xsd:documentation>

2264

<h:div>

2265

<h:p>The overall reaction in a multi-step reaction. Normally this would be the first reaction in a reactionList and the individual steps are held in a following sibling reactionList.</h:p></h:div>

2266

</xsd:documentation>

2267

</xsd:annotation>

2268

</xsd:enumeration>

2269

<xsd:enumeration value="rateDeterminingStep">

2270

<xsd:annotation>

2271

<xsd:documentation>

2272

<h:div>

2273

<h:p>The rate-determining step in a multi-step reaction. This implies also that the reaction has a role of step.</h:p></h:div>

2274

</xsd:documentation>

2275

</xsd:annotation>

2276

</xsd:enumeration>

2277

<xsd:enumeration value="step">

2278

<xsd:annotation>

2279

<xsd:documentation>

2280

<h:div>

2281

<h:p>A step in a multi-step reaction. This reaction will normally be a child of reactionList.</h:p></h:div>

2282

</xsd:documentation>

2283

</xsd:annotation>

2284

</xsd:enumeration>

2285

<xsd:enumeration value="steps">

2286

<xsd:annotation>

2287

<xsd:documentation>

2288

<h:div>

2289

<h:p>a reactionList containing steps</h:p></h:div>

2290

</xsd:documentation>

2291

</xsd:annotation>

2292

</xsd:enumeration>

2293

</xsd:restriction>

2294

</xsd:simpleType>

2295

<xsd:simpleType>

2296

<xsd:restriction base="namespaceRefType">

2297

<xsd:annotation>

2298

<xsd:documentation>

2299

<h:div>

2300

<h:p>Examples could be "myDict:step1", "foo:chainPropagation", etc.</h:p></h:div>

2301

</xsd:documentation>

2302

</xsd:annotation>

2303

</xsd:restriction>

2304

</xsd:simpleType>

2305

</xsd:union>

2306

</xsd:simpleType><xsd:simpleType id="st.reactionStepListTypeType" name="reactionStepListTypeType">

2307

<xsd:annotation>

2308

<xsd:documentation>

2309

<h:div class="summary">The sequence of steps in a reactionStepList.</h:div>

2310

<h:div class="description">By default the reactions in a reactionStepList are assumed to take place in sequence (e.g. one or more products of reaction n are used in reaction n+1 or later. However there are cases where it is known that reactions take place in parallel (e.g. if there is no overlap of molecular identities). Alternatively there are points at which there are two or more competing reactions which may depend on conditions or concentrations. A small semi-controlled vocabulary is suggested.</h:div>

2311

<h:div>The semantic of these are not fully explored, but we suggest that consecutive and simultaneous should be the first to be supported</h:div>

2312

</xsd:documentation>

2313

</xsd:annotation>

2314

<xsd:union>

2315

<xsd:simpleType>

2316

<xsd:restriction base="xsd:string">

2317

<xsd:enumeration value="unknown">

2318

<xsd:annotation>

2319

<xsd:documentation>

2320

<h:div class="summary">The order of the steps is unknown.</h:div>

2321

</xsd:documentation>

2322

</xsd:annotation>

2323

</xsd:enumeration>

2324

<xsd:enumeration value="consecutive">

2325

<xsd:annotation>

2326

<xsd:documentation>

2327

<h:div class="summary">The reaction proceeds through the steps in the order given.</h:div>

2328

</xsd:documentation>

2329

</xsd:annotation>

2330

</xsd:enumeration>

2331

<xsd:enumeration value="choice">

2332

<xsd:annotation>

2333

<xsd:documentation>

2334

<h:div class="summary">The reaction may proceed through either (or possibly both) of the contained reactions or reactionScheme, but it may not be known which.</h:div>

2335

</xsd:documentation>

2336

</xsd:annotation>

2337

</xsd:enumeration>

2338

<xsd:enumeration value="simultaneous">

2339

<xsd:annotation>

2340

<xsd:documentation>

2341

<h:div class="summary">The two or more independent reaction/List children proceed independently.</h:div>

2342

</xsd:documentation>

2343

</xsd:annotation>

2344

</xsd:enumeration>

2345

</xsd:restriction>

2346

</xsd:simpleType>

2347

<xsd:simpleType>

2348

<xsd:restriction base="namespaceRefType"/>

2349

</xsd:simpleType>

2350

</xsd:union>

2351

</xsd:simpleType><xsd:simpleType name="reactionTypeType" id="st.reactionTypeType">

2352

<xsd:annotation>

2353

<xsd:documentation>

2354

<h:div class="summary">The semantic type of the reaction.</h:div>

2355

<h:div>

2356

<h:p>This is provided for machine-understanding of the topology or logic of the reaction steps and components (i.e. not for a general classification for which <h:tt>label</h:tt> is more appropriate.)</h:p>

2357

<h:p>Semantics are semi-controlled. Some terms are appropriate to multistep reactions, and can be used with or without explicit steps.</h:p></h:div>

2358

</xsd:documentation>

2359

</xsd:annotation>

2360

<xsd:union>

2361

<xsd:simpleType>

2362

<xsd:restriction base="xsd:string">

2363

<xsd:enumeration value="chainReaction">

2364

<xsd:annotation>

2365

<xsd:documentation>

2366

<h:div>

2367

<h:p>A reaction in which one or more reactive reaction intermediates (frequently radicals) are continuously regenerated, usually through a repetitive cycle of elementary steps (the 'propagation step') (IUPAC GoldBook).</h:p></h:div>

2368

</xsd:documentation>

2369

</xsd:annotation>

2370

</xsd:enumeration>

2371

<xsd:enumeration value="initiation">

2372

<xsd:annotation>

2373

<xsd:documentation>

2374

<h:div>

2375

<h:p>

2376

A reaction or process generating free radicals (or some other reactive

2377

reaction intermediates) which then induce a chain reaction. For example,

2378

in the chlorination of alkanes by a radical mechanism the initiation step is

2379

the dissociation of molecular chlorine.

2380

IUPAC Compendium of Chemical Terminology 2nd Edition (1997).</h:p></h:div>

2381

</xsd:documentation>

2382

</xsd:annotation>

2383

</xsd:enumeration>

2384

2385

<xsd:enumeration value="termination">

2386

<xsd:annotation>

2387

<xsd:documentation>

2388

<h:div>

2389

<h:p>The steps in a chain reaction in which reactive intermediates are destroyed

2390

or rendered inactive, thus ending the chain.

2391

IUPAC Compendium of Chemical Terminology 2nd Edition (1997)

2392

.</h:p></h:div>

2393

</xsd:documentation>

2394

</xsd:annotation>

2395

</xsd:enumeration>

2396

2397

<xsd:enumeration value="reversible">

2398

<xsd:annotation>

2399

<xsd:documentation>

2400

<h:div>

2401

<h:p>A reaction which can proceed in the forward direction as readily as in the reverse direction (IUPAC GoldBook).</h:p></h:div>

2402

</xsd:documentation>

2403

</xsd:annotation>

2404

</xsd:enumeration>

2405

</xsd:restriction>

2406

</xsd:simpleType>

2407

2408

<xsd:simpleType>

2409

<xsd:restriction base="namespaceRefType"/>

2410

</xsd:simpleType>

2411

</xsd:union>

2412

</xsd:simpleType><xsd:simpleType name="refType" id="st.refType">

2413

<xsd:annotation>

2414

<xsd:documentation>

2415

<h:div class="summary">A reference to an existing object.</h:div>

2416

<h:div class="description">A reference to an existing element in the document.

2417

The target of the ref attribute must exist. The test for validity will normally

2418

occur in the element's _appinfo_. Any DOM Node created from this element will

2419

normally be a reference to another Node, so that if the target node is modified

2420

a the dereferenced content is modified. At present there are no deep copy

2421

semantics hardcoded into the schema.</h:div>

2422

<h:div class="description">The semantic of reference are normally identical to

2423

an idType (e.g. "a123b"). Howevere there are some cases where compound references

2424

are required, such as "a123b:pq456". It is likely that this will be superseded at

2425

by RDF or Xpointer, but as long as we have non-uniqueIds this is a problem</h:div>

2426

</xsd:documentation>

2427

</xsd:annotation>

2428

<xsd:restriction base="xsd:string">

2429

<xsd:pattern value="([A-Za-z_][A-Za-z0-9_\.\-]*:)?[A-Za-z_][A-Za-z0-9_\.\-]*"/>

2430

</xsd:restriction>

2431

</xsd:simpleType><xsd:simpleType id="st.relatedEntryTypeType" name="relatedEntryTypeType">

2432

<xsd:annotation>

2433

<xsd:documentation>

2434

<h:div class="summary">Type of relatedEntry.</h:div>

2435

<h:div class="description">Type represents a the type of relationship in a relatedEntry element.</h:div>

2436

</xsd:documentation>

2437

</xsd:annotation>

2438

<xsd:union>

2439

<xsd:simpleType>

2440

<xsd:restriction base="xsd:string">

2441

<xsd:enumeration value="parent"/>

2442

<xsd:enumeration value="partitiveParent"/>

2443

<xsd:enumeration value="child"/>

2444

<xsd:enumeration value="partitiveChild"/>

2445

<xsd:enumeration value="related"/>

2446

<xsd:enumeration value="synonym"/>

2447

<xsd:enumeration value="quasi-synonym"/>

2448

<xsd:enumeration value="antonym"/>

2449

<xsd:enumeration value="homonym"/>

2450

<xsd:enumeration value="see"/>

2451

<xsd:enumeration value="seeAlso"/>

2452

<xsd:enumeration value="abbreviation"/>

2453

<xsd:enumeration value="acronym"/>

2454

</xsd:restriction>

2455

</xsd:simpleType>

2456

<xsd:simpleType>

2457

<xsd:restriction base="namespaceRefType"/>

2458

</xsd:simpleType>

2459

</xsd:union>

2460

</xsd:simpleType><xsd:simpleType id="st.schemeType" name="schemeType">

2461

<xsd:annotation>

2462

<xsd:documentation>

2463

<h:div class="summary">The sequence of steps in a reactionList.</h:div>

2464

2465

</xsd:documentation>

2466

</xsd:annotation>

2467

<xsd:union>

2468

<xsd:simpleType>

2469

<xsd:restriction base="xsd:string">

2470

<xsd:enumeration value="unknown">

2471

<xsd:annotation>

2472

<xsd:documentation>

2473

<h:div class="summary">The order of the steps is unknow.</h:div>

2474

</xsd:documentation>

2475

</xsd:annotation>

2476

</xsd:enumeration>

2477

<xsd:enumeration value="sequence">

2478

<xsd:annotation>

2479

<xsd:documentation>

2480

<h:div class="summary">The reaction proceeds through the steps in the order give.</h:div>

2481

</xsd:documentation>

2482

</xsd:annotation>

2483

</xsd:enumeration>

2484

<xsd:enumeration value="choice">

2485

<xsd:annotation>

2486

<xsd:documentation>

2487

<h:div class="summary">The reaction may proceed through either of the contained reactions or reactionScheme.</h:div>

2488

</xsd:documentation>

2489

</xsd:annotation>

2490

</xsd:enumeration>

2491

<xsd:enumeration value="and">

2492

<xsd:annotation>

2493

<xsd:documentation>

2494

<h:div class="summary">The two or more independent reaction/List children proceed independently. This can be extended to synthetic chemistry where two parts of the synthesis are conducted in parallel.</h:div>

2495

</xsd:documentation>

2496

</xsd:annotation>

2497

</xsd:enumeration>

2498

</xsd:restriction>

2499

</xsd:simpleType>

2500

<xsd:simpleType>

2501

<xsd:restriction base="namespaceRefType"/>

2502

</xsd:simpleType>

2503

</xsd:union>

2504

</xsd:simpleType><xsd:simpleType name="sizeType" id="st.sizeType">

2505

<xsd:annotation>

2506

<xsd:documentation>

2507

<h:div class="summary">The size of an array.</h:div>

2508

<h:div class="description">The size of an array. Redundant, but serves as a check for processing software (useful if delimiters are used).</h:div>

2509

</xsd:documentation>

2510

</xsd:annotation>

2511

<xsd:restriction base="xsd:nonNegativeInteger"/>

2512

</xsd:simpleType><xsd:simpleType name="spaceType" id="st.spaceType">

2513

<xsd:annotation>

2514

<xsd:documentation>

2515

<h:div class="summary">Signifies real or reciprocal space.</h:div>

2516

<h:div class="description">Likely to be used on types such as lattice, plane, point.</h:div>

2517

<h:div class="example" href="space1.xml"/>

2518

</xsd:documentation>

2519

</xsd:annotation>

2520

<xsd:union>

2521

<xsd:simpleType>

2522

<xsd:restriction base="xsd:string">

2523

<xsd:enumeration value="real"/>

2524

<xsd:enumeration value="k-space">

2525

<xsd:annotation>

2526

<xsd:documentation>

2527

<h:div class="description">A synonym for reciprocal.</h:div>

2528

</xsd:documentation>

2529

</xsd:annotation>

2530

</xsd:enumeration>

2531

<xsd:enumeration value="Fourier">

2532

<xsd:annotation>

2533

<xsd:documentation>

2534

<h:div class="description">A synonym for reciprocal.</h:div>

2535

</xsd:documentation>

2536

</xsd:annotation>

2537

</xsd:enumeration>

2538

<xsd:enumeration value="reciprocal">

2539

<xsd:annotation>

2540

<xsd:documentation>

2541

<h:div class="description"/>

2542

</xsd:documentation>

2543

</xsd:annotation>

2544

</xsd:enumeration>

2545

</xsd:restriction>

2546

</xsd:simpleType>

2547

<xsd:simpleType>

2548

<xsd:restriction base="namespaceRefType">

2549

<xsd:annotation>

2550

<xsd:documentation>

2551

<h:div class="summary">User-defined space-type.</h:div>

2552

<h:div class="description">No obvious possibilities, but who know.</h:div>

2553

</xsd:documentation>

2554

</xsd:annotation>

2555

</xsd:restriction>

2556

</xsd:simpleType>

2557

</xsd:union>

2558

</xsd:simpleType><xsd:simpleType id="st.spectrumTypeType" name="spectrumTypeType">

2559

<xsd:annotation>

2560

<xsd:documentation>

2561

<h:div class="summary">The type of the spectrum.</h:div>

2562

</xsd:documentation>

2563

</xsd:annotation>

2564

<xsd:union>

2565

<xsd:simpleType>

2566

<xsd:restriction base="xsd:string">

2567

<xsd:enumeration value="infrared">

2568

<xsd:annotation>

2569

<xsd:documentation>

2570

<h:div class="summary">An infrared spectrum.</h:div>

2571

<h:div class="description">The measurement should denote transmittance or absorbanc.</h:div>

2572

</xsd:documentation>

2573

</xsd:annotation>

2574

</xsd:enumeration>

2575

<xsd:enumeration value="massSpectrum">

2576

<xsd:annotation>

2577

<xsd:documentation>

2578

<h:div class="summary">A "simple" mass spectrum.</h:div>

2579

<h:div class="description">This excludes experiments such as GC/MS, MS/MS, etc. though these could be constructed out of individual spectra with some care. The spectrum may be continuous ( <h:tt>data</h:tt> or a <h:tt>peakList</h:tt>).</h:div>

2580

</xsd:documentation>

2581

</xsd:annotation>

2582

</xsd:enumeration>

2583

<xsd:enumeration value="NMR">

2584

<xsd:annotation>

2585

<xsd:documentation>

2586

<h:div class="summary">An NMR spectrum.</h:div>

2587

<h:div class="description">This can include any experiment which creates a "1D" or "2D" data array. The symmetry of the spectrum can be specified but the details of the NMR experiment (COSY, NOESY, etc.) are not part of CMLSpect. They can be described though the normal <h:tt>dictRef</h:tt> mechanism.</h:div>

2588

</xsd:documentation>

2589

</xsd:annotation>

2590

</xsd:enumeration>

2591

<xsd:enumeration value="UV/VIS">

2592

<xsd:annotation>

2593

<xsd:documentation>

2594

<h:div class="summary">A spectrum somewhere in the UV VIS region of the spectrum.</h:div>

2595

<h:div class="description">The measurement should denote transmittance or absorbance.</h:div>

2596

</xsd:documentation>

2597

</xsd:annotation>

2598

</xsd:enumeration>

2599

</xsd:restriction>

2600

</xsd:simpleType>

2601

<xsd:simpleType>

2602

<xsd:restriction base="namespaceRefType"/>

2603

</xsd:simpleType>

2604

</xsd:union>

2605

</xsd:simpleType><xsd:simpleType name="sphere3Type" id="st.sphere3Type">

2606

<xsd:annotation>

2607

<xsd:documentation>

2608

<h:div class="summary">A sphere in 3-space.</h:div>

2609

<h:div class="description">Defined by 4 real numbers, conventionally a point3 at

2610

the centre of the sphere and a nonNegative scalar for the radius.</h:div>

2611

<h:div class="example" href="sphere31.xml"/>

2612

</xsd:documentation>

2613

</xsd:annotation>

2614

<xsd:restriction>

2615

<xsd:simpleType>

2616

<xsd:list itemType="xsd:double"/>

2617

</xsd:simpleType>

2618

<xsd:length value="4"/>

2619

</xsd:restriction>

2620

</xsd:simpleType><xsd:simpleType name="stateType" id="st.stateType">

2621

<xsd:annotation>

2622

<xsd:documentation>

2623

<h:div class="summary">State of a substance or property.</h:div>

2624

<h:div class="description">The state(s) of matter appropriate to a substance or property. It follows a partially controlled vocabulary. It can be extended through namespace codes to dictionaries.</h:div>

2625

<h:div class="example" href="stateType1.xml"/>

2626

</xsd:documentation>

2627

</xsd:annotation>

2628

<xsd:union>

2629

<xsd:simpleType>

2630

<xsd:restriction base="xsd:string">

2631

2632

<xsd:enumeration value="aqueous">

2633

<xsd:annotation>

2634

<xsd:documentation>

2635

<h:div>An aqueous solutio.</h:div>

2636

</xsd:documentation>

2637

</xsd:annotation>

2638

</xsd:enumeration>

2639

<xsd:enumeration value="gas">

2640

<xsd:annotation>

2641

<xsd:documentation>

2642

<h:div>Gas or vapor. The default state for computation on isolated molecule.</h:div>

2643

</xsd:documentation>

2644

</xsd:annotation>

2645

</xsd:enumeration>

2646

<xsd:enumeration value="glass">

2647

<xsd:annotation>

2648

<xsd:documentation>

2649

<h:div>A glassy stat.</h:div>

2650

</xsd:documentation>

2651

</xsd:annotation>

2652

</xsd:enumeration>

2653

<xsd:enumeration value="liquid">

2654

<xsd:annotation>

2655

<xsd:documentation>

2656

<h:div>Normally pure liquid (use solution where appropriate.</h:div>

2657

</xsd:documentation>

2658

</xsd:annotation>

2659

</xsd:enumeration>

2660

<xsd:enumeration value="nematic">

2661

<xsd:annotation>

2662

<xsd:documentation>

2663

<h:div>The nematic phas.</h:div>

2664

</xsd:documentation>

2665

</xsd:annotation>

2666

</xsd:enumeration>

2667

<xsd:enumeration value="smectic">

2668

<xsd:annotation>

2669

<xsd:documentation>

2670

<h:div>The smectic phas.</h:div>

2671

</xsd:documentation>

2672

</xsd:annotation>

2673

</xsd:enumeration>

2674

<xsd:enumeration value="solid">

2675

<xsd:annotation>

2676

<xsd:documentation>

2677

<h:div>A soli.</h:div>

2678

</xsd:documentation>

2679

</xsd:annotation>

2680

</xsd:enumeration>

2681

<xsd:enumeration value="solidSolution">

2682

<xsd:annotation>

2683

<xsd:documentation>

2684

<h:div>A solid solutio.</h:div>

2685

</xsd:documentation>

2686

</xsd:annotation>

2687

</xsd:enumeration>

2688

<xsd:enumeration value="solution">

2689

<xsd:annotation>

2690

<xsd:documentation>

2691

<h:div>A (liquid) solutio.</h:div>

2692

</xsd:documentation>

2693

</xsd:annotation>

2694

</xsd:enumeration>

2695

</xsd:restriction>

2696

</xsd:simpleType>

2697

2698

<xsd:simpleType>

2699

<xsd:restriction base="namespaceRefType"/>

2700

</xsd:simpleType>

2701

</xsd:union>

2702

2703

</xsd:simpleType><xsd:simpleType name="stereoType" id="st.stereoType">

2704

<xsd:annotation>

2705

<xsd:documentation>

2706

<h:div class="summary">Bond stereochemistry as a string.</h:div>

2707

<h:div class="description">This is purely conventional. There is no default value.

2708

The emptyString attribute can be used to indicate a bond of

2709

unknown or unspecified type. The interpretation of this is outside

2710

the scope of CML-based algorithms. It may be accompanied by a <h:tt>convention</h:tt>

2711

attribute which links to a dictionary.</h:div>

2712

<h:div class="example" href="bond1.xml"/>

2713

</xsd:documentation>

2714

</xsd:annotation>

2715

<xsd:restriction base="xsd:string">

2716

<xsd:enumeration value="C">

2717

<xsd:annotation>

2718

<xsd:documentation>

2719

<h:div class="summary">A cis bond.</h:div>

2720

</xsd:documentation>

2721

</xsd:annotation>

2722

</xsd:enumeration>

2723

<xsd:enumeration value="T">

2724

<xsd:annotation>

2725

<xsd:documentation>

2726

<h:div class="summary">A trans bond.</h:div>

2727

</xsd:documentation>

2728

</xsd:annotation>

2729

</xsd:enumeration>

2730

<xsd:enumeration value="W">

2731

<xsd:annotation>

2732

<xsd:documentation>

2733

<h:div class="summary">A wedge bond.</h:div>

2734

</xsd:documentation>

2735

</xsd:annotation>

2736

</xsd:enumeration>

2737

<xsd:enumeration value="H">

2738

<xsd:annotation>

2739

<xsd:documentation>

2740

<h:div class="summary">A hatch bond.</h:div>

2741

</xsd:documentation>

2742

</xsd:annotation>

2743

</xsd:enumeration>

2744

<xsd:enumeration value="">

2745

<xsd:annotation>

2746

<xsd:documentation>

2747

<h:div class="summary">empty or missing.</h:div>

2748

</xsd:documentation>

2749

</xsd:annotation>

2750

</xsd:enumeration>

2751

</xsd:restriction>

2752

</xsd:simpleType><xsd:simpleType name="stringArrayType" id="st.stringArrayType">

2753

<xsd:annotation>

2754

<xsd:documentation>

2755

<h:div class="summary">An array of strings, separated by whitespace.</h:div>

2756

<h:div class="description">An array of strings, separated by whitespace. If the strings have embedded whitespace or may be empty (zero-length), a non-whitespace single-character delimiter must be used. At present no machine validation</h:div>

2757

<h:div class="example" href="stringArrayType1.xml"/>

2758

</xsd:documentation>

2759

</xsd:annotation>

2760

<xsd:list itemType="xsd:string"/>

2761

</xsd:simpleType><xsd:simpleType id="st.substanceListTypeType" name="substanceListTypeType">

2762

<xsd:annotation>

2763

<xsd:documentation>

2764

<h:div class="summary">Type of the substanceList.</h:div>

2765

<h:div class="description">Extension is allowed through the "other" value.</h:div>

2766

</xsd:documentation>

2767

</xsd:annotation>

2768

<xsd:restriction base="xsd:string">

2769

<xsd:enumeration value="solution"/>

2770

<xsd:enumeration value="mixture"/>

2771

<xsd:enumeration value="other"/>

2772

</xsd:restriction>

2773

</xsd:simpleType><xsd:simpleType name="torsionAngleType" id="st.torsionAngleType">

2774

<xsd:annotation>

2775

<xsd:documentation>

2776

<h:div class="summary">The type of a torsion angle.</h:div>

2777

</xsd:documentation>

2778

</xsd:annotation>

2779

<xsd:restriction base="xsd:double">

2780

<xsd:minInclusive value="-360.0"/>

2781

<xsd:maxInclusive value="360.0"/>

2782

</xsd:restriction>

2783

</xsd:simpleType><xsd:simpleType name="unitListTypeType" id="st.unitListTypeType">

2784

<xsd:annotation>

2785

<xsd:documentation>

2786

<h:div class="summary">Type of unitList.</h:div>

2787

<h:div class="description">Required to differentiate between the two types of

2788

unitList (units and unitTypes)</h:div>

2789

2790

</xsd:documentation>

2791

</xsd:annotation>

2792

<xsd:restriction base="xsd:string">

2793

<xsd:enumeration value="unit">

2794

<xsd:annotation>

2795

<xsd:documentation>

2796

<h:div class="description">child elements are unit</h:div>

2797

</xsd:documentation>

2798

</xsd:annotation>

2799

</xsd:enumeration>

2800

<xsd:enumeration value="unitType">

2801

<xsd:annotation>

2802

<xsd:documentation>

2803

<h:div class="description">child elements are unitType</h:div>

2804

</xsd:documentation>

2805

</xsd:annotation>

2806

</xsd:enumeration>

2807

</xsd:restriction>

2808

</xsd:simpleType><xsd:simpleType name="unitsType" id="st.unitsType">

2809

<xsd:annotation>

2810

<xsd:documentation>

2811

<h:div class="summary">Scientific units.</h:div>

2812

<h:div class="description">These will be linked to dictionaries of

2813

units with conversion information, using namespaced references

2814

(e.g. <h:tt>si:m</h:tt>). Distinguish carefully from _unitType_

2815

which is an element describing a type of a unit in a

2816

_unitList_.</h:div>

2817

<h:div class="example" href="unit2.xml"/>

2818

</xsd:documentation>

2819

</xsd:annotation>

2820

<xsd:restriction base="namespaceRefType"/>

2821

</xsd:simpleType><xsd:simpleType name="vector3Type" id="st.vector3Type">

2822

<xsd:annotation>

2823

<xsd:documentation>

2824

<h:div class="summary">A vector in 3-space.</h:div>

2825

<h:div class="description">No constraints on magnitude (i.e. could be zero.</h:div>

2826

<h:div class="example" href="vector31.xml"/>

2827

</xsd:documentation>

2828

</xsd:annotation>

2829

<xsd:restriction>

2830

<xsd:simpleType>

2831

<xsd:list itemType="xsd:double"/>

2832

</xsd:simpleType>

2833

<xsd:length value="3"/>

2834

</xsd:restriction>

2835

</xsd:simpleType><xsd:simpleType name="xmlElementType" id="st.xmlElementType">

2836

<xsd:annotation>

2837

<xsd:documentation>

2838

<h:div class="summary">The name of an XMLElement.</h:div>

2839

<h:div class="description">

2840

<h:p>(Distinguish from a chemical element as in elementTypeType).

2841

Currently used for assigning XMLElement types to references (e.g. to='a1' toType='atom').

2842

Semantics are not controlled and in principle elements outside the CML tagSet

2843

could be used. Implementers cannot assume that namespace prefixes can be resolved

2844

and default usage is probably the local name.</h:p></h:div>

2845

</xsd:documentation>

2846

</xsd:annotation>

2847

<xsd:restriction base="refType"/>

2848

</xsd:simpleType><xsd:attributeGroup id="attGp.abbreviation" name="abbreviation">

2849

<xsd:attribute id="att.abbreviation" name="abbreviation" type="xsd:string">

2850

<xsd:annotation>

2851

<xsd:documentation>

2852

<h:div class="summary">Abbreviation.</h:div>

2853

<h:div class="description">Abbreviation for units, terms, etc.</h:div>

2854

</xsd:documentation>

2855

</xsd:annotation>

2856

</xsd:attribute>

2857

</xsd:attributeGroup><xsd:attributeGroup id="attGp.actionOrder" name="actionOrder">

2858

<xsd:attribute name="order" id="att.actionOrder" type="actionOrderType">

2859

<xsd:annotation>

2860

<xsd:documentation>

2861

<h:div class="summary">Describes whether child elements are sequential or parallel.</h:div>

2862

<h:div class="description">There is no default.</h:div>

2863

</xsd:documentation>

2864

</xsd:annotation>

2865

</xsd:attribute>

2866

</xsd:attributeGroup><xsd:attributeGroup id="attGp.alternativeType" name="alternativeType">

2867

2868

<xsd:attribute name="type" id="att.alternativeType" type="alternativeTypeType">

2869

<xsd:annotation>

2870

<xsd:documentation>

2871

<h:div class="summary">The type of an alternative.</h:div>

2872

<h:div class="general">This adds semantics to an _alternative_ and might be used by an RDF or related engine.</h:div>

2873

</xsd:documentation>

2874

</xsd:annotation>

2875

</xsd:attribute>

2876

</xsd:attributeGroup><xsd:attributeGroup id="attGp.angleUnits" name="angleUnits">

2877

2878

<xsd:attribute id="att.angleUnits" name="units" type="angleUnitsType">

2879

<xsd:annotation>

2880

<xsd:documentation>

2881

<h:div class="summary">Restricts units to radians or degrees.</h:div>

2882

<h:div class="description"/>

2883

</xsd:documentation>

2884

</xsd:annotation>

2885

</xsd:attribute>

2886

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomIDArray" name="atomIDArray">

2887

2888

<xsd:attribute name="atomID" id="att.atomIDArray" type="atomRefArrayType">

2889

<xsd:annotation>

2890

<xsd:documentation>

2891

<h:div class="summary">An array of atom IDs.</h:div>

2892

<h:div class="description">Normally an attribute of an array-based element.</h:div>

2893

</xsd:documentation>

2894

</xsd:annotation>

2895

</xsd:attribute>

2896

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomMap" name="atomMap">

2897

<xsd:attribute id="att.atomMap" name="atomMap" type="idType">

2898

<xsd:annotation>

2899

<xsd:documentation>

2900

<h:div class="summary">A reference to a map providing mappings between atoms</h:div>

2901

<h:div class="description">The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking atoms. The topology of the linking is defined by the application - it could be overlay of molecular fragments, reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of atoms are of equal size and have 1:1 mapping between each id. This is another way of saying that the atoms mapped by a given ID are "the same atom". </h:div>

2902

</xsd:documentation>

2903

</xsd:annotation>

2904

</xsd:attribute>

2905

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomRef" name="atomRef">

2906

<xsd:attribute id="att.atomRef" name="atomRef" type="atomRefType">

2907

<xsd:annotation>

2908

<xsd:documentation>

2909

<h:div class="summary">A reference to an atom.</h:div>

2910

<h:div class="description">Used by bond, electron, etc.</h:div>

2911

</xsd:documentation>

2912

</xsd:annotation>

2913

</xsd:attribute>

2914

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomRef1Array" name="atomRef1Array">

2915

2916

<xsd:attribute name="atomRef1" id="att.atomRef1Array" type="atomRefArrayType">

2917

<xsd:annotation>

2918

<xsd:documentation>

2919

<h:div class="summary">The first atoms in each bond.</h:div>

2920

<h:div class="description">Currently only used in bondArray in CML2 array mode.</h:div>

2921

</xsd:documentation>

2922

</xsd:annotation>

2923

</xsd:attribute>

2924

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomRef2Array" name="atomRef2Array">

2925

2926

<xsd:attribute name="atomRef2" id="att.atomRef2Array" type="atomRefArrayType">

2927

<xsd:annotation>

2928

<xsd:documentation>

2929

<h:div class="summary">The second atoms in each bond.</h:div>

2930

<h:div class="general">Only used in bondArray in CML2 array mode.</h:div>

2931

</xsd:documentation>

2932

</xsd:annotation>

2933

</xsd:attribute>

2934

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomRefArray" name="atomRefArray">

2935

<xsd:attribute id="att.atomRefArray" name="atomRefArray" type="atomRefArrayType">

2936

<xsd:annotation>

2937

<xsd:documentation>

2938

<h:div class="summary">An array of references to atoms.</h:div>

2939

<h:div class="description">Typical use would be to atoms defining a plane.</h:div>

2940

</xsd:documentation>

2941

</xsd:annotation>

2942

</xsd:attribute>

2943

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomRefGroup" name="atomRefGroup">

2944

<xsd:attribute id="att.atomRefGroup" name="atomRefGroup" type="atomIDType"/>

2945

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomRefs" name="atomRefs">

2946

<xsd:attribute name="atomRefs" id="att.atomRefs" type="atomRefArrayType">

2947

<xsd:annotation>

2948

<xsd:documentation>

2949

<h:div class="summary">A reference to a list of atoms.</h:div>

2950

<h:div class="description">Used by bonds, electrons, atomSets, etc.</h:div>

2951

</xsd:documentation>

2952

</xsd:annotation>

2953

</xsd:attribute>

2954

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomRefs2" name="atomRefs2">

2955

<xsd:attribute name="atomRefs2" id="att.atomRefs2" type="atomRefs2Type">

2956

<xsd:annotation>

2957

<xsd:documentation>

2958

<h:div class="summary">References to two different atoms.</h:div>

2959

<h:div class="description">Available for any reference to atoms but normally will be the normal reference attribute on the bond element. The order of atoms is preserved and may matter for some conventions (e.g. wedge/hatch or donor bonds.</h:div>

2960

</xsd:documentation>

2961

</xsd:annotation>

2962

</xsd:attribute>

2963

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomRefs3" name="atomRefs3">

2964

<xsd:attribute id="att.atomRefs3" name="atomRefs3" type="atomRefs3Type">

2965

<xsd:annotation>

2966

<xsd:documentation>

2967

<h:div class="summary">A list of three references to atoms.</h:div>

2968

<h:div class="description">Typically used for defining angles,

2969

but could also be used to define a three-centre bond.</h:div>

2970

</xsd:documentation>

2971

</xsd:annotation>

2972

</xsd:attribute>

2973

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomRefs4" name="atomRefs4">

2974

<xsd:attribute id="att.atomRefs4" name="atomRefs4" type="atomRefs4Type">

2975

<xsd:annotation>

2976

<xsd:documentation>

2977

<h:div class="summary">A list of 4 references to atoms.</h:div>

2978

<h:div class="description">Typically used for defining torsions and atomParities,

2979

but could also be used to define a four-centre bond.</h:div>

2980

</xsd:documentation>

2981

</xsd:annotation>

2982

</xsd:attribute>

2983

</xsd:attributeGroup><xsd:attributeGroup id="attGp.atomSetRef" name="atomSetRef">

2984

<xsd:attribute name="atomSetRef" type="refType" id="att.atomSetRef">

2985

<xsd:annotation>

2986

<xsd:documentation>

2987

<h:div class="summary">An atomSet describing the region.</h:div>

2988

<h:div class="description">Any point falling within atomOffset of any atom in the set lies within the region. This means the region could consist of disjoint fragments.</h:div>

2989

</xsd:documentation>

2990

</xsd:annotation>

2991

</xsd:attribute>

2992

</xsd:attributeGroup><xsd:attributeGroup id="attGp.bondIDArray" name="bondIDArray">

2993

2994

<xsd:attribute name="bondID" id="att.bondIDArray" type="bondRefArrayType">

2995

<xsd:annotation>

2996

<xsd:documentation>

2997

<h:div class="summary">The IDs for an array of bond.</h:div>

2998

<h:div class="general">Required in CML2 array mode.</h:div>

2999

</xsd:documentation>

3000

</xsd:annotation>

3001

</xsd:attribute>

3002

</xsd:attributeGroup><xsd:attributeGroup id="attGp.bondMap" name="bondMap">

3003

<xsd:attribute id="att.bondMap" name="bondMap" type="xsd:QName">

3004

<xsd:annotation>

3005

<xsd:documentation>

3006

<h:div class="summary">A reference to a map providing mappings between bonds</h:div>

3007

<h:div class="description">The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking bonds. The topology of the linking is defined by the application - it could be overlay of molecular fragments, reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of bonds are of equal size and have 1:1 mapping between each id. This is another way of saying that the bonds mapped by a given ID are "the same bond". </h:div>

3008

</xsd:documentation>

3009

</xsd:annotation>

3010

</xsd:attribute>

3011

</xsd:attributeGroup><xsd:attributeGroup id="attGp.bondRef" name="bondRef">

3012

<xsd:attribute name="bondRef" id="att.bondRef" type="bondRefType">

3013

<xsd:annotation>

3014

<xsd:documentation>

3015

<h:div class="summary">A reference to a bond.</h:div>

3016

<h:div class="description">used by electron, etc.</h:div>

3017

</xsd:documentation>

3018

</xsd:annotation>

3019

</xsd:attribute>

3020

</xsd:attributeGroup><xsd:attributeGroup id="attGp.bondRefs" name="bondRefs">

3021

<xsd:attribute name="bondRefs" id="att.bondRefs" type="bondRefArrayType">

3022

<xsd:annotation>

3023

<xsd:documentation>

3024

<h:div class="summary">A reference to a list of bonds.</h:div>

3025

<h:div class="description">Used by electrons, bondSets, etc.</h:div>

3026

</xsd:documentation>

3027

</xsd:annotation>

3028

</xsd:attribute>

3029

</xsd:attributeGroup><xsd:attributeGroup id="attGp.box3" name="box3">

3030

<xsd:attribute name="box3" type="box3Type" id="att.box3">

3031

<xsd:annotation>

3032

<xsd:documentation>

3033

<h:div class="summary">A parallelipiped box.</h:div>

3034

<h:div class="description">By default the box uses isometric Cartesians axes but can also be linked to lattice Vector. Any point falling within the box or on a boundary is within the regio.</h:div>

3035

</xsd:documentation>

3036

</xsd:annotation>

3037

</xsd:attribute>

3038

</xsd:attributeGroup><xsd:attributeGroup id="attGp.builtin" name="builtin">

3039

<xsd:attribute name="builtin" id="att.builtin" type="xsd:string">

3040

<xsd:annotation>

3041

<xsd:documentation>

3042

<h:div class="summary">builtin children.</h:div>

3043

<h:div class="description">CML1-only - now deprecated.</h:div>

3044

</xsd:documentation>

3045

</xsd:annotation>

3046

</xsd:attribute>

3047

</xsd:attributeGroup><xsd:attributeGroup id="attGp.chirality" name="chirality">

3048

<xsd:attribute name="chirality" id="att.chirality" type="chiralityType">

3049

<xsd:annotation>

3050

<xsd:documentation>

3051

<h:div class="summary">The chirality of a system or molecule.</h:div>

3052

<h:div class="description">This is being actively investigated by a IUPAC committee (2002) so the convention is likely to change. No formal default.</h:div>

3053

</xsd:documentation>

3054

</xsd:annotation>

3055

</xsd:attribute>

3056

</xsd:attributeGroup><xsd:attributeGroup id="attGp.columns" name="columns">

3057

<xsd:attribute name="columns" id="att.columns" type="sizeType">

3058

<xsd:annotation>

3059

<xsd:documentation>

3060

<h:div class="summary">Number of columns.</h:div>

3061

</xsd:documentation>

3062

</xsd:annotation>

3063

</xsd:attribute>

3064

</xsd:attributeGroup><xsd:attributeGroup id="attGp.concise" name="concise">

3065

<xsd:attribute name="concise" id="att.concise" type="formulaType">

3066

<xsd:annotation>

3067

<xsd:documentation>

3068

<h:div class="summary">A concise formula.</h:div>

3069

<h:div class="general">The string represents an (unstructured) formula i.e. no submolecules.

3070

Recommended to use the format "H 2 O 1", etc.</h:div>

3071

</xsd:documentation>

3072

</xsd:annotation>

3073

</xsd:attribute>

3074

</xsd:attributeGroup><xsd:attributeGroup id="attGp.constantToData" name="constantToData">

3075

<xsd:attribute id="att.constantToData" name="constantToData" type="xsd:double" default="0.0">

3076

<xsd:annotation>

3077

<xsd:documentation>

3078

<h:div class="summary">The constant to add to the raw data.</h:div>

3079

<h:div class="description"> add *after* applying any multiplier.</h:div>

3080

</xsd:documentation>

3081

</xsd:annotation>

3082

</xsd:attribute>

3083

</xsd:attributeGroup><xsd:attributeGroup id="attGp.constantToSI" name="constantToSI">

3084

<xsd:attribute id="att.constantToSI" name="constantToSI" type="xsd:double">

3085

<xsd:annotation>

3086

<xsd:documentation>

3087

<h:div class="summary">Additive constant to generate SI equivalent.</h:div>

3088

<h:div class="description">The amount to add to a quantity in non-SI units to convert its representation to SI Units. This is applied *after* multiplierToSI. It is necessarily zero for SI units.</h:div>

3089

</xsd:documentation>

3090

</xsd:annotation>

3091

</xsd:attribute>

3092

</xsd:attributeGroup><xsd:attributeGroup id="attGp.constraint" name="constraint">

3093

<xsd:attribute name="constraint" id="att.constraint" type="xsd:string">

3094

<xsd:annotation>

3095

<xsd:documentation>

3096

<h:div class="summary">Constraint on a parameter.</h:div>

3097

<h:div class="description">Semantics not yet finalised. We anticipate "fixed",

3098

"none" and symbolic relationships to other parameters.</h:div>

3099

</xsd:documentation>

3100

</xsd:annotation>

3101

</xsd:attribute>

3102

</xsd:attributeGroup><xsd:attributeGroup id="attGp.content" name="content">

3103

<xsd:attribute name="content" type="xsd:string" id="att.content">

3104

<xsd:annotation>

3105

<xsd:documentation>

3106

<h:div class="summary">content of metadata.</h:div>

3107

</xsd:documentation>

3108

</xsd:annotation>

3109

</xsd:attribute>

3110

</xsd:attributeGroup><xsd:attributeGroup name="convention" id="attGp.convention">

3111

<xsd:attribute id="att.convention" name="convention" type="refType">

3112

<xsd:annotation>

3113

<xsd:documentation>

3114

<h:div class="summary">A reference to a convention.</h:div>

3115

<h:div class="description">There is no controlled vocabulary for conventions, but the author must ensure that the semantics are openly available and that there are mechanisms for implementation. The convention is inherited by all the subelements,

3116

so that a convention for <h:tt>molecule</h:tt> would by default extend to its <h:tt>bond</h:tt> and <h:tt>atom</h:tt> children. This can be overwritten

3117

if necessary by an explicit <h:tt>convention</h:tt>.

3118

<h:p>It may be useful to create conventions with namespaces (e.g. <h:tt>iupac:name</h:tt>).

3119

Use of <h:tt>convention</h:tt> will normally require non-STMML semantics, and should be used with

3120

caution. We would expect that conventions prefixed with "ISO" would be useful,

3121

such as ISO8601 for dateTimes.</h:p>

3122

<h:p>There is no default, but the conventions of STMML or the related language (e.g. CML) will be assumed.</h:p></h:div>

3123

<h:div class="example" id="ex" href="convGroup1.xml"/>

3124

</xsd:documentation>

3125

</xsd:annotation>

3126

</xsd:attribute>

3127

</xsd:attributeGroup><xsd:attributeGroup id="attGp.conventionValue" name="conventionValue">

3128

<xsd:attribute name="conventionValue" id="att.conventionValue" type="xsd:string">

3129

<xsd:annotation>

3130

<xsd:documentation>

3131

<h:div class="summary">The value of an element with a _convention_.</h:div>

3132

<h:div class="description">When convention is used this attribute must be present and element content must be empty.</h:div>

3133

</xsd:documentation>

3134

</xsd:annotation>

3135

</xsd:attribute>

3136

</xsd:attributeGroup><xsd:attributeGroup id="attGp.count" name="count">

3137

<xsd:attribute id="att.count" name="count" type="positiveNumberType">

3138

<xsd:annotation>

3139

<xsd:documentation>

3140

<h:div class="summary">The count of the object.</h:div>

3141

<h:div class="description">No fixed semantics or default, normally integers.

3142

It is presumed that the element can be multiplied by the count value.</h:div>

3143

</xsd:documentation>

3144

</xsd:annotation>

3145

</xsd:attribute>

3146

</xsd:attributeGroup><xsd:attributeGroup id="attGp.countArray" name="countArray">

3147

<xsd:attribute id="att.countArray" name="count" type="countArrayType">

3148

<xsd:annotation>

3149

<xsd:documentation>

3150

<h:div class="summary">Array of object counts.</h:div>

3151

<h:div class="description">No fixed semantics or default, normally integral. It is presumed that the element can be multiplied by the count value.</h:div>

3152

</xsd:documentation>

3153

</xsd:annotation>

3154

</xsd:attribute>

3155

</xsd:attributeGroup><xsd:attributeGroup id="attGp.dataType" name="dataType">

3156

<xsd:attribute id="att.dataType" name="dataType" type="dataTypeType">

3157

<xsd:annotation>

3158

<xsd:documentation>

3159

<h:div class="summary">The data type of the object.</h:div>

3160

<h:div class="description">Normally applied to scalar/array

3161

objects but may extend to more complex one.</h:div>

3162

</xsd:documentation>

3163

</xsd:annotation>

3164

</xsd:attribute>

3165

</xsd:attributeGroup><xsd:attributeGroup id="attGp.default" name="default">

3166

<xsd:attribute name="default" type="xsd:string" id="att.default">

3167

<xsd:annotation>

3168

<xsd:documentation>

3169

<h:div class="summary">default value in an enumeration.</h:div>

3170

<h:div class="description">A non-whitespace string (value is irrelevant) indicates that the content of this enumeration is the default value (usually of a scalar). It is an error to have more than one default. If the scalar in an instance document has no value (i.e. is empty or contains only whitespace) its value is given by the default. If the scalar in the instance is empty and no enumerations have a default attribute, an application may throw an error.</h:div>

3171

</xsd:documentation>

3172

</xsd:annotation>

3173

</xsd:attribute>

3174

</xsd:attributeGroup><xsd:attributeGroup id="attGp.delimiter" name="delimiter">

3175

<xsd:attribute id="att.delimiter" name="delimiter" type="delimiterType">

3176

<xsd:annotation>

3177

<xsd:documentation>

3178

<h:div class="summary">A delimiter character for arrays and matrices.</h:div>

3179

<h:div class="description">By default array components ('elements' in the non-XML sense) are whitespace-separated. This fails for components with embedded whitespace or missing completely:

3180

<h:pre>

3181

Example:

3182

In the protein database ' CA' and 'CA' are different atom types, and and array could be:

3183

3184

</h:pre>

3185

Note that the array starts and ends with the delimiter, which must be chosen to avoid accidental use. There is currently no syntax for escaping delimiters.</h:div>

3186

</xsd:documentation>

3187

</xsd:annotation>

3188

</xsd:attribute>

3189

</xsd:attributeGroup><xsd:attributeGroup id="attGp.dictionaryPrefix" name="dictionaryPrefix">

3190

<xsd:attribute id="att.dictionaryPrefix" name="dictionaryPrefix" type="dictionaryPrefixType">

3191

<xsd:annotation>

3192

<xsd:documentation>

3193

<h:div class="summary">The namespacePrefix for a data item.</h:div>

3194

<h:div class="description">The dictionaryPrefix is associated with elements

3195

such as dictionaries and units and allows them to be referenced namespaces.

3196

The dictionaryPrefix is normally unbound but it may be necessary to hardcode them

3197

occasionally. Thus if a value is fixed (e.g. "xsd:double") the prefix must

3198

be identified and fixed.</h:div>

3199

</xsd:documentation>

3200

</xsd:annotation>

3201

</xsd:attribute>

3202

</xsd:attributeGroup><xsd:attributeGroup name="dictRef" id="attGp.dictRef">

3203

<xsd:attribute id="att.dictRef" name="dictRef" type="namespaceRefType">

3204

<xsd:annotation>

3205

<xsd:documentation>

3206

<h:div class="summary">A reference to a dictionary entry.</h:div>

3207

<h:div class="description">Elements in data instances such as _scalar_ may have a <h:tt>dictRef</h:tt> attribute to point to an entry in a dictionary. To avoid excessive use of (mutable) filenames and URIs we recommend a namespace prefix, mapped to a namespace URI in the normal manner. In this case, of course, the namespace URI must point to a real XML document containing _entry_ elements and validated against STMML Schema.

3208

<h:p>Where there is concern about the dictionary becoming separated from the document the dictionary entries can be physically included as part of the data instance and the normal XPointer addressing mechanism can be used.</h:p>

3209

<h:p>This attribute can also be used on _dictionary_ elements to define the namespace prefix</h:p></h:div>

3210

3211

<h:div class="example" href="dictRefGroup1.xml"/>

3212

<!--

3213

<h:div class="example" href="dictRefGroup2.xml"></h:div>

3214

-->

3215

</xsd:documentation>

3216

</xsd:annotation>

3217

</xsd:attribute>

3218

</xsd:attributeGroup><xsd:attributeGroup id="attGp.dimensionality" name="dimensionality">

3219

<xsd:attribute name="dimensionality" id="att.dimensionality" type="xsd:positiveInteger">

3220

<xsd:annotation>

3221

<xsd:documentation>

3222

<h:div class="summary">Dimensionality of a coordinate system.</h:div>

3223

<h:div class="description">Note that this means that coordinates of higher dimensionality

3224

are ignored or an error is flagged. Thus z3 and dimensionality='2' are incompatible.

3225

At present higher dimensionalities than 3 (cf. Wondratschek) are not supported.

3226

The labelling of the axes id not controlled. ?? should we have an explicit

3227

attribute for labelling convention?.</h:div>

3228

</xsd:documentation>

3229

</xsd:annotation>

3230

</xsd:attribute>

3231

</xsd:attributeGroup><xsd:attributeGroup id="attGp.dimensionBasis" name="dimensionBasis">

3232

<xsd:attribute name="dimensionBasis" type="dimensionType" id="att.dimensionBasis">

3233

<xsd:annotation>

3234

<xsd:documentation>

3235

<h:div class="summary">The basis of the dimension.</h:div>

3236

<h:div class="description">Normally taken from the seven SI types but possibly expandable.</h:div>

3237

</xsd:documentation>

3238

</xsd:annotation>

3239

</xsd:attribute>

3240

</xsd:attributeGroup><xsd:attributeGroup name="duration" id="attGp.duration">

3241

<xsd:attribute name="duration" type="xsd:string" id="att.duration">

3242

<xsd:annotation>

3243

<xsd:documentation>

3244

<h:div class="summary">The duration of the action.</h:div>

3245

<h:div class="description">Semantics undefined.</h:div>

3246

</xsd:documentation>

3247

</xsd:annotation>

3248

</xsd:attribute>

3249

</xsd:attributeGroup><xsd:attributeGroup id="attGp.eigenOrientation" name="eigenOrientation">

3250

3251

<xsd:attribute name="orientation" type="eigenOrientationType" id="att.eigenOrientation">

3252

<xsd:annotation>

3253

<xsd:documentation>

3254

<h:div class="summary">The orientation of the eigenvector matrix.</h:div>

3255

<h:div class="description">Describes whether the vectors are columns or

3256

rows. No default, so effectively mandatory unless you want to make implementers

3257

guess and break applications.</h:div>

3258

</xsd:documentation>

3259

</xsd:annotation>

3260

</xsd:attribute>

3261

</xsd:attributeGroup><xsd:attributeGroup id="attGp.electronMap" name="electronMap">

3262

<xsd:attribute id="att.electronMap" name="electronMap" type="idType">

3263

<xsd:annotation>

3264

<xsd:documentation>

3265

<h:div class="summary">A reference to a map providing mappings between electrons</h:div>

3266

<h:div class="description">The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking electrons. The topology of the linking is defined by the application - it could be reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of electrons are of equal size and have 1:1 mapping between each id. This is another way of saying that the electrons mapped by a given ID are "the same electron". </h:div>

3267

</xsd:documentation>

3268

</xsd:annotation>

3269

</xsd:attribute>

3270

</xsd:attributeGroup><xsd:attributeGroup id="attGp.elementType" name="elementType">

3271

<xsd:attribute id="att.elementType" name="elementType" type="elementTypeType">

3272

<xsd:annotation>

3273

<xsd:documentation>

3274

<h:div class="summary">The identity of a chemical element.</h:div>

3275

<h:div class="description">Normally mandatory on _atom_, _isotope_, etc.</h:div>

3276

</xsd:documentation>

3277

</xsd:annotation>

3278

</xsd:attribute>

3279

</xsd:attributeGroup><xsd:attributeGroup id="attGp.elementTypeArray" name="elementTypeArray">

3280

3281

<xsd:attribute id="att.elementTypeArray" name="elementType" type="elementTypeArrayType">

3282

<xsd:annotation>

3283

<xsd:documentation>

3284

<h:div class="summary">The identity of a chemical element.</h:div>

3285

<h:div class="description">Normally mandatory on _atom_, _isotope_, etc.</h:div>

3286

</xsd:documentation>

3287

</xsd:annotation>

3288

</xsd:attribute>

3289

</xsd:attributeGroup><xsd:attributeGroup name="end" id="attGp.end">

3290

<xsd:attribute name="end" type="xsd:string" id="att.end">

3291

<xsd:annotation>

3292

<xsd:documentation>

3293

<h:div class="summary">The end time.</h:div>

3294

<h:div class="description">The start time in any allowable XSD representation of date, time or dateTime. This will normally be a clock time or date.</h:div>

3295

</xsd:documentation>

3296

</xsd:annotation>

3297

</xsd:attribute>

3298

</xsd:attributeGroup><xsd:attributeGroup name="endCondition" id="attGp.endCondition">

3299

<xsd:attribute name="endCondition" type="xsd:string" id="att.endCondition">

3300

<xsd:annotation>

3301

<xsd:documentation>

3302

<h:div class="summary">The end condition.</h:div>

3303

<h:div class="description">

3304

<h:p>At present a human-readable string describing some condition when the

3305

ac tion should end. As XML develops it may be possible to add machine-processable

3306

semantics in this field.</h:p></h:div>

3307

</xsd:documentation>

3308

</xsd:annotation>

3309

</xsd:attribute>

3310

</xsd:attributeGroup><xsd:attributeGroup id="attGp.errorBasis" name="errorBasis">

3311

<xsd:attribute id="att.errorBasis" name="errorBasis" type="errorBasisType">

3312

<xsd:annotation>

3313

<xsd:documentation>

3314

<h:div class="summary">Basis of the error estimate.</h:div>

3315

<h:div class="description"/>

3316

</xsd:documentation>

3317

</xsd:annotation>

3318

</xsd:attribute>

3319

</xsd:attributeGroup><xsd:attributeGroup id="attGp.errorValue" name="errorValue">

3320

<xsd:attribute id="att.errorValue" name="errorValue" type="errorValueType">

3321

<xsd:annotation>

3322

<xsd:documentation>

3323

<h:div class="summary">Value of the error.</h:div>

3324

<h:div class="description">Reports the author's estimate of the error in a scalar value. Only meaningful for dataTypes mapping to real number.</h:div>

3325

</xsd:documentation>

3326

</xsd:annotation>

3327

</xsd:attribute>

3328

</xsd:attributeGroup><xsd:attributeGroup id="attGp.errorValueArray" name="errorValueArray">

3329

<xsd:attribute id="att.errorValueArray" name="errorValueArray" type="errorValueArrayType">

3330

<xsd:annotation>

3331

<xsd:documentation>

3332

<h:div class="summary">Array of error values.</h:div>

3333

<h:div class="description">Reports the author's estimate of the error in an array of values. Only meaningful for dataTypes mapping to real number.</h:div>

3334

</xsd:documentation>

3335

</xsd:annotation>

3336

</xsd:attribute>

3337

</xsd:attributeGroup><xsd:attributeGroup id="attGp.fileId" name="fileId">

3338

<xsd:attribute id="att.fileId" name="fileId" type="xsd:string">

3339

<xsd:annotation>

3340

<xsd:documentation>

3341

<h:div class="summary">Information identifying the name of a file or other resource.</h:div>

3342

<h:div class="description">This allows an element (such as cml) to carry limited

3343

information about provenance such as the name of the document used to provide the

3344

content. It is not a complete solution but can help to protect a document becoming

3345

separated from its external metadata. It is restricted to the basic XML character set

3346

(printable ANSI) and whitespace (which should anyway be discouraged) is normalized to

3347

single space (attribute values cannot carry newlines).

3348

Quotation marks and other horrors (as used in some OS)

3349

should be avoided. </h:div>

3350

</xsd:documentation>

3351

</xsd:annotation>

3352

</xsd:attribute>

3353

</xsd:attributeGroup><xsd:attributeGroup id="attGp.form" name="form">

3354

<xsd:attribute name="form" id="att.form" type="namespaceRefType">

3355

<xsd:annotation>

3356

<xsd:documentation>

3357

<h:div class="summary">A reference to a functional form.</h:div>

3358

<h:div class="description">Currently used for potential.</h:div>

3359

</xsd:documentation>

3360

</xsd:annotation>

3361

</xsd:attribute>

3362

</xsd:attributeGroup><xsd:attributeGroup id="attGp.formalCharge" name="formalCharge">

3363

<xsd:attribute id="att.formalCharge" name="formalCharge" type="formalChargeType">

3364

<xsd:annotation>

3365

<xsd:documentation>

3366

<h:div class="summary">The formalCharge on the object.</h:div>

3367

<h:div class="description">NOT the calculated charge or oxidation state. No formal default, but assumed to be zero if omitted. It may become good practice to include it.</h:div>

3368

</xsd:documentation>

3369

</xsd:annotation>

3370

</xsd:attribute>

3371

</xsd:attributeGroup><xsd:attributeGroup id="attGp.formalChargeArray" name="formalChargeArray">

3372

3373

<xsd:attribute id="att.formalChargeArray" name="formalCharge" type="formalChargeArrayType">

3374

<xsd:annotation>

3375

<xsd:documentation>

3376

<h:div class="summary">An array of formalCharges.</h:div>

3377

<h:div class="description">Used in CML2 Array mode. NOT the calculated charge or oxidation state. No formal defaults, but assumed to be zero if omitted. It may become good practice to include it.</h:div>

3378

</xsd:documentation>

3379

</xsd:annotation>

3380

</xsd:attribute>

3381

</xsd:attributeGroup><xsd:attributeGroup id="attGp.format" name="format">

3382

<xsd:attribute id="att.format" name="format" type="formatType">

3383

<xsd:annotation>

3384

<xsd:documentation>

3385

<h:div class="summary">Format of a spectrum.</h:div>

3386

<h:div class="description">The data structure of the spectrum. (Not the format of the data). This describes how the data structure is to be interpreted.</h:div>

3387

</xsd:documentation>

3388

</xsd:annotation>

3389

</xsd:attribute>

3390

</xsd:attributeGroup><xsd:attributeGroup id="attGp.formula" name="formula">

3391

<xsd:attribute id="att.formula" name="formula" type="formulaType">

3392

<xsd:annotation>

3393

<xsd:documentation>

3394

<h:div class="summary">Simple chemical formula.</h:div>

3395

<h:div class="general">

3396

This attribute should only be used for simple formulae (i.e. without brackets or other nesting for which a _formula_ child element should be used. The attribute might be used as a check on the child elements or for ease of representation. Essentially the same as _concise_ attribute on _formula.</h:div>

3397

</xsd:documentation>

3398

</xsd:annotation>

3399

</xsd:attribute>

3400

</xsd:attributeGroup><xsd:attributeGroup id="attGp.fractionDigits" name="fractionDigits">

3401

<xsd:attribute id="att.fractionDigits" name="fractionDigits" type="xsd:nonNegativeInteger">

3402

<xsd:annotation>

3403

<xsd:documentation>

3404

<h:div class="summary">Number of digits after the point.</h:div>

3405

<h:div class="description">This is used in dictionaries to define precision. However it might be replaced by xsd:facet.</h:div>

3406

</xsd:documentation>

3407

</xsd:annotation>

3408

</xsd:attribute>

3409

</xsd:attributeGroup><xsd:attributeGroup id="attGp.from" name="from">

3410

<xsd:attribute id="att.from" name="from" type="refType">

3411

<xsd:annotation>

3412

<xsd:documentation>

3413

<h:div class="summary">The base of one or more links.</h:div>

3414

<h:div class="description">On link elements the value is the single id of an element within the document or context specified in map@fromRef attributes. It must identify the element uniquely. The reserved value 'null' implies that no mapping has been provided for the object(s) in the 'to' attribute. This implies no semantics but may be used by software to keep count of which elements have been mapped. For multiple targets use 'fromSet'.</h:div>

3415

<h:div class="curation">2005-06-18: updated docs</h:div>

3416

</xsd:documentation>

3417

</xsd:annotation>

3418

</xsd:attribute>

3419

</xsd:attributeGroup><xsd:attributeGroup id="attGp.fromContext" name="fromContext">

3420

<xsd:attribute id="att.fromContext" name="fromContext" type="idType">

3421

<xsd:annotation>

3422

<xsd:documentation>

3423

<h:div class="summary">The context for the 'from' links in a map.</h:div>

3424

<h:div class="description"><h:p>A reference to the unique 'id' attribute of an element defining the context for links in a map. This may be required when id attributes may not be unique within a document. The id should either reference an element uniquely or should be taken as the first ancestor (of the map) with such an id.</h:p>

3425

<h:p>This is fairly horrid but may be required when documents are assembled without establishing unique ids (e.g. concatenation of files). As an example a map referencing linked atoms in two molecules might use the containing 'reaction' element as its uniquifying context.</h:p>

3426

</h:div>

3427

<h:div class="curation">2005-06-18: created</h:div>

3428

</xsd:documentation>

3429

</xsd:annotation>

3430

</xsd:attribute>

3431

</xsd:attributeGroup><xsd:attributeGroup id="attGp.fromSet" name="fromSet">

3432

<xsd:attribute id="att.fromSet" name="fromSet" type="idArrayType">

3433

<xsd:annotation>

3434

<xsd:documentation>

3435

<h:div class="summary">A set of ids representing the base of a link.</h:div>

3436

<h:div class="description"><h:p>For a partial mapping where a number of 'from' elements are known to link to a number of 'to' elements it can be useful to aggregate these into a single attribute value. The primary use is to assert that n links exist between a set of n 'from' elements and n 'to' elements but that the precise links are unknown. The semantics of the reference are the same as for 'from' and all the elements must be of the same type (which can be specified with 'fromType' either on the link or the containing map). No order information is implied. In general there will be the same number of idRefs in the 'toSet' and all implicit links will share the same attributes (e.g. 'role'). In many cases the sets will be later split into discrete links thorugh further calculation or experiment (e.g. peak assignment). Sets should never be used as a lazy or concise alternative where the all the links are explicitly known. </h:p>

3437

</h:div>

3438

<h:div class="curation">2005-06-18: created</h:div>

3439

</xsd:documentation>

3440

</xsd:annotation>

3441

</xsd:attribute>

3442

</xsd:attributeGroup><xsd:attributeGroup id="attGp.fromType" name="fromType">

3443

<xsd:attribute id="att.fromType" name="fromType" type="xmlElementType">

3444

<xsd:annotation>

3445

<xsd:documentation>

3446

<h:div class="summary">The type of the base of a link.</h:div>

3447

<h:div class="description"><h:p>The local tagname of the referenced element (e.g. 'molecule' or 'peakGroup'). This acts as a partial check on the integrity of the link. Software can assume that the referenced element is of a given tytpe and can create an object supporting that type. </h:p>

3448

<h:p>This attribute can be attached to the 'map' attribute and requires all contained links to be of this type. This can be overridden by a 'toType' attribute on indivdual links, but it may also be useful to split the map into maps od different link types.</h:p>

3449

</h:div>

3450

<h:div class="curation">2005-06-18: created</h:div>

3451

</xsd:documentation>

3452

</xsd:annotation>

3453

</xsd:attribute>

3454

</xsd:attributeGroup><xsd:attributeGroup id="attGp.ft" name="ft">

3455

<xsd:attribute id="att.ft" name="ft" default="none" type="ftType">

3456

<xsd:annotation>

3457

<xsd:documentation>

3458

<h:div class="summary">Domain of an FT spectrum.</h:div>

3459

<h:div class="description">Indicates whether a spectrum is raw FID or has been transforme.</h:div>

3460

</xsd:documentation>

3461

</xsd:annotation>

3462

</xsd:attribute>

3463

</xsd:attributeGroup><xsd:attributeGroup id="attGp.href" name="href">

3464

<xsd:attribute id="att.href" name="href" type="xsd:anyURI">

3465

<xsd:annotation>

3466

<xsd:documentation>

3467

<h:div class="summary">address of a resource.</h:div>

3468

<h:div class="description">Links to another element in the same or other file. For dictionary/@dictRef requires the prefix and the physical URI

3469

address to be contained within the same file. We can anticipate that

3470

better mechanisms will arise - perhaps through XMLCatalogs.

3471

At least it works at present.</h:div>

3472

</xsd:documentation>

3473

</xsd:annotation>

3474

</xsd:attribute>

3475

</xsd:attributeGroup><xsd:attributeGroup id="attGp.hydrogenCount" name="hydrogenCount">

3476

<xsd:attribute id="att.hydrogenCount" name="hydrogenCount" type="hydrogenCountType">

3477

<xsd:annotation>

3478

<xsd:documentation>

3479

<h:div class="summary">Number of hydrogens.</h:div>

3480

<h:div class="description">The total number of hydrogens bonded to the atom or molecule. It is preferable to include hydrogens explicitly, and where this is done their count represents the minimum (and may thus override this attribute). It is dangerous to use this attribute for electron-deficient molecules (e.g. diborane) or hydrogen bonds. There is NO DEFAULT and the absence of this attribute must not be given any meaning.</h:div>

3481

</xsd:documentation>

3482

</xsd:annotation>

3483

</xsd:attribute>

3484

</xsd:attributeGroup><xsd:attributeGroup id="attGp.hydrogenCountArray" name="hydrogenCountArray">

3485

3486

<xsd:attribute id="att.hydrogenCountArray" name="hydrogenCount" type="hydrogenCountArrayType">

3487

<xsd:annotation>

3488

<xsd:documentation>

3489

<h:div class="summary">Array of hydrogenCounts.</h:div>

3490

<h:div class="description">Normally used in CML2 array mode. The total number of hydrogens bonded to the atom or molecule. It is preferable to include hydrogens explicitly, and where this is done their count represents the minimum (and may thus override this attribute). It is dangerous to use this attribute for electron-deficient molecules (e.g. diborane) or hydrogen bonds. There is NO DEFAULT and the absence of this attribute must not be given any meaning.</h:div>

3491

</xsd:documentation>

3492

</xsd:annotation>

3493

</xsd:attribute>

3494

</xsd:attributeGroup><xsd:attributeGroup id="attGp.id" name="id">

3495

<xsd:attribute id="att.id" name="id" type="idType">

3496

<xsd:annotation>

3497

<xsd:documentation>

3498

<h:div class="summary">A unique ID for an element.</h:div>

3499

<h:div class="description">Id is used for machine identification of elements and

3500

in general should not have application semantics. It is similar to the XML ID type

3501

as containing only alphanumerics, '_', ',' and '-' and and must start with an

3502

alphabetic character. Ids are case sensitive. Ids should be unique within local scope,

3503

thus all atoms within a molecule should have unique ids, but separated molecules within a

3504

document (such as a published article) might have identical ids. Software

3505

should be able to search local scope (e.g. all atoms within a molecule).

3506

However this is under constant review.</h:div>

3507

</xsd:documentation>

3508

</xsd:annotation>

3509

</xsd:attribute>

3510

</xsd:attributeGroup><xsd:attributeGroup id="attGp.inherit" name="inherit">

3511

<xsd:attribute id="att.inherit" name="inherit" type="inheritType">

3512

<xsd:annotation>

3513

<xsd:documentation>

3514

<h:div class="summary">Inheritance mechanism.</h:div>

3515

3516

<h:pre>

3517

3518

3519

3520

</atomArray>

3521

</molecule>

3522

3523

3524

3525

3526

</atomArray>

3527

</molecule>

3528

3529

3530

3531

3532

</atomArray>

3533

</molecule>

3534

3535

3536

3537

3538

</atomArray>

3539

</molecule>

3540

</h:pre>

3541

<h:p>

3542

The first <h:tt>molecule/@ref</h:tt> adds complementary information, the second

3543

changes the values. Software is allowed to generate two independent copies of the molecule and reference them by different IDs (<h:tt>m1</h:tt> and <h:tt>m2</h:tt>).

3544

</h:p>

3545

<h:p>This mechanism is necessary to manage the implied inheritance of partial information during minimisations and dynamics. It requires careful software implementation.

3546

</h:p></h:div>

3547

</xsd:documentation>

3548

</xsd:annotation>

3549

</xsd:attribute>

3550

</xsd:attributeGroup><xsd:attributeGroup id="attGp.inline" name="inline">

3551

<xsd:attribute name="inline" id="att.inline" type="xsd:string">

3552

<xsd:annotation>

3553

<xsd:documentation>

3554

<h:div class="summary">An inline representation of the object.</h:div>

3555

<h:div class="general">This can represent a wide range of information from formal serialization

3556

as ASCII through to domain-specific textual representations. It will often be used in conjunction

3557

with the "convention" attribute. For example it could be used to represent IUPAC formula,

3558

SMILES strings, TeX equations, etc. Characters should conforma to the XML character set,

3559

and XML markup (lt and amp) should be escaped. <h:b>IT SHOULD NEVER BE USED FOR INLINE XML</h:b></h:div>

3560

<h:div class="example" href="attributeGroups/inline.xml"/>

3561

</xsd:documentation>

3562

</xsd:annotation>

3563

</xsd:attribute>

3564

</xsd:attributeGroup><xsd:attributeGroup id="attGp.integral" name="integral">

3565

<xsd:attribute id="att.integral" name="integral" type="xsd:string">

3566

<xsd:annotation>

3567

<xsd:documentation>

3568

<h:div class="summary">Area under a peak.</h:div>

3569

<h:div class="description">Unfortunately units are usually arbitrary and not related to the x- and y- axis units, and in this case _peakUnits_ should be use.</h:div>

3570

</xsd:documentation>

3571

</xsd:annotation>

3572

</xsd:attribute>

3573

3574

</xsd:attributeGroup><xsd:attributeGroup id="attGp.irreducibleRepresentation" name="irreducibleRepresentation">

3575

<xsd:attribute name="irreducibleRepresentation" id="att.irreducibleRepresentation" type="xsd:string">

3576

<xsd:annotation>

3577

<xsd:documentation>

3578

<h:div class="summary">A symmetry species.</h:div>

3579

<h:div class="description">No fixed semantics, though we may provide a controlled-extensible list in the future.</h:div>

3580

</xsd:documentation>

3581

</xsd:annotation>

3582

</xsd:attribute>

3583

</xsd:attributeGroup><xsd:attributeGroup id="attGp.isotope" name="isotope">

3584

<xsd:attribute id="att.isotope" name="isotope" type="xsd:double">

3585

<xsd:annotation>

3586

<xsd:documentation>

3587

<h:div class="summary">The isotope for an element.</h:div>

3588

<h:div class="description">A real number describing the isotope. Probably obsolet.</h:div>

3589

</xsd:documentation>

3590

</xsd:annotation>

3591

</xsd:attribute>

3592

</xsd:attributeGroup><xsd:attributeGroup id="attGp.isotopeListRef" name="isotopeListRef">

3593

<xsd:attribute id="att.isotopeListRef" name="isotopeListRef" type="idType">

3594

<xsd:annotation>

3595

<xsd:documentation>

3596

<h:div class="summary">Reference to a description of the isotopic composition of an atom.</h:div>

3597

<h:div class="description">Used when more than one atom shares the same isotopic composition (e.g. when H/D have been scrambled over some or all of the atoms in a molecule..</h:div>

3598

<h:div class="example" href="isotope1.xml"/>

3599

</xsd:documentation>

3600

</xsd:annotation>

3601

</xsd:attribute>

3602

</xsd:attributeGroup><xsd:attributeGroup id="attGp.isotopeNumber" name="isotopeNumber">

3603

<xsd:attribute id="att.isotopeNumber" name="isotopeNumber" type="xsd:positiveInteger">

3604

<xsd:annotation>

3605

<xsd:documentation>

3606

<h:div class="summary">The integer number for an isotope.</h:div>

3607

<h:div class="description">The number representing the isotope. By default it does not point to a fuller description of the isotope (use isotopeRef).</h:div>

3608

</xsd:documentation>

3609

</xsd:annotation>

3610

</xsd:attribute>

3611

</xsd:attributeGroup><xsd:attributeGroup id="attGp.isotopeRef" name="isotopeRef">

3612

<xsd:attribute id="att.isotopeRef" name="isotopeRef" type="refType">

3613

<xsd:annotation>

3614

<xsd:documentation>

3615

<h:div class="summary">Reference to a fuller description of the isotope.</h:div>

3616

<h:div class="general">The description may be found in an external collection (e.g. IUPAC) or within the current document.</h:div>

3617

<h:div class="example" href="isotope2.xml"/>

3618

</xsd:documentation>

3619

</xsd:annotation>

3620

</xsd:attribute>

3621

</xsd:attributeGroup><xsd:attributeGroup id="attGp.isSI" name="isSI">

3622

<xsd:attribute name="isSI" id="att.isSI" type="xsd:boolean">

3623

<xsd:annotation>

3624

<xsd:documentation>

3625

<h:div class="summary">indicates whether a unit is an SI or derived SI unit.</h:div>

3626

<h:div class="description">required on SI unit elements with value 'true'.

3627

Optional on other units with attribute 'false'. A unitList should contain either

3628

SI units or non-SI units but not both.</h:div>

3629

</xsd:documentation>

3630

</xsd:annotation>

3631

</xsd:attribute>

3632

</xsd:attributeGroup><xsd:attributeGroup id="attGp.kpoint" name="kpoint">

3633

<xsd:attribute name="kpoint" type="vector3Type" id="att.kpoint">

3634

<xsd:annotation>

3635

<xsd:documentation>

3636

<h:div class="summary">The k vector.</h:div>

3637

<h:div class="description">The k-vector with 3 components.</h:div>

3638

</xsd:documentation>

3639

</xsd:annotation>

3640

</xsd:attribute>

3641

</xsd:attributeGroup><xsd:attributeGroup id="attGp.kpointRef" name="kpointRef">

3642

<xsd:attribute id="att.kpointRef" name="kpointRef" type="refType">

3643

<xsd:annotation>

3644

<xsd:documentation>

3645

<h:div class="summary">A reference to a kpoint.</h:div>

3646

<h:div class="description">Used by band, etc.</h:div>

3647

<h:div class="curation">2006-01-21: PMR. Created</h:div>

3648

</xsd:documentation>

3649

</xsd:annotation>

3650

</xsd:attribute>

3651

</xsd:attributeGroup><xsd:attributeGroup id="attGp.l" name="l">

3652

<xsd:attribute name="l" id="att.l" type="xsd:nonNegativeInteger">

3653

<xsd:annotation>

3654

<xsd:documentation>

3655

<h:div class="summary">The secondary quantum number.</h:div>

3656

<h:div class="description">takes values 0, 1, etc.</h:div>

3657

</xsd:documentation>

3658

</xsd:annotation>

3659

</xsd:attribute>

3660

</xsd:attributeGroup><xsd:attributeGroup id="attGp.label" name="label">

3661

<xsd:attribute name="label" type="xsd:string" id="att.label">

3662

<xsd:annotation>

3663

<xsd:documentation>

3664

<h:div class="summary">A label.</h:div>

3665

<h:div class="description">The semantics of label are not defined in the schema but are normally commonly used standard or semi-standard text strings. This attribute has the the same semantics as the more common _label_ element.</h:div>

3666

</xsd:documentation>

3667

</xsd:annotation>

3668

</xsd:attribute>

3669

</xsd:attributeGroup><xsd:attributeGroup id="attGp.latticeType" name="latticeType">

3670

<xsd:attribute id="att.latticeType" name="latticeType" type="latticeType">

3671

<xsd:annotation>

3672

<xsd:documentation>

3673

<h:div class="summary">The primitivity of a lattice.</h:div>

3674

<h:div class="description">No default. The semantics of this are software-dependent (i.e. this Schema does not check for consistency between spacegroups, symmetry operators, etc.</h:div>

3675

</xsd:documentation>

3676

</xsd:annotation>

3677

</xsd:attribute>

3678

</xsd:attributeGroup><xsd:attributeGroup id="attGp.length" name="length">

3679

<xsd:attribute id="att.length" name="length" type="xsd:nonNegativeInteger">

3680

<xsd:annotation>

3681

<xsd:documentation>

3682

<h:div class="summary">Length of a scalar.</h:div>

3683

<h:div class="description">Probably will be replaced with xsd:schema tool.</h:div>

3684

</xsd:documentation>

3685

</xsd:annotation>

3686

</xsd:attribute>

3687

</xsd:attributeGroup><xsd:attributeGroup id="attGp.linkType" name="linkType">

3688

<xsd:attribute name="linkType" id="att.linkType" type="linkTypeType">

3689

<xsd:annotation>

3690

<xsd:documentation>

3691

<h:div class="summary">The type of the link.</h:div>

3692

</xsd:documentation>

3693

</xsd:annotation>

3694

</xsd:attribute>

3695

3696

</xsd:attributeGroup><xsd:attributeGroup id="attGp.lm" name="lm">

3697

<xsd:attribute name="lm" id="att.lm" type="lmType">

3698

<xsd:annotation>

3699

<xsd:documentation>

3700

<h:div class="summary">symbolic represention of l amd m.</h:div>

3701

<h:div class="description">takes avlues of s, p, px, dxy, dx2y2, f, etc.</h:div>

3702

</xsd:documentation>

3703

</xsd:annotation>

3704

</xsd:attribute>

3705

</xsd:attributeGroup><xsd:attributeGroup id="attGp.m" name="m">

3706

<xsd:attribute name="m" id="att.m" type="xsd:integer">

3707

<xsd:annotation>

3708

<xsd:documentation>

3709

<h:div class="summary">The azimuthal quantum number.</h:div>

3710

<h:div class="description">takes values -1, 0, 1, etc.</h:div>

3711

</xsd:documentation>

3712

</xsd:annotation>

3713

</xsd:attribute>

3714

</xsd:attributeGroup><xsd:attributeGroup id="attGp.mandatoryId" name="mandatoryId">

3715

3716

<xsd:attribute id="att.mandatoryId" name="id" type="idType" use="required">

3717

<xsd:annotation>

3718

<xsd:documentation>

3719

<h:div class="summary">An attribute providing a mandatory unique ID for an element.</h:div>

3720

<h:div class="description">This is a horrible hack. It should be possible to add 'required' to

3721

the attributeGroup where used... (Maybe it is and I am still fighting Schema Wars.</h:div>

3722

</xsd:documentation>

3723

</xsd:annotation>

3724

</xsd:attribute>

3725

</xsd:attributeGroup><xsd:attributeGroup id="attGp.matrixType" name="matrixType">

3726

<xsd:attribute name="matrixType" type="matrixType" id="att.matrixType">

3727

<xsd:annotation>

3728

<xsd:documentation>

3729

<h:div class="summary">Type of matrix.</h:div>

3730

<h:div class="description">Mainly square, but extensible through the _xsd:union_ mechanis.</h:div>

3731

</xsd:documentation>

3732

</xsd:annotation>

3733

</xsd:attribute>

3734

</xsd:attributeGroup><xsd:attributeGroup id="attGp.max" name="max">

3735

<xsd:attribute id="att.max" name="max" type="maxType">

3736

<xsd:annotation>

3737

<xsd:documentation>

3738

<h:div class="summary">Maximum value allowed for an element or attribute.</h:div>

3739

<h:div class="description"/>

3740

</xsd:documentation>

3741

</xsd:annotation>

3742

</xsd:attribute>

3743

</xsd:attributeGroup><xsd:attributeGroup id="attGp.maxExclusive" name="maxExclusive">

3744

<xsd:attribute id="att.maxExclusive" name="maxExclusive" type="xsd:double">

3745

<xsd:annotation>

3746

<xsd:documentation>

3747

<h:div class="summary">maximum exclusive value.</h:div>

3748

<h:div class="description">by analogy with xsd:schema.</h:div>

3749

</xsd:documentation>

3750

</xsd:annotation>

3751

</xsd:attribute>

3752

</xsd:attributeGroup><xsd:attributeGroup id="attGp.maxInclusive" name="maxInclusive">

3753

<xsd:attribute id="att.maxInclusive" name="maxInclusive" type="xsd:double">

3754

<xsd:annotation>

3755

<xsd:documentation>

3756

<h:div class="summary">minimum inclusive value.</h:div>

3757

<h:div class="description">by analogy with xsd:schem.</h:div>

3758

</xsd:documentation>

3759

</xsd:annotation>

3760

</xsd:attribute>

3761

</xsd:attributeGroup><xsd:attributeGroup id="attGp.maxLength" name="maxLength">

3762

<xsd:attribute id="att.maxLength" name="maxLength" type="xsd:positiveInteger">

3763

<xsd:annotation>

3764

<xsd:documentation>

3765

<h:div class="summary">maximum length of a scalar.</h:div>

3766

<h:div class="description">by analogy with xsd:schem.</h:div>

3767

</xsd:documentation>

3768

</xsd:annotation>

3769

</xsd:attribute>

3770

</xsd:attributeGroup><xsd:attributeGroup id="attGp.maxValueArray" name="maxValueArray">

3771

<xsd:attribute name="maxValueArray" type="floatArrayType" id="att.maxValueArray">

3772

<xsd:annotation>

3773

<xsd:documentation>

3774

<h:div class="summary">Maximum values for numeric _matrix_ or _array.</h:div>

3775

<h:div class="description">A whitespace-separated list of the same length as the array in the parent element.</h:div>

3776

</xsd:documentation>

3777

</xsd:annotation>

3778

</xsd:attribute>

3779

</xsd:attributeGroup><xsd:attributeGroup id="attGp.measurement" name="measurement">

3780

<xsd:attribute id="att.measurement" name="measurement" type="measurementType">

3781

<xsd:annotation>

3782

<xsd:documentation>

3783

<h:div class="summary">Type of spectral measurement.</h:div>

3784

<h:div class="description">The nature of the measured data. This is not an exhaustive list and should only be used if it affects the storage or immediate processing.</h:div>

3785

</xsd:documentation>

3786

</xsd:annotation>

3787

</xsd:attribute>

3788

</xsd:attributeGroup><xsd:attributeGroup id="attGp.metadataType" name="metadataType">

3789

3790

<xsd:attribute name="name" type="metadataType" id="att.metadataType">

3791

<xsd:annotation>

3792

<xsd:documentation>

3793

<h:div class="summary">The metadata type.</h:div>

3794

<h:div class="description">This is likely to be the Dublin Core

3795

name or something similar. The use of "type" is an infelicitous

3796

misnomer and we shall try to remove it.</h:div>

3797

</xsd:documentation>

3798

</xsd:annotation>

3799

</xsd:attribute>

3800

</xsd:attributeGroup><xsd:attributeGroup id="attGp.min" name="min">

3801

<xsd:attribute id="att.min" name="min" type="minType">

3802

<xsd:annotation>

3803

<xsd:documentation>

3804

<h:div class="summary">The minimum value allowed for an element or attribute.</h:div>

3805

<h:div class="description"/>

3806

</xsd:documentation>

3807

</xsd:annotation>

3808

</xsd:attribute>

3809

</xsd:attributeGroup><xsd:attributeGroup id="attGp.minExclusive" name="minExclusive">

3810

<xsd:attribute id="att.minExclusive" name="minExclusive" type="xsd:double">

3811

<xsd:annotation>

3812

<xsd:documentation>

3813

<h:div class="summary">minimum exclusive value.</h:div>

3814

<h:div class="description">by analogy with xsd:schema.</h:div>

3815

</xsd:documentation>

3816

</xsd:annotation>

3817

</xsd:attribute>

3818

</xsd:attributeGroup><xsd:attributeGroup id="attGp.minInclusive" name="minInclusive">

3819

<xsd:attribute id="att.minInclusive" name="minInclusive" type="xsd:double">

3820

<xsd:annotation>

3821

<xsd:documentation>

3822

<h:div class="summary">minimum inclusive value.</h:div>

3823

<h:div class="description">by analogy with xsd:schema.</h:div>

3824

</xsd:documentation>

3825

</xsd:annotation>

3826

</xsd:attribute>

3827

</xsd:attributeGroup><xsd:attributeGroup id="attGp.minLength" name="minLength">

3828

<xsd:attribute id="att.minLength" name="minLength" type="xsd:nonNegativeInteger">

3829

<xsd:annotation>

3830

<xsd:documentation>

3831

<h:div class="summary">minimum length of a scalar.</h:div>

3832

<h:div class="description">by analogy with xsd:schema.</h:div>

3833

</xsd:documentation>

3834

</xsd:annotation>

3835

</xsd:attribute>

3836

</xsd:attributeGroup><xsd:attributeGroup id="attGp.minValueArray" name="minValueArray">

3837

<xsd:attribute name="minValueArray" type="floatArrayType" id="att.minValueArray">

3838

<xsd:annotation>

3839

<xsd:documentation>

3840

<h:div class="summary">Minimum values for numeric _matrix_ or _array.</h:div>

3841

<h:div class="description">A whitespace-separated lists of the same length as the array in the parent element.</h:div>

3842

</xsd:documentation>

3843

</xsd:annotation>

3844

</xsd:attribute>

3845

</xsd:attributeGroup><xsd:attributeGroup id="attGp.moleculeRef" name="moleculeRef">

3846

<xsd:attribute id="att.moleculeRef" name="moleculeRef" type="moleculeRefType">

3847

<xsd:annotation>

3848

<xsd:documentation>

3849

<h:div class="summary">A reference to a molecule.</h:div>

3850

<h:div class="description">Used by spectrum, etc.</h:div>

3851

</xsd:documentation>

3852

</xsd:annotation>

3853

</xsd:attribute>

3854

</xsd:attributeGroup><xsd:attributeGroup id="attGp.moleculeRefs" name="moleculeRefs">

3855

<xsd:attribute name="moleculeRefs" id="att.moleculeRefs" type="moleculeRefArrayType">

3856

<xsd:annotation>

3857

<xsd:documentation>

3858

<h:div class="summary">A reference to one or more molecules.</h:div>

3859

<h:div class="description">Uses the id attribute as the target identification.

3860

The order of molecules is preserved. It is not necessarily an error to have repeated

3861

references to the same molecule</h:div>

3862

<h:div class="curation">2005-11-22: PMR. added this attribute.</h:div>

3863

</xsd:documentation>

3864

</xsd:annotation>

3865

</xsd:attribute>

3866

</xsd:attributeGroup><xsd:attributeGroup id="attGp.multiplierToData" name="multiplierToData">

3867

<xsd:attribute id="att.multiplierToData" name="multiplierToData" type="xsd:double" default="1.0">

3868

<xsd:annotation>

3869

<xsd:documentation>

3870

<h:div class="summary">The scale by which to multiply raw data or a unit.</h:div>

3871

<h:div class="description">The scale is applied *before* adding any constant.

3872

The attribute may be found on a data item (scalar, array, matrix, etc.) or

3873

a user-defined unit.</h:div>

3874

</xsd:documentation>

3875

</xsd:annotation>

3876

</xsd:attribute>

3877

</xsd:attributeGroup><xsd:attributeGroup id="attGp.multiplierToSI" name="multiplierToSI">

3878

<xsd:attribute id="att.multiplierToSI" name="multiplierToSI" type="xsd:double">

3879

<xsd:annotation>

3880

<xsd:documentation>

3881

<h:div class="summary">Multiplier to generate SI equivalent.</h:div>

3882

<h:div class="description">The factor by which the non-SI unit should be multiplied to convert a quantity to its representation in SI Units. This is applied *before* _constantToSI_. Necessarily unity for SI unit.</h:div>

3883

</xsd:documentation>

3884

</xsd:annotation>

3885

</xsd:attribute>

3886

</xsd:attributeGroup><xsd:attributeGroup id="attGp.n" name="n">

3887

<xsd:attribute name="n" id="att.n" type="xsd:nonNegativeInteger">

3888

<xsd:annotation>

3889

<xsd:documentation>

3890

<h:div class="summary">The principal quantum number.</h:div>

3891

<h:div class="description">Takes values 1, 2, 3, etc.</h:div>

3892

</xsd:documentation>

3893

</xsd:annotation>

3894

</xsd:attribute>

3895

</xsd:attributeGroup><xsd:attributeGroup id="attGp.name" name="name">

3896

<xsd:attribute id="att.name" name="name" type="xsd:string">

3897

<xsd:annotation>

3898

<xsd:documentation>

3899

<h:div class="summary">Name of the object.</h:div>

3900

<h:div class="description">A string by which the object is known. Often a required attribute. The may or may not be a semi-controlled vocabulary.</h:div>

3901

</xsd:documentation>

3902

</xsd:annotation>

3903

</xsd:attribute>

3904

</xsd:attributeGroup><xsd:attributeGroup id="attGp.namespace" name="namespace">

3905

<xsd:attribute id="att.namespace" name="namespace" type="namespaceType">

3906

<xsd:annotation>

3907

<xsd:documentation>

3908

<h:div class="summary">The namespace for a data item.</h:div>

3909

<h:div class="description">The namespace is associated with elements such as dictionaries

3910

and units and allows them to be referenced through free namespace prefixes.</h:div>

3911

</xsd:documentation>

3912

</xsd:annotation>

3913

</xsd:attribute>

3914

</xsd:attributeGroup><xsd:attributeGroup id="attGp.number" name="number">

3915

<xsd:attribute id="att.number" name="number" type="xsd:nonNegativeInteger">

3916

<xsd:annotation>

3917

<xsd:documentation>

3918

<h:div class="summary">A number determined by context</h:div>

3919

<h:div class="description">Used for isotope number in isotope, and rotational symmetry number in symmetry for calculation of entropy, etc.</h:div>

3920

<h:div class="curation">2003-03-30: added number attribut.</h:div>

3921

</xsd:documentation>

3922

</xsd:annotation>

3923

</xsd:attribute>

3924

</xsd:attributeGroup><xsd:attributeGroup id="attGp.objectClass" name="objectClass">

3925

<xsd:attribute name="objectClass" type="xsd:string" id="att.objectClass">

3926

<xsd:annotation>

3927

<xsd:documentation>

3928

<h:div class="summary">The class of an object.</h:div>

3929

<h:div class="description">The type of this information. This is not controlled, but examples might include:

3930

<h:ul>

3931

<h:li>label</h:li>

3932

<h:li>summary</h:li>

3933

<h:li>note</h:li>

3934

<h:li>usage</h:li>

3935

<h:li>qualifier</h:li>

3936

</h:ul>

3937

It might be used to control display or XSL filtering.</h:div>

3938

<h:div class="note">The attribute is named 'objectClass' to avoid clashes with other class attributes and inappropriate conversion to foo.getClass().</h:div>

3939

</xsd:documentation>

3940

</xsd:annotation>

3941

</xsd:attribute>

3942

</xsd:attributeGroup><xsd:attributeGroup id="attGp.occupancy" name="occupancy">

3943

<xsd:attribute id="att.occupancy" name="occupancy" type="occupancyType">

3944

<xsd:annotation>

3945

<xsd:documentation>

3946

<h:div class="summary">Occupancy for an atom.</h:div>

3947

<h:div class="description">Normally only found in crystallography. Defaults to 1.0. The occupancy is required to calculate the molecular formaula from the atoms.</h:div>

3948

</xsd:documentation>

3949

</xsd:annotation>

3950

</xsd:attribute>

3951

</xsd:attributeGroup><xsd:attributeGroup id="attGp.occupancyArray" name="occupancyArray">

3952

3953

<xsd:attribute id="att.occupancyArray" name="occupancy" type="occupancyArrayType">

3954

<xsd:annotation>

3955

<xsd:documentation>

3956

<h:div class="summary">Array of occupancies.</h:div>

3957

<h:div class="description">Normally only found in crystallography. Defaults to 1.0. The occupancy is required to calculate the molecular formula from the atoms.</h:div>

3958

</xsd:documentation>

3959

</xsd:annotation>

3960

</xsd:attribute>

3961

</xsd:attributeGroup><xsd:attributeGroup id="attGp.order" name="order">

3962

<xsd:attribute id="att.order" name="order" type="orderType">

3963

<xsd:annotation>

3964

<xsd:documentation>

3965

<h:div class="summary">The order of the bond.</h:div>

3966

<h:div class="description">There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations.</h:div>

3967

</xsd:documentation>

3968

</xsd:annotation>

3969

</xsd:attribute>

3970

</xsd:attributeGroup><xsd:attributeGroup id="attGp.orderArray" name="orderArray">

3971

3972

<xsd:attribute name="order" id="att.orderArray" type="orderArrayType">

3973

<xsd:annotation>

3974

<xsd:documentation>

3975

<h:div class="summary">The order of the bond.</h:div>

3976

<h:div class="description">There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations.</h:div>

3977

</xsd:documentation>

3978

</xsd:annotation>

3979

</xsd:attribute>

3980

</xsd:attributeGroup><xsd:attributeGroup id="attGp.parentSI" name="parentSI">

3981

<xsd:attribute id="att.parentSI" name="parentSI" type="namespaceRefType">

3982

<xsd:annotation>

3983

<xsd:documentation>

3984

<h:div class="summary">A dictRef-like reference to the id of the parent SI unit.</h:div>

3985

<h:div class="description">This parent should occur in this or another dictionary

3986

and be accessible through the dictRef mechanism. This attribute is forbidden

3987

for SI Units themselves. The mechanism holds for base SI units (7) and

3988

all compound (derived) units made by combinations of base Units.</h:div>

3989

<h:div class="example" href="unit3.xml"/>

3990

</xsd:documentation>

3991

</xsd:annotation>

3992

</xsd:attribute>

3993

</xsd:attributeGroup><xsd:attributeGroup id="attGp.pattern" name="pattern">

3994

<xsd:attribute id="att.pattern" name="pattern" type="xsd:string">

3995

<xsd:annotation>

3996

<xsd:documentation>

3997

<h:div class="summary">Pattern constraint.</h:div>

3998

<h:div class="description">Based on xsd:schema.</h:div>

3999

</xsd:documentation>

4000

</xsd:annotation>

4001

</xsd:attribute>

4002

</xsd:attributeGroup><xsd:attributeGroup id="attGp.peakHeight" name="peakHeight">

4003

<xsd:attribute id="att.peakHeight" name="peakHeight" type="xsd:double">

4004

<xsd:annotation>

4005

<xsd:documentation>

4006

<h:div class="summary">Height of a peak.</h:div>

4007

<h:div class="description">For 1-dimensional data

4008

(e.g. y vs x) hould use the same units as the appropriate

4009

axis (e.g. y).</h:div>

4010

</xsd:documentation>

4011

</xsd:annotation>

4012

</xsd:attribute>

4013

</xsd:attributeGroup><xsd:attributeGroup id="attGp.peakMultiplicity" name="peakMultiplicity">

4014

<xsd:attribute id="att.peakMultiplicity" name="peakMultiplicity" type="peakMultiplicityType">

4015

<xsd:annotation>

4016

<xsd:documentation>

4017

<h:div class="summary">Multiplicity of a peak.</h:div>

4018

<h:div class="description">Uses a semi-controlled vocabulary.</h:div>

4019

</xsd:documentation>

4020

</xsd:annotation>

4021

4022

</xsd:attribute>

4023

4024

</xsd:attributeGroup><xsd:attributeGroup id="attGp.peakShape" name="peakShape">

4025

<xsd:attribute id="att.peakShape" name="peakShape" type="peakShapeType">

4026

<xsd:annotation>

4027

<xsd:documentation>

4028

<h:div class="summary">Shape of a peak.</h:div>

4029

<h:div class="description">Semi-controlled vocabulary such as broad or sharp.</h:div>

4030

</xsd:documentation>

4031

</xsd:annotation>

4032

</xsd:attribute>

4033

4034

</xsd:attributeGroup><xsd:attributeGroup id="attGp.peakStructureType" name="peakStructureType">

4035

<xsd:attribute id="att.peakStructureType" name="type" type="peakStructureTypeType">

4036

<xsd:annotation>

4037

<xsd:documentation>

4038

<h:div class="summary">Type of this structure.</h:div>

4039

<h:div class="description">Semi-controlled vocabulary such as coupling

4040

or splitting.</h:div>

4041

</xsd:documentation>

4042

</xsd:annotation>

4043

</xsd:attribute>

4044

4045

</xsd:attributeGroup><xsd:attributeGroup id="attGp.peakUnits" name="peakUnits">

4046

<xsd:attribute id="att.peakUnits" name="peakUnits" type="unitsType">

4047

<xsd:annotation>

4048

<xsd:documentation>

4049

<h:div class="summary">Units for a peak or peak integral.</h:div>

4050

<h:div class="description">For 2-dimensional spectra the units represent the observation. For an integral they are usually arbitrary and not related to the x- and y- axis units. Thus NMR spectra may use hydrogen count as the units for the peak area.</h:div>

4051

</xsd:documentation>

4052

</xsd:annotation>

4053

</xsd:attribute>

4054

4055

</xsd:attributeGroup><xsd:attributeGroup id="attGp.periodic" name="periodic">

4056

<xsd:attribute name="periodic" type="xsd:boolean" id="att.periodic" default="true">

4057

<xsd:annotation>

4058

<xsd:documentation>

4059

<h:div class="summary">Is the axis periodic.</h:div>

4060

<h:div class="description">Any or all of the axes may be periodic or aperiodic. An example could be a surface where 2 periodic axes (not necessarily orthogonal) are used to describe the coordinates in the surface, perhaps representing lattice vectors of a 3D crystal or 2D layer. The third vector is orthogonal and represents coordinates normal to the surface. In this case only the direction, not the magnitude of the vector is important.</h:div>

4061

</xsd:documentation>

4062

</xsd:annotation>

4063

</xsd:attribute>

4064

</xsd:attributeGroup><xsd:attributeGroup id="attGp.periodicity" name="periodicity">

4065

<xsd:attribute name="periodicity" id="att.periodicity" type="xsd:positiveInteger">

4066

<xsd:annotation>

4067

<xsd:documentation>

4068

<h:div class="summary">Periodicity of the system.</h:div>

4069

<h:div class="summary">This represents the number of dimensions (or coordinate axes) along periodic behaviour occurs and can be supported by symmetry operators or other transformations. Periodicity must never exceed dimensionality.</h:div>

4070

</xsd:documentation>

4071

</xsd:annotation>

4072

</xsd:attribute>

4073

</xsd:attributeGroup><xsd:attributeGroup id="attGp.point3" name="point3">

4074

<xsd:attribute name="point3" type="point3Type" id="att.point3">

4075

<xsd:annotation>

4076

<xsd:documentation>

4077

<h:div class="summary">A point in 3 dimensions.</h:div>

4078

<h:div class="description">can be used for any complex geometrical object,

4079

such as line.</h:div>

4080

</xsd:documentation>

4081

</xsd:annotation>

4082

</xsd:attribute>

4083

</xsd:attributeGroup><xsd:attributeGroup id="attGp.pointGroup" name="pointGroup">

4084

<xsd:attribute id="att.pointGroup" name="pointGroup" type="xsd:string">

4085

<xsd:annotation>

4086

<xsd:documentation>

4087

<h:div class="summary">A point group.</h:div>

4088

<h:div class="description">No fixed semantics, though Schoenflies is recommended over Hermann-Mauguin. We may provide a controlled-extensible list in the future.</h:div>

4089

</xsd:documentation>

4090

</xsd:annotation>

4091

</xsd:attribute>

4092

</xsd:attributeGroup><xsd:attributeGroup id="attGp.pointGroupMultiplicity" name="pointGroupMultiplicity">

4093

<xsd:attribute id="att.pointGroupMultiplicity" name="pointGroupMultiplicity" type="xsd:positiveInteger">

4094

<xsd:annotation>

4095

<xsd:documentation>

4096

<h:div class="summary">SpaceGroup multiplicity.</h:div>

4097

<h:div class="description">Normally for an atom. This attribute gives the pointGroup multiplicity of the molecule and is independent of any atomic information. No default, and it may take any positive integer value

4098

(though values are normally between 1 and 60 (for icosahedral). It represents the number of symmetry operations

4099

(without any translations) that transform the atom into itself.

4100

Thus an atom on a centre of symmetry can have a pointGroupMultiplicity of 2.

4101

The pointGroupMultiplicity can be deduced from a knowledge of the

4102

coordinates and the pointGroup operators and so is formally redundant but this is a

4103

useful convenience operator.

4104

Distinguish carefully from occupancy which represents incomplete occupation of a

4105

site.</h:div>

4106

</xsd:documentation>

4107

</xsd:annotation>

4108

</xsd:attribute>

4109

</xsd:attributeGroup><xsd:attributeGroup id="attGp.power" name="power">

4110

<xsd:attribute name="power" type="xsd:double" use="required" id="att.power">

4111

<xsd:annotation>

4112

<xsd:documentation>

4113

<h:div class="summary">The power to which a dimension should be raised.</h:div>

4114

<h:div class="description">Normally an integer. Must be included, even if unity.</h:div>

4115

</xsd:documentation>

4116

</xsd:annotation>

4117

</xsd:attribute>

4118

</xsd:attributeGroup><xsd:attributeGroup id="attGp.preserve" name="preserve">

4119

<xsd:attribute name="preserve" type="xsd:boolean" id="att.preserve">

4120

<xsd:annotation>

4121

<xsd:documentation>

4122

<h:div class="summary">Is the dimension preserved during algebra.</h:div>

4123

<h:div class="dimension">Experimental. The idea is to support

4124

concepts like volume/volume where algebraically these cancel out.

4125

preserve="yes" is intending to support preservation during

4126

derivation of new unitTypes.</h:div>

4127

</xsd:documentation>

4128

</xsd:annotation>

4129

</xsd:attribute>

4130

</xsd:attributeGroup><xsd:attributeGroup id="attGp.ratio" name="ratio">

4131

<xsd:attribute name="ratio" id="att.ratio" type="occupancyType">

4132

<xsd:annotation>

4133

<xsd:documentation>

4134

<h:div class="summary">A ratio in the range 0 to 1.</h:div>

4135

<h:div class="description">Currently used for ratios between brached reactions but re-usable for other concepts.</h:div>

4136

</xsd:documentation>

4137

</xsd:annotation>

4138

</xsd:attribute>

4139

</xsd:attributeGroup><xsd:attributeGroup id="attGp.reactionFormat" name="reactionFormat">

4140

4141

<xsd:attribute id="att.reactionFormat" name="format" type="reactionFormatType">

4142

<xsd:annotation>

4143

<xsd:documentation>

4144

<h:div class="summary">Format of the reaction component.</h:div>

4145

<h:div class="description">Indicates how the components of reactionScheme, reactionStepList, etc. should be processed. No controlled vocabulary. One example is format="cmlSnap" asserts that the processor can assume that the reactants and products can be rendered using the CMLSnap design. Note that the reaction can be interpreted without reference to the format, which is primarily a processing instruction.</h:div>

4146

</xsd:documentation>

4147

</xsd:annotation>

4148

</xsd:attribute>

4149

</xsd:attributeGroup><xsd:attributeGroup id="attGp.reactionRole" name="reactionRole">

4150

4151

<xsd:attribute name="role" id="att.reactionRole" type="reactionRoleType">

4152

<xsd:annotation>

4153

<xsd:documentation>

4154

<h:div class="summary">Role of the reaction.</h:div>

4155

</xsd:documentation>

4156

</xsd:annotation>

4157

</xsd:attribute>

4158

</xsd:attributeGroup><xsd:attributeGroup id="attGp.reactionStepListType" name="reactionStepListType">

4159

4160

<xsd:attribute name="type" id="att.reactionStepListType" default="consecutive" type="reactionStepListTypeType">

4161

<xsd:annotation>

4162

<xsd:documentation>

4163

<h:div class="summary">The sequence of steps in a reactionStepList.</h:div>

4164

4165

<h:div>The semantic of these are not fully explored, but we suggest that consecutive and simultaneous should be the first to be supported</h:div>

4166

</xsd:documentation>

4167

</xsd:annotation>

4168

</xsd:attribute>

4169

</xsd:attributeGroup><xsd:attributeGroup id="attGp.reactionType" name="reactionType">

4170

4171

<xsd:attribute id="att.reactionType" name="type" type="reactionTypeType">

4172

<xsd:annotation>

4173

<xsd:documentation>

4174

<h:div class="summary">Type of the reaction.</h:div>

4175

</xsd:documentation>

4176

</xsd:annotation>

4177

</xsd:attribute>

4178

</xsd:attributeGroup><xsd:attributeGroup id="attGp.recommendedUnits" name="recommendedUnits">

4179

<xsd:attribute id="att.recommendedUnits" name="recommendedUnits" type="unitsType">

4180

<xsd:annotation>

4181

<xsd:documentation>

4182

<h:div class="summary">Recommended unit.</h:div>

4183

<h:div class="description">a facet on a numeric dictionary entry.</h:div>

4184

</xsd:documentation>

4185

</xsd:annotation>

4186

</xsd:attribute>

4187

</xsd:attributeGroup><xsd:attributeGroup id="attGp.ref" name="ref">

4188

<xsd:attribute id="att.ref" name="ref" type="refType">

4189

<xsd:annotation>

4190

<xsd:documentation>

4191

<h:div class="summary">A reference to an element of given type.</h:div>

4192

<h:div class="description"><h:tt>ref</h:tt> modifies an element into a reference to an existing element of that type within the document. This is similar to a pointer and it can be thought of a strongly typed hyperlink. It may also be used for "subclassing" or "overriding" elements.<br xmlns=""/>

4193

When referring to an element most of the "data" such as attribute values and element content will be on the full instantiated element. Therefore ref (and possibly id) will normally be the only attributes on the pointing element. However there may be some attributes (title, count, etc.) which have useful semantics, but these are element-specific</h:div>

4194

4195

<h:div class="example" href="refGroup1.xml"/>

4196

</xsd:documentation>

4197

</xsd:annotation>

4198

</xsd:attribute>

4199

</xsd:attributeGroup><xsd:attributeGroup id="attGp.regionRefs" name="regionRefs">

4200

<xsd:attribute name="regionRefs" type="refType" id="att.regionRefs">

4201

<xsd:annotation>

4202

<xsd:documentation>

4203

<h:div class="summary">A list of regions creating a union.</h:div>

4204

<h:div class="description">The union of a series of regions produces a larger region (possibly disjoint). Any point belonging to any of the referenced regions is a member of this region.</h:div>

4205

</xsd:documentation>

4206

</xsd:annotation>

4207

</xsd:attribute>

4208

</xsd:attributeGroup><xsd:attributeGroup id="attGp.relatedEntryType" name="relatedEntryType">

4209

4210

<xsd:attribute id="att.relatedEntryType" name="type" type="relatedEntryTypeType">

4211

<xsd:annotation>

4212

<xsd:documentation>

4213

<h:div class="summary">Type of relatedEntry.</h:div>

4214

<h:div class="description">Type represents a the type of relationship in a relatedEntry element.</h:div>

4215

</xsd:documentation>

4216

</xsd:annotation>

4217

</xsd:attribute>

4218

</xsd:attributeGroup><xsd:attributeGroup id="attGp.role" name="role">

4219

<xsd:attribute id="att.role" name="role" type="xsd:string">

4220

<xsd:annotation>

4221

<xsd:documentation>

4222

<h:div class="summary">Role of the object.</h:div>

4223

<h:div class="description">How the object functions or its position in the architecture. No controlled vocabulary.</h:div>

4224

</xsd:documentation>

4225

</xsd:annotation>

4226

</xsd:attribute>

4227

</xsd:attributeGroup><xsd:attributeGroup id="attGp.rows" name="rows">

4228

<xsd:attribute name="rows" id="att.rows" type="sizeType">

4229

<xsd:annotation>

4230

<xsd:documentation>

4231

<h:div class="summary">Number of rows.</h:div>

4232

</xsd:documentation>

4233

</xsd:annotation>

4234

</xsd:attribute>

4235

</xsd:attributeGroup><xsd:attributeGroup id="attGp.scheme" name="scheme">

4236

<xsd:attribute name="scheme" id="att.reactionStepList.scheme" default="sequence" type="schemeType">

4237

<xsd:annotation>

4238

<xsd:documentation>

4239

<h:div class="summary">The sequence of steps in a reactionList.</h:div>

4240

4241

</xsd:documentation>

4242

</xsd:annotation>

4243

</xsd:attribute>

4244

</xsd:attributeGroup><xsd:attributeGroup id="attGp.serial" name="serial">

4245

<xsd:attribute name="serial" id="att.serial" type="xsd:string">

4246

<xsd:annotation>

4247

<xsd:documentation>

4248

<h:div class="summary">Serial number or other id.</h:div>

4249

<h:div class="summary">Currently only on module. Modules with the same _role_ attribute can be distinguished by _serial_. This is often an integer but other schemes may be used.</h:div>

4250

</xsd:documentation>

4251

</xsd:annotation>

4252

</xsd:attribute>

4253

</xsd:attributeGroup><xsd:attributeGroup id="attGp.siNamespace" name="siNamespace">

4254

<xsd:attribute id="att.siNamespace" name="siNamespace" type="namespaceType">

4255

<xsd:annotation>

4256

<xsd:documentation>

4257

<h:div class="summary">The namespace for SI Units dictionary.</h:div>

4258

<h:div class="description">Main use is on unitList to identify the

4259

dictionary holding the SI Units.</h:div>

4260

</xsd:documentation>

4261

</xsd:annotation>

4262

</xsd:attribute>

4263

</xsd:attributeGroup><xsd:attributeGroup id="attGp.siNamespaceArray" name="siNamespaceArray">

4264

<xsd:attribute id="att.siNamespaceArray" name="siNamespaceArray" type="namespaceArrayType">

4265

<xsd:annotation>

4266

<xsd:documentation>

4267

<h:div class="summary">Array of namespaces locating SI Units dictionaries.</h:div>

4268

<h:div class="description">Main use is on unitList to identify the

4269

dictionaries holding the SI Units.</h:div>

4270

</xsd:documentation>

4271

</xsd:annotation>

4272

</xsd:attribute>

4273

</xsd:attributeGroup><xsd:attributeGroup id="attGp.size" name="size">

4274

<xsd:attribute id="att.size" name="size" type="sizeType">

4275

<xsd:annotation>

4276

<xsd:documentation>

4277

<h:div class="summary">The size of an array or matrix.</h:div>

4278

</xsd:documentation>

4279

</xsd:annotation>

4280

</xsd:attribute>

4281

</xsd:attributeGroup><xsd:attributeGroup id="attGp.spaceGroup" name="spaceGroup">

4282

<xsd:attribute id="att.spaceGroup" name="spaceGroup" type="xsd:string">

4283

<xsd:annotation>

4284

<xsd:documentation>

4285

<h:div class="summary">A space group.</h:div>

4286

<h:div class="description">No fixed semantics, though Hermann-Mauguin or Hall is recommended over Schoenflies. We may provide a controlled-extensible list in the future.</h:div>

4287

</xsd:documentation>

4288

</xsd:annotation>

4289

</xsd:attribute>

4290

</xsd:attributeGroup><xsd:attributeGroup id="attGp.spaceGroupMultiplicity" name="spaceGroupMultiplicity">

4291

<xsd:attribute id="att.spaceGroupMultiplicity" name="spaceGroupMultiplicity" type="xsd:positiveInteger">

4292

<xsd:annotation>

4293

<xsd:documentation>

4294

<h:div class="summary">SpaceGroup multiplicity.</h:div>

4295

<h:div class="description">Normally for an atom. This attribute gives the spaceGroup multiplicity of the molecule and is independent of any atomic information. No default, and it may take any positive integer value

4296

(though values are normally between 1 and 192. It represents the number of symmetry operations

4297

(without cell translations) that transform the atom into itself.

4298

Thus an atom on a centre of symmetry can have a spaceGroupMultiplicity of 2.

4299

The spaceGroupMultiplicity can be deduced from a knowledge of the

4300

coordinates and the spaceGroup operators and so is formally redundant but this is a

4301

useful convenience operator. Some crystallographic experiments report this attribute

4302

as, for example, the IUCr CIF item 'atom_site_symmetry_multiplicity'.

4303

Distinguish carefully from occupancy which represents incomplete occupation of a

4304

site.</h:div>

4305

</xsd:documentation>

4306

</xsd:annotation>

4307

</xsd:attribute>

4308

</xsd:attributeGroup><xsd:attributeGroup id="attGp.spaceType" name="spaceType">

4309

<xsd:attribute id="att.spaceType" name="spaceType" type="spaceType">

4310

<xsd:annotation>

4311

<xsd:documentation>

4312

<h:div class="summary">The spaceType of the lattice.</h:div>

4313

<h:div class="description">Usually real or reciprocal. No default. The semantics of this are software-dependent (i.e. this Schema does not check for consistency for unitTypes, etc.</h:div>

4314

</xsd:documentation>

4315

</xsd:annotation>

4316

</xsd:attribute>

4317

</xsd:attributeGroup><xsd:attributeGroup id="attGp.spectrumType" name="spectrumType">

4318

<xsd:attribute name="type" id="att.spectrumType" type="spectrumTypeType">

4319

<xsd:annotation>

4320

<xsd:documentation>

4321

<h:div class="summary">The type of the spectrum.</h:div>

4322

</xsd:documentation>

4323

</xsd:annotation>

4324

</xsd:attribute>

4325

</xsd:attributeGroup><xsd:attributeGroup id="attGp.sphere3" name="sphere3">

4326

<xsd:attribute name="sphere3" type="sphere3Type" id="att.sphere3">

4327

<xsd:annotation>

4328

<xsd:documentation>

4329

<h:div class="summary">A sphere.</h:div>

4330

<h:div class="description">Currently describes a region. Any point falling within the sphere or on its surface is within the region.</h:div>

4331

</xsd:documentation>

4332

</xsd:annotation>

4333

</xsd:attribute>

4334

</xsd:attributeGroup><xsd:attributeGroup id="attGp.spin" name="spin">

4335

<xsd:attribute id="att.spin" name="spin" type="isotopicSpinType">

4336

<xsd:annotation>

4337

<xsd:documentation>

4338

<h:div class="summary">The spin of a system.</h:div>

4339

<h:div class="description">Supports fractional values. Currently the spin of a nucleus. The normal fraction representing the spin of the isotope.</h:div>

4340

<h:div class="example" href="spin1.xml"/>

4341

</xsd:documentation>

4342

</xsd:annotation>

4343

</xsd:attribute>

4344

</xsd:attributeGroup><xsd:attributeGroup id="attGp.spinMultiplicity" name="spinMultiplicity">

4345

<xsd:attribute id="att.spinMultiplicity" name="spinMultiplicity" type="xsd:positiveInteger">

4346

<xsd:annotation>

4347

<xsd:documentation>

4348

<h:div class="summary">Spin multiplicity.</h:div>

4349

<h:div class="description">Normally for a molecule. This attribute gives the spin multiplicity of the molecule and is independent of any atomic information. No default, and it may take any positive integer value (though values are normally between 1 and 5.</h:div>

4350

</xsd:documentation>

4351

</xsd:annotation>

4352

</xsd:attribute>

4353

</xsd:attributeGroup><xsd:attributeGroup name="start" id="attGp.start">

4354

<xsd:attribute name="start" type="xsd:string" id="att.start">

4355

<xsd:annotation>

4356

<xsd:documentation>

4357

<h:div class="summary">The start time.</h:div>

4358

<h:div class="description">The start time in any allowable XSD representation of date, time or dateTime. This will normally be a clock time or date.</h:div>

4359

</xsd:documentation>

4360

</xsd:annotation>

4361

</xsd:attribute>

4362

</xsd:attributeGroup><xsd:attributeGroup name="startCondition" id="attGp.startCondition">

4363

<xsd:attribute name="startCondition" type="xsd:string" id="att.startCondition">

4364

<xsd:annotation>

4365

<xsd:documentation>

4366

<h:div class="summary">The start condition.</h:div>

4367

<h:div class="description">This can describe the condition(s) that has to be met before an action can begin, such as in a recipe. Semantics are unexplored but could be used to control robotic operations.</h:div>

4368

</xsd:documentation>

4369

</xsd:annotation>

4370

</xsd:attribute>

4371

</xsd:attributeGroup><xsd:attributeGroup id="attGp.state" name="state">

4372

<xsd:attribute name="state" type="stateType" id="att.state">

4373

<xsd:annotation>

4374

<xsd:documentation>

4375

<h:div class="summary">The physical state of the substance.</h:div>

4376

<h:div class="description">No fixed semantics or default.</h:div>

4377

</xsd:documentation>

4378

</xsd:annotation>

4379

</xsd:attribute>

4380

</xsd:attributeGroup><xsd:attributeGroup id="attGp.substanceListType" name="substanceListType">

4381

4382

<xsd:attribute id="att.substanceListType" name="type" type="substanceListTypeType">

4383

<xsd:annotation>

4384

<xsd:documentation>

4385

<h:div class="summary">Type of the substanceList.</h:div>

4386

<h:div class="description">Extension is allowed through the "other" value.</h:div>

4387

</xsd:documentation>

4388

</xsd:annotation>

4389

</xsd:attribute>

4390

</xsd:attributeGroup><xsd:attributeGroup id="attGp.symbol" name="symbol">

4391

<xsd:attribute name="symbol" id="att.symbol" type="xsd:string">

4392

<xsd:annotation>

4393

<xsd:documentation>

4394

<h:div class="summary">A symbol.</h:div>

4395

<h:div class="description">No semantics. However it should contain only

4396

ASCII characters and we may have to develop an escaping mechanism.

4397

Used on _atomicBasisFunction_, _unit_, etc.</h:div>

4398

</xsd:documentation>

4399

</xsd:annotation>

4400

</xsd:attribute>

4401

</xsd:attributeGroup><xsd:attributeGroup id="attGp.symmetryOriented" name="symmetryOriented">

4402

<xsd:attribute id="att.symmetryOriented" name="symmetryOriented" type="xsd:boolean">

4403

<xsd:annotation>

4404

<xsd:documentation>

4405

<h:div class="summary">Is the molecule oriented to the symmetry</h:div>

4406

<h:div class="description">No formal default, but a molecule is assumed to be oriented according to any _symmetry_ children. This is required for crystallographic data, but some systems for isolated molecules allow specification of arbitrary Cartesian or internal coordinates, which must be fitted or refined to a prescribed symmetry. In this case the attribute value is false.</h:div>

4407

</xsd:documentation>

4408

</xsd:annotation>

4409

</xsd:attribute>

4410

</xsd:attributeGroup><xsd:attributeGroup id="attGp.tautomeric" name="tautomeric">

4411

<xsd:attribute id="att.tautomeric" name="tautomeric" type="xsd:string">

4412

<xsd:annotation>

4413

<xsd:documentation>

4414

<h:div class="summary">Indicates whether the structure is a tautomer.</h:div>

4415

<h:div class="general">Currently used with IChI _identifier_ element. Semantics, vocabulary and usage are application-dependent.</h:div>

4416

</xsd:documentation>

4417

</xsd:annotation>

4418

</xsd:attribute>

4419

</xsd:attributeGroup><xsd:attributeGroup id="attGp.term" name="term">

4420

<xsd:attribute id="att.term" name="term" type="xsd:string" use="required">

4421

<xsd:annotation>

4422

<xsd:documentation>

4423

<h:div class="summary">A term in a dictionary.</h:div>

4424

<h:div class="description">The term should be a noun or nounal phrase, with a separate definition and further description.</h:div>

4425

</xsd:documentation>

4426

</xsd:annotation>

4427

</xsd:attribute>

4428

</xsd:attributeGroup><xsd:attributeGroup id="attGp.title" name="title">

4429

<xsd:attribute id="att.title" name="title" type="xsd:string">

4430

<xsd:annotation>

4431

<xsd:documentation>

4432

<h:div class="summary">A title on an element.</h:div>

4433

<h:div class="description">No controlled value.</h:div>

4434

<h:div class="example" href="title1.xml"/>

4435

</xsd:documentation>

4436

</xsd:annotation>

4437

</xsd:attribute>

4438

</xsd:attributeGroup><xsd:attributeGroup id="attGp.to" name="to">

4439

<xsd:attribute id="att.to" name="to" type="refType">

4440

<xsd:annotation>

4441

<xsd:documentation>

4442

<h:div class="summary">The target of one or more links.</h:div>

4443

<h:div class="summary">On link elements the value is the single id of an element within the document or context specified in map@toContext attributes. It must identify the element uniquely. The reserved value 'null' implies that no mapping has been provided for the object(s) in the 'from' attribute. This implies no semantics but may be used by software to keep count of which elements have been mapped. For multiple targets use 'toSet'.</h:div>

4444

<h:div class="curation">2005-06-18: updated docs</h:div>

4445

</xsd:documentation>

4446

</xsd:annotation>

4447

</xsd:attribute>

4448

</xsd:attributeGroup><xsd:attributeGroup id="attGp.toContext" name="toContext">

4449

<xsd:attribute id="att.toContext" name="toContext" type="idType">

4450

<xsd:annotation>

4451

<xsd:documentation>

4452

<h:div class="summary">The context for the 'from' links in a map.</h:div>

4453

4454

4455

</h:div>

4456

<h:div class="curation">2005-06-18: created</h:div>

4457

</xsd:documentation>

4458

</xsd:annotation>

4459

</xsd:attribute>

4460

</xsd:attributeGroup><xsd:attributeGroup id="attGp.toSet" name="toSet">

4461

<xsd:attribute id="att.toSet" name="toSet" type="idArrayType">

4462

<xsd:annotation>

4463

<xsd:documentation>

4464

<h:div class="summary">A set of ids representing the base of a link.</h:div>

4465

<h:div class="description"><h:p>For a partial mapping where a number of 'to' elements are known to link to a number of 'from' elements it can be useful to aggregate these into a single attribute value. The primary use is to assert that n links exist between a set of n 'to' elements and n 'from' elements but that the precise links are unknown. The semantics of the reference are the same as for 'to' and all the elements must be of the same type (which can be specified with 'toType' either on the link or the containing map). No order information is implied. In general there will be the same number of idRefs in the 'fromSet' and all implicit links will share the same attributes (e.g. 'role'). In many cases the sets will be later split into discrete links thorugh further calculation or experiment (e.g. peak assignment). Sets should never be used as a lazy or concise alternative where the all the links are explicitly known. </h:p>

4466

</h:div>

4467

<h:div class="curation">2005-06-18: created</h:div>

4468

</xsd:documentation>

4469

</xsd:annotation>

4470

</xsd:attribute>

4471

</xsd:attributeGroup><xsd:attributeGroup id="attGp.totalDigits" name="totalDigits">

4472

<xsd:attribute id="att.totalDigits" name="totalDigits" type="xsd:positiveInteger">

4473

<xsd:annotation>

4474

<xsd:documentation>

4475

<h:div class="summary">total digits in a scalar.</h:div>

4476

<h:div class="description">based on xsd:schema.</h:div>

4477

</xsd:documentation>

4478

</xsd:annotation>

4479

</xsd:attribute>

4480

</xsd:attributeGroup><xsd:attributeGroup id="attGp.toType" name="toType">

4481

<xsd:attribute id="att.toType" name="toType" type="xmlElementType">

4482

<xsd:annotation>

4483

<xsd:documentation>

4484

<h:div class="summary">The type of the base of a link.</h:div>

4485

<h:div class="description">

4486

<h:p>The local tagname of the referenced element (e.g. 'molecule' or 'peakGroup'). This acts as a partial check on the integrity of the link. Software can assume that the referenced element is of a given tytpe and can create an object supporting that type.</h:p>

4487

4488

</h:div>

4489

<h:div class="curation">2005-06-18: created</h:div>

4490

</xsd:documentation>

4491

</xsd:annotation>

4492

</xsd:attribute>

4493

</xsd:attributeGroup><xsd:attributeGroup id="attGp.type" name="type">

4494

<xsd:attribute name="type" id="att.type" type="xsd:string">

4495

<xsd:annotation>

4496

<xsd:documentation>

4497

<h:div class="summary">Type of the object.</h:div>

4498

<h:div class="description">A qualifier which may affect the semantics of the object.</h:div>

4499

</xsd:documentation>

4500

</xsd:annotation>

4501

</xsd:attribute>

4502

</xsd:attributeGroup><xsd:attributeGroup id="attGp.unitListType" name="unitListType">

4503

<xsd:attribute id="att.unitListType" name="type" type="unitListTypeType">

4504

<xsd:annotation>

4505

<xsd:documentation>

4506

<h:div class="summary">A reference to the type of a unit.</h:div>

4507

<h:div class="description">Needed to differentiate the rather unhappy

4508

polymorphism of unitList/unit and unitList/unitType.</h:div>

4509

<h:div class="curation">2005-12-17 PMR: Added</h:div>

4510

</xsd:documentation>

4511

</xsd:annotation>

4512

</xsd:attribute>

4513

</xsd:attributeGroup><xsd:attributeGroup id="attGp.units" name="units">

4514

<xsd:attribute id="att.units" name="units" type="unitsType">

4515

<xsd:annotation>

4516

<xsd:documentation>

4517

<h:div class="summary">Scientific units on an element.</h:div>

4518

<h:div class="description">These must be taken from a dictionary

4519

of units. There should be some mechanism for validating the type

4520

of the units against the possible values of the element.</h:div>

4521

</xsd:documentation>

4522

</xsd:annotation>

4523

</xsd:attribute>

4524

</xsd:attributeGroup><xsd:attributeGroup id="attGp.unitsRef" name="unitsRef">

4525

<xsd:attribute name="unitsRef" id="att.unitsRef" type="xsd:string">

4526

<xsd:annotation>

4527

<xsd:documentation>

4528

<h:div class="summary">unitsRef attribute on CML1 elements.</h:div>

4529

<h:div class="description">CML1-only - now deprecated.</h:div>

4530

</xsd:documentation>

4531

</xsd:annotation>

4532

</xsd:attribute>

4533

</xsd:attributeGroup><xsd:attributeGroup id="attGp.unitType" name="unitType">

4534

<xsd:attribute id="att.unitType" name="unitType" type="xsd:string">

4535

<xsd:annotation>

4536

<xsd:documentation>

4537

<h:div class="summary">A reference to the type of a unit.</h:div>

4538

<h:div class="description">Used in defining the unit and doing

4539

symbolic algebra on the dimensionality.</h:div>

4540

</xsd:documentation>

4541

</xsd:annotation>

4542

</xsd:attribute>

4543

</xsd:attributeGroup><xsd:attributeGroup id="attGp.value" name="value">

4544

<xsd:attribute name="value" id="att.value" type="xsd:string">

4545

<xsd:annotation>

4546

<xsd:documentation>

4547

<h:div class="summary">Value of a scalar object.</h:div>

4548

<h:div class="description">The value must be consistent with the dataType of the object.</h:div>

4549

</xsd:documentation>

4550

</xsd:annotation>

4551

</xsd:attribute>

4552

</xsd:attributeGroup><xsd:attributeGroup id="attGp.vector3" name="vector3">

4553

<xsd:attribute name="vector3" type="vector3Type" id="att.vector3">

4554

<xsd:annotation>

4555

<xsd:documentation>

4556

<h:div class="summary">A vector in 3 dimensions.</h:div>

4557

<h:div class="description">can be used for any complex geometrical object,

4558

such as line.</h:div>

4559

</xsd:documentation>

4560

</xsd:annotation>

4561

</xsd:attribute>

4562

</xsd:attributeGroup><xsd:attributeGroup id="attGp.version" name="version">

4563

<xsd:attribute id="att.version" name="version" type="xsd:string">

4564

<xsd:annotation>

4565

<xsd:documentation>

4566

<h:div class="summary">The version of the identifier.</h:div>

4567

<h:div class="general">The IChI or other identifier may be dependent on the date of release and this attribute is highly recommended.</h:div>

4568

</xsd:documentation>

4569

</xsd:annotation>

4570

</xsd:attribute>

4571

</xsd:attributeGroup><xsd:attributeGroup id="attGp.weight" name="weight">

4572

<xsd:attribute name="weight" type="xsd:double" id="att.weight">

4573

<xsd:annotation>

4574

<xsd:documentation>

4575

<h:div class="summary">Weight of the element.</h:div>

4576

<h:div class="description">Currently the weight of the kPoint, derived from the symmetry such as the inverse of the multiplicity in real space. Thus a point at 0,0,0 in monoclinic space might be 0.25. The lowest value possible is probably 1/48.0 (in m3m).</h:div>

4577

<h:div class="curation">2003-09-15 (added at suggestion of Jon Wakelin).</h:div>

4578

</xsd:documentation>

4579

</xsd:annotation>

4580

</xsd:attribute>

4581

</xsd:attributeGroup><xsd:attributeGroup id="attGp.whiteSpace" name="whiteSpace">

4582

<xsd:attribute id="att.whiteSpace" name="whiteSpace" type="xsd:string">

4583

<xsd:annotation>

4584

<xsd:documentation>

4585

<h:div class="summary">Whitespace.</h:div>

4586

<h:div class="description">Attached to entry. This may be obsolete.</h:div>

4587

</xsd:documentation>

4588

</xsd:annotation>

4589

</xsd:attribute>

4590

4591

</xsd:attributeGroup><xsd:attributeGroup id="attGp.x2" name="x2">

4592

<xsd:attribute name="x2" id="att.x2" type="xsd:double">

4593

<xsd:annotation>

4594

<xsd:documentation>

4595

<h:div class="summary">x2 coordinate for an object.</h:div>

4596

<h:div class="description">Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object.</h:div>

4597

</xsd:documentation>

4598

</xsd:annotation>

4599

</xsd:attribute>

4600

</xsd:attributeGroup><xsd:attributeGroup id="attGp.x2Array" name="x2Array">

4601

4602

<xsd:attribute name="x2" id="att.x2Array" type="coordinateComponentArrayType">

4603

<xsd:annotation>

4604

<xsd:documentation>

4605

<h:div class="summary">array of x2 coordinate.</h:div>

4606

<h:div class="description">Normally used in CML2 array mode. Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object.</h:div>

4607

</xsd:documentation>

4608

</xsd:annotation>

4609

</xsd:attribute>

4610

</xsd:attributeGroup><xsd:attributeGroup id="attGp.x3" name="x3">

4611

<xsd:attribute id="att.x3" name="x3" type="xsd:double">

4612

<xsd:annotation>

4613

<xsd:documentation>

4614

<h:div class="summary">The x coordinate of a 3 dimensional object.</h:div>

4615

<h:div class="description">The default units are Angstrom. (The provision

4616

for other units is weak at present.) Objects are always described

4617

with a right-handed coordinate system.</h:div>

4618

</xsd:documentation>

4619

</xsd:annotation>

4620

</xsd:attribute>

4621

</xsd:attributeGroup><xsd:attributeGroup id="attGp.x3Array" name="x3Array">

4622

4623

<xsd:attribute id="att.x3Array" name="x3" type="coordinateComponentArrayType">

4624

<xsd:annotation>

4625

<xsd:documentation>

4626

<h:div class="summary">An array of x3 coordinate.</h:div>

4627

<h:div class="summary">Normally used in CML2 array mode.</h:div>

4628

</xsd:documentation>

4629

</xsd:annotation>

4630

</xsd:attribute>

4631

</xsd:attributeGroup><xsd:attributeGroup id="attGp.xFract" name="xFract">

4632

<xsd:attribute id="att.xFract" name="xFract" type="xsd:double">

4633

<xsd:annotation>

4634

<xsd:documentation>

4635

<h:div class="summary">Fractional x coordinate.</h:div>

4636

<h:div class="description">normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.</h:div>

4637

</xsd:documentation>

4638

</xsd:annotation>

4639

</xsd:attribute>

4640

</xsd:attributeGroup><xsd:attributeGroup id="attGp.xFractArray" name="xFractArray">

4641

4642

<xsd:attribute id="att.xFractArray" name="xFract" type="coordinateComponentArrayType">

4643

<xsd:annotation>

4644

<xsd:documentation>

4645

<h:div class="summary">Array of fractional x coordinate.</h:div>

4646

<h:div class="description">normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.</h:div>

4647

</xsd:documentation>

4648

</xsd:annotation>

4649

</xsd:attribute>

4650

</xsd:attributeGroup><xsd:attributeGroup id="attGp.xMax" name="xMax">

4651

<xsd:attribute id="att.xMax" name="xMax" type="xsd:double">

4652

<xsd:annotation>

4653

<xsd:documentation>

4654

<h:div class="summary">Maximum xValue.</h:div>

4655

<h:div class="description">Annotates x-axis data with a maximum

4656

value. This need not be algorithmically deducible from the data

4657

and is typically used for the extent of a _peak_ or _peakGroup_.

4658

It uses xUnits or the same units as the data. There may or may not

4659

be a _xMin_ attribute but if so xMax should be greater than or

4660

equals to it.</h:div>

4661

</xsd:documentation>

4662

</xsd:annotation>

4663

</xsd:attribute>

4664

</xsd:attributeGroup><xsd:attributeGroup id="attGp.xMin" name="xMin">

4665

<xsd:attribute id="att.xMin" name="xMin" type="xsd:double">

4666

<xsd:annotation>

4667

<xsd:documentation>

4668

<h:div class="summary">Minimum xValue.</h:div>

4669

<h:div class="description">Annotates x-axis data with a minimum

4670

value. This need not be algorithmically deducible from the data

4671

and is typically used for the extent of a _peak_ or _peakGroup_.

4672

It uses xUnits or the same units as the data. There may or may not

4673

be a _xMax_ attribute but if so xMin should be less than or equals

4674

to it.</h:div>

4675

</xsd:documentation>

4676

</xsd:annotation>

4677

</xsd:attribute>

4678

</xsd:attributeGroup><xsd:attributeGroup id="attGp.xUnits" name="xUnits">

4679

<xsd:attribute id="att.xUnits" name="xUnits" type="unitsType">

4680

<xsd:annotation>

4681

<xsd:documentation>

4682

<h:div class="summary">Units for x axis.</h:div>

4683

<h:div class="description">All x-axis data must have unambiguous units. Ideally the data and _xMin_ or _xValue_ should share the same units but different xUnits can be used as long as it is clear..</h:div>

4684

</xsd:documentation>

4685

</xsd:annotation>

4686

</xsd:attribute>

4687

</xsd:attributeGroup><xsd:attributeGroup id="attGp.xValue" name="xValue">

4688

<xsd:attribute id="att.xValue" name="xValue" type="xsd:double">

4689

<xsd:annotation>

4690

<xsd:documentation>

4691

<h:div class="summary">Value along an x axis.</h:div>

4692

<h:div class="description">Annotates x-axis data with a value. It

4693

is typically used for the location of a _peak_ or _peakGroup_. It

4694

uses xUnits or the same units as the data.</h:div>

4695

</xsd:documentation>

4696

</xsd:annotation>

4697

</xsd:attribute>

4698

</xsd:attributeGroup><xsd:attributeGroup id="attGp.xWidth" name="xWidth">

4699

<xsd:attribute id="att.xWidth" name="xWidth" type="xsd:double">

4700

<xsd:annotation>

4701

<xsd:documentation>

4702

<h:div class="summary">An unsigned interval along an x axis.</h:div>

4703

<h:div class="description">It is typically used for the width of

4704

a _peak_ or _peakGroup_ but could be used for any range. It uses

4705

xUnits or the same units as the data.</h:div>

4706

</xsd:documentation>

4707

</xsd:annotation>

4708

</xsd:attribute>

4709

</xsd:attributeGroup><xsd:attributeGroup id="attGp.y2" name="y2">

4710

<xsd:attribute id="att.y2" name="y2" type="xsd:double">

4711

<xsd:annotation>

4712

<xsd:documentation>

4713

<h:div class="summary">y2 coordinate for an object.</h:div>

4714

<h:div class="description">Used for displaying the object in 2

4715

dimensions. Unrelated to the 3-D coordinates for the object. The

4716

orientation of the axes matters as it can affect the chirality of

4717

object.</h:div>

4718

</xsd:documentation>

4719

</xsd:annotation>

4720

</xsd:attribute>

4721

</xsd:attributeGroup><xsd:attributeGroup id="attGp.y2Array" name="y2Array">

4722

4723

<xsd:attribute id="att.y2Array" name="y2" type="coordinateComponentArrayType">

4724

<xsd:annotation>

4725

<xsd:documentation>

4726

<h:div class="summary">array of y2 coordinate.</h:div>

4727

4728

</xsd:documentation>

4729

</xsd:annotation>

4730

</xsd:attribute>

4731

</xsd:attributeGroup><xsd:attributeGroup id="attGp.y3" name="y3">

4732

<xsd:attribute id="att.y3" name="y3" type="xsd:double">

4733

<xsd:annotation>

4734

<xsd:documentation>

4735

<h:div class="summary">The y coordinate of a 3 dimensional object.</h:div>

4736

<h:div class="description">The default units are Angstrom. (The

4737

provision for other units is weak at present.) Objects are always

4738

described with a right-handed coordinate system.</h:div>

4739

</xsd:documentation>

4740

</xsd:annotation>

4741

</xsd:attribute>

4742

</xsd:attributeGroup><xsd:attributeGroup id="attGp.y3Array" name="y3Array">

4743

4744

<xsd:attribute id="att.y3Array" name="y3" type="coordinateComponentArrayType">

4745

<xsd:annotation>

4746

<xsd:documentation>

4747

<h:div class="summary">An array of y3 coordinate.</h:div>

4748

<h:div class="summary">Normally used in CML2 array mode.</h:div>

4749

</xsd:documentation>

4750

</xsd:annotation>

4751

</xsd:attribute>

4752

</xsd:attributeGroup><xsd:attributeGroup id="attGp.yFract" name="yFract">

4753

<xsd:attribute id="att.yFract" name="yFract" type="xsd:double">

4754

<xsd:annotation>

4755

<xsd:documentation>

4756

<h:div class="summary">Fractional y coordinate.</h:div>

4757

<h:div class="description">normally xFract, yFract and zFract

4758

should all be present or absent. If present a _crystal_ element

4759

should also occur.</h:div>

4760

</xsd:documentation>

4761

</xsd:annotation>

4762

</xsd:attribute>

4763

</xsd:attributeGroup><xsd:attributeGroup id="attGp.yFractArray" name="yFractArray">

4764

4765

<xsd:attribute id="att.yFractArray" name="yFract" type="coordinateComponentArrayType">

4766

<xsd:annotation>

4767

<xsd:documentation>

4768

<h:div class="summary">Array of fractional y coordinate.</h:div>

4769

<h:div class="description">normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.</h:div>

4770

</xsd:documentation>

4771

</xsd:annotation>

4772

</xsd:attribute>

4773

</xsd:attributeGroup><xsd:attributeGroup id="attGp.yield" name="yield">

4774

<xsd:attribute name="yield" id="att.yield" type="occupancyType">

4775

<xsd:annotation>

4776

<xsd:documentation>

4777

<h:div class="summary">Yield of a reaction or reactionStep.</h:div>

4778

<h:div class="description">Yields can be given on either element. They should lie in the range 0 to 1 inclusive (i.e. percentages will need to be converted). Software may use yield to calculate amounts of substances created during a reaction or series of reactions.</h:div>

4779

</xsd:documentation>

4780

</xsd:annotation>

4781

</xsd:attribute>

4782

</xsd:attributeGroup><xsd:attributeGroup id="attGp.yMax" name="yMax">

4783

<xsd:attribute id="att.yMax" name="yMax" type="xsd:double">

4784

<xsd:annotation>

4785

<xsd:documentation>

4786

<h:div class="summary">Maximum yValue.</h:div>

4787

<h:div class="description">Annotates y-axis data with a maximum

4788

value. This need not be algorithmically deducible from the data

4789

and is typically used for the extent of a _peak_ or _peakGroup_.

4790

It uses yUnits or the same units as the data. There may or may not

4791

be a _yMin_ attribute but if so yMax should be greater than or

4792

equals to it.</h:div>

4793

</xsd:documentation>

4794

</xsd:annotation>

4795

</xsd:attribute>

4796

</xsd:attributeGroup><xsd:attributeGroup id="attGp.yMin" name="yMin">

4797

<xsd:attribute id="att.yMin" name="yMin" type="xsd:double">

4798

<xsd:annotation>

4799

<xsd:documentation>

4800

<h:div class="summary">Minimum yValue.</h:div>

4801

<h:div class="description">Annotates y-axis data with a minimum

4802

value. This need not be algorithmically deducible from the data

4803

and is typically used for the extent of a _peak_ or _peakGroup_.

4804

It uses yUnits or the same units as the data. There may or may

4805

not be a _yMax_ attribute but if so yMin should be less than or

4806

equal to it.</h:div>

4807

</xsd:documentation>

4808

</xsd:annotation>

4809

</xsd:attribute>

4810

</xsd:attributeGroup><xsd:attributeGroup id="attGp.yUnits" name="yUnits">

4811

<xsd:attribute id="att.yUnits" name="yUnits" type="unitsType">

4812

<xsd:annotation>

4813

<xsd:documentation>

4814

<h:div class="summary">Units for y axis.</h:div>

4815

<h:div class="description">All y-axis data must have unambiguous units. Ideally the data and _yMin_ or _yValue_ should share the same units but different yUnits can be used as long as it is clear.</h:div>

4816

</xsd:documentation>

4817

</xsd:annotation>

4818

</xsd:attribute>

4819

</xsd:attributeGroup><xsd:attributeGroup id="attGp.yValue" name="yValue">

4820

<xsd:attribute id="att.yValue" name="yValue" type="xsd:double">

4821

<xsd:annotation>

4822

<xsd:documentation>

4823

<h:div class="summary">Value along a y axis.</h:div>

4824

<h:div class="description">Annotates y-axis data with a value. It

4825

is typically used for the location of a _peak_ or _peakGroup_. It

4826

uses yUnits or the same units as the data.</h:div>

4827

</xsd:documentation>

4828

</xsd:annotation>

4829

</xsd:attribute>

4830

</xsd:attributeGroup><xsd:attributeGroup id="attGp.yWidth" name="yWidth">

4831

<xsd:attribute id="att.yWidth" name="yWidth" type="xsd:double">

4832

<xsd:annotation>

4833

<xsd:documentation>

4834

<h:div class="summary">An unsigned interval along a y axis.</h:div>

4835

<h:div class="description">It is typically used for the width of

4836

a _peak_ or _peakGroup_ but could be used for any range. It uses

4837

yUnits or the same units as the data.</h:div>

4838

</xsd:documentation>

4839

</xsd:annotation>

4840

</xsd:attribute>

4841

</xsd:attributeGroup><xsd:attributeGroup id="attGp.z" name="z">

4842

<xsd:attribute id="att.z" name="z" type="xsd:nonNegativeInteger">

4843

<xsd:annotation>

4844

<xsd:documentation>

4845

<h:div class="summary">The number of molecules per cell.</h:div>

4846

<h:div class="description">Molecules are defined as the _molecule_ which directly contains the _crystal_ element.</h:div>

4847

</xsd:documentation>

4848

</xsd:annotation>

4849

</xsd:attribute>

4850

</xsd:attributeGroup><xsd:attributeGroup id="attGp.z3" name="z3">

4851

<xsd:attribute id="att.z3" name="z3" type="xsd:double">

4852

<xsd:annotation>

4853

<xsd:documentation>

4854

<h:div class="summary">The z coordinate of a 3 dimensional object.</h:div>

4855

<h:div class="description">The default units are Angstrom. (The

4856

provision for other units is weak at present.) Objects are always

4857

described with a right-handed coordinate system.</h:div>

4858

</xsd:documentation>

4859

</xsd:annotation>

4860

</xsd:attribute>

4861

</xsd:attributeGroup><xsd:attributeGroup id="attGp.z3Array" name="z3Array">

4862

4863

<xsd:attribute id="att.z3Array" name="z3" type="coordinateComponentArrayType">

4864

<xsd:annotation>

4865

<xsd:documentation>

4866

<h:div class="summary">An array of z3 coordinate.</h:div>

4867

<h:div class="summary">Normally used in CML2 array mode.</h:div>

4868

</xsd:documentation>

4869

</xsd:annotation>

4870

</xsd:attribute>

4871

</xsd:attributeGroup><xsd:attributeGroup id="attGp.zFract" name="zFract">

4872

<xsd:attribute id="att.zFract" name="zFract" type="xsd:double">

4873

<xsd:annotation>

4874

<xsd:documentation>

4875

<h:div class="summary">Fractional y coordinate.</h:div>

4876

<h:div class="description">normally xFract, yFract and zFract

4877

should all be present or absent. If present a _crystal_ element

4878

should also occur.</h:div>

4879

</xsd:documentation>

4880

</xsd:annotation>

4881

</xsd:attribute>

4882

</xsd:attributeGroup><xsd:attributeGroup id="attGp.zFractArray" name="zFractArray">

4883

4884

<xsd:attribute id="att.zFractArray" name="zFract" type="coordinateComponentArrayType">

4885

<xsd:annotation>

4886

<xsd:documentation>

4887

<h:div class="summary">Array of fractional z coordinate.</h:div>

4888

<h:div class="description">normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.</h:div>

4889

</xsd:documentation>

4890

</xsd:annotation>

4891

</xsd:attribute>

4892

</xsd:attributeGroup><xsd:element name="abundance" id="el.abundance">

4893

<xsd:annotation>

4894

<xsd:documentation>

4895

<h:div class="summary">The abundance of an isotope.</h:div>

4896

<h:div class="description">The abundance of an isotope in an isotopeList.

4897

Values are expressed in percentages.</h:div>

4898

<h:div class="example" href="isotope1.xml"/>

4899

</xsd:documentation>

4900

</xsd:annotation>

4901

<xsd:complexType>

4902

<xsd:simpleContent>

4903

<xsd:extension base="xsd:double">

4904

<xsd:attributeGroup ref="title"/>

4905

<xsd:attributeGroup ref="id"/>

4906

<xsd:attributeGroup ref="convention"/>

4907

<xsd:attributeGroup ref="dictRef"/>

4908

<xsd:attributeGroup ref="min"/>

4909

<xsd:attributeGroup ref="max"/>

4910

<xsd:attributeGroup ref="units"/>

4911

</xsd:extension>

4912

</xsd:simpleContent>

4913

</xsd:complexType>

4914

</xsd:element><xsd:element name="action" id="el.action">

4915

<xsd:annotation>

4916

<xsd:documentation>

4917

<h:div class="summary">An action which might occur in scientific data or narrative.</h:div>

4918

<h:div class="description">

4919

An action which might occur in scientific data or narrative. The definition is deliberately vague, intending to collect examples of possible usage. Thus an action could be addition of materials, measurement, application of heat or radiation. The content model is unrestricted. _action_ iself is normally a child of _actionList_.

4920

4921

<h:p>The start, end and duration attributes should be interpreted as

4922

</h:p>

4923

<h:ul>

4924

<h:li>XSD dateTimes and XSD durations. This allows precise recording of time of day, etc, or duration after start of actionList. A <h:tt>convention="xsd"</h:tt> attribute should be used to enforce XSD.</h:li>

4925

<h:li>a numerical value, with a units attribute linked to a dictionary.</h:li>

4926

<h:li>a human-readable string (unlikely to be machine processable)</h:li>

4927

</h:ul>

4928

<h:p>

4929

<h:tt>startCondition</h:tt> and <h:tt>endCondition</h:tt> values are not constrained, which allows XSL-like <h:tt>test</h:tt> attribute values. The semantics of the conditions are yet to be defined and at present are simply human readable.

4930

</h:p>

4931

<h:p>The order of the <h:tt>action</h:tt> elements in the document may, but will not always, define

4932

the order that they actually occur in.</h:p>

4933

<h:p>A delay can be shown by an <h:tt>action</h:tt> with no content. Repeated actions or

4934

actionLists are indicated through the count attribute.</h:p>

4935

</h:div>

4936

4937

<h:div class="example" href="action1.xml"/>

4938

<!--

4939

<h:div class="example" href="action2.xml"></h:div>

4940

-->

4941

</xsd:documentation>

4942

</xsd:annotation>

4943

4944

<xsd:complexType mixed="true">

4945

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

4946

<xsd:any processContents="lax"/>

4947

</xsd:sequence>

4948

4949

<xsd:attributeGroup ref="title"/>

4950

<xsd:attributeGroup ref="id"/>

4951

<xsd:attributeGroup ref="convention"/>

4952

<xsd:attributeGroup ref="dictRef"/>

4953

<xsd:attributeGroup ref="units"/>

4954

<xsd:attributeGroup ref="start"/>

4955

<xsd:attributeGroup ref="startCondition"/>

4956

<xsd:attributeGroup ref="duration"/>

4957

<xsd:attributeGroup ref="end"/>

4958

<xsd:attributeGroup ref="endCondition"/>

4959

<xsd:attributeGroup ref="type"/>

4960

<xsd:attributeGroup ref="actionOrder"/>

4961

<xsd:attributeGroup ref="count">

4962

<xsd:annotation>

4963

<xsd:documentation>

4964

<h:div class="specific">Number of times the action should be repeated.</h:div>

4965

</xsd:documentation>

4966

</xsd:annotation>

4967

</xsd:attributeGroup>

4968

<xsd:attributeGroup ref="ref"/>

4969

</xsd:complexType>

4970

4971

</xsd:element><xsd:element name="actionList" id="el.actionList">

4972

<xsd:annotation>

4973

<xsd:documentation>

4974

<h:div class="summary">A container for a group of actions.</h:div>

4975

<h:div class="description"><h:tt>ActionList</h:tt> contains a series of<h:tt>action</h:tt>s or

4976

nested<h:tt>actionList</h:tt>s.</h:div>

4977

<h:div class="example" href="actionList1.xml"/>

4978

</xsd:documentation>

4979

</xsd:annotation>

4980

<xsd:complexType mixed="true">

4981

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

4982

<xsd:any processContents="lax"/>

4983

</xsd:sequence>

4984

<xsd:attributeGroup ref="title"/>

4985

<xsd:attributeGroup ref="id"/>

4986

<xsd:attributeGroup ref="convention"/>

4987

<xsd:attributeGroup ref="dictRef"/>

4988

<xsd:attributeGroup ref="start"/>

4989

<xsd:attributeGroup ref="startCondition"/>

4990

<xsd:attributeGroup ref="duration"/>

4991

<xsd:attributeGroup ref="end"/>

4992

<xsd:attributeGroup ref="endCondition"/>

4993

<xsd:attributeGroup ref="units"/>

4994

<xsd:attributeGroup ref="count"/>

4995

<xsd:attributeGroup ref="type"/>

4996

<xsd:attributeGroup ref="actionOrder"/>

4997

</xsd:complexType>

4998

</xsd:element><xsd:element name="alternative" id="el.alternative">

4999

<xsd:annotation>

5000

<xsd:documentation>

5001

<h:div class="summary">An alternative name for an entry.</h:div>

5002

<h:div class="description">

5003

At present a child of _entry_ which represents an alternative string that refers to the concept. There is a partial controlled vocabulary in _alternativeType_ with values such as :

5004

<h:ul>

5005

<h:li>synonym</h:li>

5006

<h:li>acronym</h:li>

5007

<h:li>abbreviation</h:li>

5008

</h:ul>

5009

</h:div>

5010

5011

<h:div class="example" href="alternative1.xml"/>

5012

</xsd:documentation>

5013

</xsd:annotation>

5014

<xsd:complexType>

5015

<xsd:simpleContent>

5016

<xsd:extension base="xsd:string">

5017

<xsd:attributeGroup ref="id"/>

5018

<xsd:attributeGroup ref="convention"/>

5019

<xsd:attributeGroup ref="alternativeType"/>

5020

</xsd:extension>

5021

</xsd:simpleContent>

5022

</xsd:complexType>

5023

</xsd:element><xsd:element name="amount" id="el.amount">

5024

<xsd:annotation>

5025

<xsd:documentation>

5026

<h:div class="summary">The amount of a substance.</h:div>

5027

<h:div class="description">The <h:tt>units</h:tt> attribute is mandatory and

5028

can be customised to support mass, volumes, moles, percentages, or ratios

5029

(e.g. ppm).</h:div>

5030

<h:div class="example" href="amount1.xml"/>

5031

</xsd:documentation>

5032

</xsd:annotation>

5033

<xsd:complexType>

5034

<xsd:simpleContent>

5035

<xsd:extension base="xsd:double">

5036

<xsd:attributeGroup ref="title"/>

5037

<xsd:attributeGroup ref="id"/>

5038

<xsd:attributeGroup ref="convention"/>

5039

<xsd:attributeGroup ref="dictRef"/>

5040

<xsd:attributeGroup ref="units" id="att.amount.units"/>

5041

</xsd:extension>

5042

</xsd:simpleContent>

5043

</xsd:complexType>

5044

</xsd:element><xsd:element name="angle" id="el.angle">

5045

<xsd:annotation>

5046

<xsd:documentation>

5047

<h:div class="summary">An angle between three atoms.</h:div>

5048

<h:div class="description">

5049

<h:p>It can be used for:</h:p>

5050

<h:ul>

5051

<h:li>Recording experimentally determined bond angles (e.g. in

5052

a crystallographic paper).</h:li>

5053

<h:li>Providing the angle component for internal coordinates (e.g.

5054

z-matrix).</h:li>

5055

</h:ul></h:div>

5056

<h:div class="example" href="angle1.xml"/>

5057

</xsd:documentation>

5058

</xsd:annotation>

5059

<xsd:complexType>

5060

<xsd:simpleContent>

5061

<xsd:extension base="nonNegativeAngleType">

5062

<xsd:attributeGroup ref="title"/>

5063

<xsd:attributeGroup ref="id"/>

5064

<xsd:attributeGroup ref="convention"/>

5065

<xsd:attributeGroup ref="dictRef"/>

5066

<xsd:attributeGroup ref="atomRefs3"/>

5067

<xsd:attributeGroup ref="angleUnits"/>

5068

<xsd:attributeGroup ref="errorValue"/>

5069

<xsd:attributeGroup ref="errorBasis"/>

5070

<xsd:attributeGroup ref="min"/>

5071

<xsd:attributeGroup ref="max"/>

5072

<xsd:attributeGroup ref="ref"/>

5073

</xsd:extension>

5074

</xsd:simpleContent>

5075

</xsd:complexType>

5076

</xsd:element><xsd:element name="annotation" id="el.annotation">

5077

<xsd:annotation>

5078

<xsd:documentation>

5079

<h:div class="summary">A documentation container similar to annotation in XML Schema.</h:div>

5080

5081

<h:div class="description">A documentation container similar to <h:tt>annotation</h:tt> in XML Schema. At present this is experimental and designed to be used for dictionaries, units, etc. One approach is to convert these into XML Schemas when the <h:tt>documentation</h:tt> and <h:tt>appinfo</h:tt> children will emerge in their correct position in the derived schema.

5082

<h:p>It is possible that this may develop as a useful tool for annotating components

5083

of complex objects such as molecules. </h:p></h:div>

5084

5085

<h:div class="example" href="annotation1.xml"/>

5086

</xsd:documentation>

5087

</xsd:annotation>

5088

5089

<xsd:complexType mixed="true">

5090

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5091

<xsd:element ref="documentation"/>

5092

<xsd:element ref="appinfo"/>

5093

</xsd:choice>

5094

</xsd:complexType>

5095

5096

</xsd:element><xsd:element name="appinfo" id="el.appinfo">

5097

<xsd:annotation>

5098

<xsd:documentation>

5099

<h:div class="summary">A container similar to appinfo in XML Schema.</h:div>

5100

5101

<h:div class="description">A container for machine processable documentation for an entry. This is likely to be platform and/or language specific. It is possible that XSLT, RDF or XBL will emerge as generic languages. See _annotation_ and _documentation_ for further information.</h:div>

5102

5103

<h:div class="example" href="appinfo1.xml">

5104

<h:p>An example in XSLT where an element _foo_ calls a bespoke template</h:p>.</h:div>

5105

</xsd:documentation>

5106

</xsd:annotation>

5107

<xsd:complexType mixed="true">

5108

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

5109

<xsd:any processContents="lax"/>

5110

</xsd:sequence>

5111

<xsd:attributeGroup ref="role">

5112

<xsd:annotation>

5113

<xsd:documentation>

5114

<h:div class="specific">Allows a processor to inspect the role of the appinfo and process accordingly.</h:div>

5115

</xsd:documentation>

5116

</xsd:annotation>

5117

</xsd:attributeGroup>

5118

</xsd:complexType>

5119

5120

</xsd:element><xsd:element name="arg" id="el.arg">

5121

<xsd:annotation>

5122

<xsd:documentation>

5123

<h:div class="summary">An argument for a function.</h:div>

5124

<h:div class="description">Arguments can be typed and have explicit or free values.</h:div>

5125

<h:div class="example" href="potential1.xml"/>

5126

</xsd:documentation>

5127

</xsd:annotation>

5128

5129

<xsd:complexType>

5130

<xsd:sequence>

5131

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5132

<xsd:element ref="atom"/>

5133

<xsd:element ref="scalar"/>

5134

<xsd:element ref="array"/>

5135

<xsd:element ref="matrix"/>

5136

<xsd:element ref="expression"/>

5137

<xsd:any processContents="lax"/>

5138

</xsd:choice>

5139

</xsd:sequence>

5140

<xsd:attributeGroup ref="title"/>

5141

<xsd:attributeGroup ref="id"/>

5142

<xsd:attributeGroup ref="convention"/>

5143

<xsd:attributeGroup ref="dictRef"/>

5144

<xsd:attributeGroup ref="ref"/>

5145

<xsd:attributeGroup ref="name"/>

5146

<xsd:attributeGroup ref="dataType"/>

5147

</xsd:complexType>

5148

</xsd:element><xsd:element name="array" id="el.array">

5149

<xsd:annotation>

5150

<xsd:documentation>

5151

<h:div class="summary">A homogenous 1 dimensional array of similar object.</h:div>

5152

<h:div class="description">These can be encoded as strings (i.e. XSD-like datatypes) and are concatenated as string content. The size of the array should always be >= 1. The default delimiter is whitespace. The _normalize-space()_ function of XSLT could be used to normalize all whitespace to single spaces and this should not affect the value of the array elements. To extract the elements __java.lang.StringTokenizer__ could be used. If the elements themselves contain whitespace then a different delimiter must be used and is identified through the <h:tt>delimiter</h:tt> attribute. This method is mandatory if it is required to represent empty strings. If a delimiter is used it MUST start and end the array - leading and trailing whitespace is ignored. Thus <h:tt>size+1</h:tt> occurrences of the delimiter character are required. If non-normalized whitespace is to be encoded (e.g. newlines, tabs, etc) you are recommended to translate it character-wise to XML character entities.

5153

<h:p>Note that normal Schema validation tools cannot validate the elements

5154

of <h:b>array</h:b> (they are defined as <h:tt>string</h:tt>) However if the string is

5155

split, a temporary schema

5156

can be constructed from the type and used for validation. Also the type

5157

can be contained in a dictionary and software could decide to retrieve this

5158

and use it for validation.</h:p>

5159

<h:p>When the elements of the <h:tt>array</h:tt> are not simple scalars

5160

(e.g. <h:a href="el.scalar">scalar</h:a>s with a value and an error, the

5161

<h:tt>scalar</h:tt>s should be used as the elements. Although this is

5162

verbose, it is simple to understand. If there is a demand for

5163

more compact representations, it will be possible to define the

5164

syntax in a later version.</h:p></h:div>

5165

<h:div class="example" href="array1.xml">

5166

<h:p>the <h:tt>size</h:tt> attribute is not mandatory but provides a useful validity

5167

check): </h:p></h:div>

5168

<!--

5169

<h:div class="example" href="array2.xml">

5170

<h:p>Note that the second array-element is the empty string ''.</h:p></h:div>

5171

<h:div class="example" href="array3.xml"></h:div>

5172

-->

5173

</xsd:documentation>

5174

</xsd:annotation>

5175

<xsd:complexType>

5176

<xsd:simpleContent>

5177

<xsd:extension base="xsd:string">

5178

<xsd:attributeGroup ref="title"/>

5179

<xsd:attributeGroup ref="id"/>

5180

<xsd:attributeGroup ref="convention"/>

5181

<xsd:attributeGroup ref="dictRef"/>

5182

<xsd:attributeGroup ref="dataType"/>

5183

<xsd:attributeGroup ref="errorValueArray"/>

5184

<xsd:attributeGroup ref="errorBasis"/>

5185

<xsd:attributeGroup ref="minValueArray"/>

5186

<xsd:attributeGroup ref="maxValueArray"/>

5187

<xsd:attributeGroup ref="units"/>

5188

<xsd:attributeGroup ref="delimiter"/>

5189

<xsd:attributeGroup ref="size"/>

5190

<xsd:attributeGroup ref="ref"/>

5191

<xsd:attributeGroup ref="constantToSI">

5192

<xsd:annotation>

5193

<xsd:documentation>

5194

<h:div class="specific">Alternative to units</h:div>

5195

<h:div class="description">Must be used in conjunction with unitType</h:div>

5196

<h:div class="curation">2005-10-26: added</h:div>

5197

</xsd:documentation>

5198

</xsd:annotation>

5199

</xsd:attributeGroup>

5200

<xsd:attributeGroup ref="multiplierToSI">

5201

<xsd:annotation>

5202

<xsd:documentation>

5203

<h:div class="specific">Alternative to units</h:div>

5204

<h:div class="description">Must be used in conjunction with unitType</h:div>

5205

<h:div class="curation">2005-10-26: added</h:div>

5206

</xsd:documentation>

5207

</xsd:annotation>

5208

</xsd:attributeGroup>

5209

<xsd:attributeGroup ref="unitType">

5210

<xsd:annotation>

5211

<xsd:documentation>

5212

<h:div class="specific">Alternative to units</h:div>

5213

<h:div class="description">Must be used in conjunction with multiplierToSI and/or constantToSI</h:div>

5214

<h:div class="curation">2005-10-26: added</h:div>

5215

</xsd:documentation>

5216

</xsd:annotation>

5217

</xsd:attributeGroup>

5218

</xsd:extension>

5219

</xsd:simpleContent>

5220

</xsd:complexType>

5221

</xsd:element><xsd:element name="atom" id="el.atom">

5222

<xsd:annotation>

5223

<xsd:documentation>

5224

<h:div class="summary">An atom.</h:div>

5225

<h:div documentation="general">Usually within an _atomArray_.</h:div>

5226

<h:div class="example" href="atom1.xml"/>

5227

<h:div class="curation">2006-01-12: PMR. Added vector3 child to support

5228

accelerations, velocities, dipole, etc.</h:div>

5229

</xsd:documentation>

5230

<xsd:appinfo/>

5231

</xsd:annotation>

5232

<xsd:complexType>

5233

5234

<xsd:choice>

5235

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5236

<xsd:annotation>

5237

<xsd:documentation>

5238

<h:div class="general">

5239

<h:p>The main content model of the atom.</h:p>

5240

<h:ul>

5241

<h:li>

5242

<h:b>name</h:b> can be used for atom labels, etc. More than one name can be used if required.</h:li>

5243

<h:li>

5244

<h:b>scalar</h:b> contains any scalar properties of the atom (examples are chemical shift, B-value, etc.) linked through <h:tt>dictRef</h:tt> (CmlDictRefType).</h:li>

5245

<h:li>

5246

<h:b>array</h:b> contains any properties of the atom describable by a homogeneous array linked through <h:tt>dictRef</h:tt> (CmlDictRefType).</h:li>

5247

<h:li>

5248

<h:b>matrix</h:b> contains any properties of the atom describable by a homogeneous matrix linked through <h:tt>dictRef</h:tt> (CmlDictRefType). An example is the polarizability tensor</h:li>

5249

<h:li>

5250

<h:b>atomParity</h:b> (CmlAtomParityElement) the required way of defining atom-based chirality</h:li>

5251

<h:li>

5252

<h:b>electron</h:b> a away of associating electron(s) with the atom</h:li>

5253

</h:ul></h:div>

5254

</xsd:documentation>

5255

</xsd:annotation>

5256

<xsd:element ref="name"/>

5257

<xsd:element ref="label"/>

5258

<xsd:element ref="atomType"/>

5259

<xsd:element ref="array"/>

5260

<xsd:element ref="matrix"/>

5261

<xsd:element ref="scalar"/>

5262

<xsd:element ref="atomParity"/>

5263

<xsd:element ref="electron"/>

5264

<xsd:element ref="particle"/>

5265

<xsd:element ref="vector3"/>

5266

</xsd:choice>

5267

</xsd:choice>

5268

5269

<xsd:attributeGroup ref="id"/>

5270

<xsd:attributeGroup ref="count">

5271

<xsd:annotation>

5272

<xsd:documentation>

5273

<h:div class="specific">Most useful in _formula_ but possibly useful in _atomArray_ where coordinates and connectivity is not defined. No formal default, but assumed to be 1.</h:div>

5274

</xsd:documentation>

5275

</xsd:annotation>

5276

</xsd:attributeGroup>

5277

<xsd:attributeGroup ref="elementType"/>

5278

<xsd:attributeGroup ref="formalCharge"/>

5279

<xsd:attributeGroup ref="hydrogenCount"/>

5280

<xsd:attributeGroup ref="isotope"/>

5281

<xsd:attributeGroup ref="isotopeNumber"/>

5282

<xsd:attributeGroup ref="isotopeRef"/>

5283

<xsd:attributeGroup ref="isotopeListRef"/>

5284

<xsd:attributeGroup ref="occupancy"/>

5285

<xsd:attributeGroup ref="spinMultiplicity"/>

5286

<xsd:attributeGroup ref="x2"/>

5287

<xsd:attributeGroup ref="y2"/>

5288

<xsd:attributeGroup ref="x3"/>

5289

<xsd:attributeGroup ref="y3"/>

5290

<xsd:attributeGroup ref="z3"/>

5291

<xsd:attributeGroup ref="xFract"/>

5292

<xsd:attributeGroup ref="yFract"/>

5293

<xsd:attributeGroup ref="zFract"/>

5294

<xsd:attributeGroup ref="title"/>

5295

<xsd:attributeGroup ref="convention"/>

5296

<xsd:attributeGroup ref="dictRef"/>

5297

<xsd:attributeGroup ref="ref"/>

5298

<xsd:attributeGroup ref="role">

5299

<xsd:annotation>

5300

<xsd:documentation>

5301

<h:div class="specific">This can be used to describe the purpose of atoms whose _elementType_s are __dummy__ or __locant__. Vocabulary not controlled.</h:div>

5302

</xsd:documentation>

5303

</xsd:annotation>

5304

</xsd:attributeGroup>

5305

<xsd:attributeGroup ref="spaceGroupMultiplicity">

5306

<xsd:annotation>

5307

<xsd:documentation>

5308

<h:div class="curation">2005-11-27: Added PMR </h:div>

5309

</xsd:documentation>

5310

</xsd:annotation>

5311

</xsd:attributeGroup>

5312

<xsd:attributeGroup ref="pointGroupMultiplicity">

5313

<xsd:annotation>

5314

<xsd:documentation>

5315

<h:div class="curation">2005-11-27: Added PMR </h:div>

5316

</xsd:documentation>

5317

</xsd:annotation>

5318

</xsd:attributeGroup>

5319

</xsd:complexType>

5320

</xsd:element><xsd:element name="atomArray" id="el.atomArray">

5321

<xsd:annotation>

5322

<xsd:documentation>

5323

<h:div class="summary">A container for a list of atoms.</h:div>

5324

<h:div class="description">A child of _molecule_ and contains _atom_ information. There are two strategies:

5325

<h:ul>

5326

<h:li>Create individual _atom_ elements under _atomArray_ (in any order). This gives the greatest flexibility but is the most verbose.</h:li>

5327

<h:li>Create <h:tt>*Array</h:tt> attributes (e.g. of _elementTypeArrayType_ under _atomArray_. This requires all arrays to be of identical lengths with explicit values for all atoms in every array. This is NOT suitable for complexType atom children such as _atomParity_. It also cannot be checked as easily by schema- and schematron validation. The _atomIDArray_ attribute is mandatory. It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_

5328

</h:li>

5329

</h:ul>

5330

The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info.</h:div>

5331

<h:div class="example" href="atomArray1.xml">

5332

<h:p>Example - these are exactly equivalent representations</h:p></h:div>

5333

</xsd:documentation>

5334

</xsd:annotation>

5335

<xsd:complexType>

5336

<xsd:sequence>

5337

<xsd:element ref="atom" minOccurs="0" maxOccurs="unbounded"/>

5338

<xsd:element ref="array" minOccurs="0" maxOccurs="unbounded"/>

5339

</xsd:sequence>

5340

5341

<xsd:attributeGroup ref="title"/>

5342

<xsd:attributeGroup ref="id"/>

5343

<xsd:attributeGroup ref="convention"/>

5344

<xsd:attributeGroup ref="dictRef"/>

5345

<xsd:attributeGroup ref="ref"/>

5346

5347

<xsd:attributeGroup ref="elementTypeArray"/>

5348

<xsd:attributeGroup ref="countArray"/>

5349

<xsd:attributeGroup ref="formalChargeArray"/>

5350

<xsd:attributeGroup ref="hydrogenCountArray"/>

5351

<xsd:attributeGroup ref="occupancyArray"/>

5352

<xsd:attributeGroup ref="x2Array"/>

5353

<xsd:attributeGroup ref="y2Array"/>

5354

<xsd:attributeGroup ref="x3Array"/>

5355

<xsd:attributeGroup ref="y3Array"/>

5356

<xsd:attributeGroup ref="z3Array"/>

5357

<xsd:attributeGroup ref="xFractArray"/>

5358

<xsd:attributeGroup ref="yFractArray"/>

5359

<xsd:attributeGroup ref="zFractArray"/>

5360

<xsd:attributeGroup ref="atomIDArray"/>

5361

5362

</xsd:complexType>

5363

</xsd:element><xsd:element name="atomicBasisFunction" id="el.atomicBasisFunction">

5364

<xsd:annotation>

5365

<xsd:documentation>

5366

<h:div class="summary">An atomicBasisFunction.</h:div>

5367

<h:div class="description">

5368

<h:p>An atomic atomicBasisFunction which can be linked to atoms,

5369

eigenvalues/vectors etc. Normally contained within _basisSet_

5370

</h:p>

5371

<h:p>Normally these are atom-centered functions, but they can also serve as

5372

"ghost" functions which are centered on points. These can be dummy atoms so

5373

that the atomRef mechanism can still be used.</h:p>

5374

<h:p>This information is required to interpret the eignevector components

5375

and map them onto the atom list. However this mapping is normally implicit

5376

in the program and so it may be necessary to generate <h:tt>basisSet</h:tt>

5377

information for some programs before XML technology can be automatically used

5378

to link the components of the CCML document.</h:p></h:div>

5379

<h:div class="example" href="atomicBasisFunction1.xml"/>

5380

</xsd:documentation>

5381

</xsd:annotation>

5382

5383

<xsd:complexType>

5384

<xsd:sequence>

5385

<xsd:choice minOccurs="0" maxOccurs="unbounded"/>

5386

<xsd:choice minOccurs="0" maxOccurs="1">

5387

<xsd:element ref="gradient"/>

5388

</xsd:choice>

5389

</xsd:sequence>

5390

<xsd:attributeGroup ref="atomRef">

5391

<xsd:annotation>

5392

<xsd:documentation>

5393

<h:div class="specific">The atom owning this atomicBasisFunction.

5394

This reference is required to tie the reported eigenvector components to

5395

the list of atoms.</h:div>

5396

</xsd:documentation>

5397

</xsd:annotation>

5398

</xsd:attributeGroup>

5399

<xsd:attributeGroup ref="title"/>

5400

<xsd:attributeGroup ref="id"/>

5401

<xsd:attributeGroup ref="convention"/>

5402

<xsd:attributeGroup ref="dictRef"/>

5403

<xsd:attributeGroup ref="n"/>

5404

<xsd:attributeGroup ref="l"/>

5405

<xsd:attributeGroup ref="m">

5406

<xsd:annotation>

5407

<xsd:documentation>

5408

<h:div class="specific">This is provided for completeness but we do not see

5409

it being widely used and the symbolic representation (lm) is more valuable.</h:div>

5410

</xsd:documentation>

5411

</xsd:annotation>

5412

</xsd:attributeGroup>

5413

<xsd:attributeGroup ref="symbol">

5414

<xsd:annotation>

5415

<xsd:documentation>

5416

<h:div class="specific">This is a local annotation of the ABF and unlikely to

5417

be enumeratable. Thus a split s-orbital could have 3 ABFs with "s", "s'", "s''"

5418

but they would all have lm="s".</h:div>

5419

</xsd:documentation>

5420

</xsd:annotation>

5421

</xsd:attributeGroup>

5422

<xsd:attributeGroup ref="lm">

5423

<xsd:annotation>

5424

<xsd:documentation>

5425

<h:div class="specific">This is a "standard" representation of the ABF, but

5426

not enumerated until we decide whether it can be formalised. Examples are "px",

5427

"dxy", etc. Note that d-orbitals and higher may be represented with redundant

5428

ABFs, e.g. 6 d-orbitals. The more standard the representation, the more useful

5429

this will be for searching.</h:div>

5430

</xsd:documentation>

5431

</xsd:annotation>

5432

</xsd:attributeGroup>

5433

</xsd:complexType>

5434

</xsd:element><xsd:element name="atomParity" id="el.atomParity">

5435

<xsd:annotation>

5436

<xsd:documentation>

5437

<h:div class="summary">The stereochemistry round an atom centre.</h:div>

5438

<h:div class="description">It follows the convention of the MIF format,

5439

and uses 4 distinct atoms to define the chirality. These can be any

5440

atoms (though they are normally bonded to the current atom). There is

5441

no default order and the order is defined by the atoms in the atomRefs4

5442

attribute. If there are only 3 ligands, the current atom should be

5443

included in the 4 atomRefs.

5444

<h:p>The value of the parity is a signed number. (It can only be

5445

zero if two or more atoms are coincident or the configuration is

5446

planar). The sign is the sign of the chiral volume created by the

5447

four atoms (a1, a2, a3, a4):</h:p>

5448

<h:pre>

5449

| 1 1 1 1 |

5450

| x1 x2 x3 x4 |

5451

| y1 y2 y3 y4 |

5452

| z1 z2 z3 z4 |

5453

</h:pre>

5454

<h:p>Note that <h:tt>atomParity</h:tt> cannot be used with the

5455

*Array syntax for atoms.</h:p></h:div>

5456

<h:div class="example" href="atomParity1.xml"/>

5457

</xsd:documentation>

5458

</xsd:annotation>

5459

<xsd:complexType>

5460

<xsd:simpleContent>

5461

<xsd:extension base="xsd:double">

5462

<xsd:attributeGroup ref="title"/>

5463

<xsd:attributeGroup ref="id"/>

5464

<xsd:attributeGroup ref="convention"/>

5465

<xsd:attributeGroup ref="dictRef"/>

5466

<xsd:attributeGroup ref="atomRefs4"/>

5467

</xsd:extension>

5468

</xsd:simpleContent>

5469

</xsd:complexType>

5470

</xsd:element><xsd:element name="atomSet" id="el.atomSet">

5471

<xsd:annotation>

5472

<xsd:documentation>

5473

<h:div class="summary">A set of references to atoms.</h:div>

5474

<h:div class="description">An atomSet consists of a number of unique references to atoms throught their ids. atomSets need not be related to molecules (which are generally created by aggregation of explicit atoms). Two or more atomSets may reference the same atom, and atomSets may be empty.

5475

<h:p>atomSets have many potential uses such as:

5476

<h:ul>

5477

<h:li>identifying functional groups</h:li>

5478

<h:li>results of substructure matching</h:li>

5479

<h:li>identifying atoms with particular roles in a calculation</h:li>

5480

</h:ul>

5481

</h:p>

5482

<h:p>The atomSet may be referenced from elsewhere in the document and you are encouraged to use locally unique id attributes on atomSets.

5483

</h:p></h:div>

5484

<h:div class="example" href="atomSet1.xml"/>

5485

</xsd:documentation>

5486

</xsd:annotation>

5487

<xsd:complexType>

5488

<xsd:simpleContent>

5489

<xsd:extension base="atomRefArrayType">

5490

<xsd:attributeGroup ref="title"/>

5491

<xsd:attributeGroup ref="id"/>

5492

<xsd:attributeGroup ref="convention"/>

5493

<xsd:attributeGroup ref="dictRef"/>

5494

<xsd:attributeGroup ref="size"/>

5495

</xsd:extension>

5496

</xsd:simpleContent>

5497

</xsd:complexType>

5498

</xsd:element><xsd:element name="atomType" id="el.atomType">

5499

<xsd:annotation>

5500

<xsd:documentation>

5501

<h:div class="summary">An atomType.</h:div>

5502

<h:div class="description">

5503

<h:p>atomTypes are used in a wide variety of ways in computational chemistry.

5504

They are normally labels added to existing atoms (or dummy atoms)

5505

in the molecule and have a number of defined properties.

5506

These properties are usually in addition to those deducible from the

5507

elementType of the atom. AtomTypes usually depend on the chemical or

5508

geometrical environment of the atom and are frequently assigned by

5509

algorithms with chemical perception. However they are often frequently

5510

set or "tweaked" by humans initiating a program run.</h:p>

5511

<h:p>AtomTypes on an atom have no formal relation to its <h:tt>elementType</h:tt>,

5512

which only describe the number of protons in the nucleus. It is not unknown

5513

(though potentially misleading) to use an "incompatible" atomType to

5514

alter the computational properties of an atom (e.g. pretend this K+

5515

is a Ca++ to increase its effective charge). <h:tt>atomTypes</h:tt>

5516

will also be required to describe pseudoAtoms such as "halogen"

5517

(generic) or "methyl group" (unified atom). Atoms in computations

5518

can therefore have an <h:tt>atomType</h:tt> child with a "ref"

5519

attribute.</h:p>

5520

<h:p>An atomType contains numeric or other quantities associated with

5521

it (charges, masses, use in force-fields, etc.) and also description

5522

of any perception algorithms (chemical and/or geometrical) which could

5523

be used to compute or constrain it. This is still experimental.</h:p>

5524

<h:p>atomTypes are referred to by their mandatory <h:tt>name</h:tt>

5525

attribute. An atom refers to one or more atomTypes through

5526

atomType/@ref children</h:p></h:div>

5527

<h:div class="example" href="atomType1.xml"/>

5528

<h:div class="note">examples not yet teste.</h:div>

5529

</xsd:documentation>

5530

</xsd:annotation>

5531

5532

<xsd:complexType>

5533

<xsd:sequence>

5534

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5535

<xsd:element ref="molecule"/>

5536

<xsd:element ref="atom"/>

5537

<xsd:element ref="label"/>

5538

</xsd:choice>

5539

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5540

<xsd:element ref="scalar"/>

5541

<xsd:element ref="array"/>

5542

<xsd:element ref="matrix"/>

5543

<xsd:element ref="property"/>

5544

</xsd:choice>

5545

</xsd:sequence>

5546

<xsd:attributeGroup ref="name">

5547

<xsd:annotation>

5548

<xsd:documentation>

5549

<h:div class="specific">The name will usually be namespaced as 'gulp:si', 'tripos:c.3', etc. It must occur except for atomType/@re.</h:div>

5550

</xsd:documentation>

5551

</xsd:annotation>

5552

</xsd:attributeGroup>

5553

<xsd:attributeGroup ref="ref"/>

5554

5555

<xsd:attributeGroup ref="atomRef"/>

5556

<xsd:attributeGroup ref="title"/>

5557

<xsd:attributeGroup ref="id"/>

5558

<xsd:attributeGroup ref="convention"/>

5559

<xsd:attributeGroup ref="dictRef"/>

5560

</xsd:complexType>

5561

</xsd:element><xsd:element name="atomTypeList" id="el.atomTypeList">

5562

<xsd:annotation>

5563

<xsd:documentation>

5564

<h:div class="summary">A container for one or more atomTypes.</h:div>

5565

<h:div class="description">It can contain several atomTypes.</h:div>

5566

<h:div class="example" href="atomTypeList1.xml"/>

5567

</xsd:documentation>

5568

</xsd:annotation>

5569

5570

<xsd:complexType>

5571

<xsd:sequence>

5572

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

5573

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

5574

<xsd:element ref="atomType" minOccurs="0" maxOccurs="unbounded"/>

5575

</xsd:sequence>

5576

<xsd:attributeGroup ref="dictRef"/>

5577

<xsd:attributeGroup ref="convention"/>

5578

<xsd:attributeGroup ref="title"/>

5579

<xsd:attributeGroup ref="id"/>

5580

<xsd:attributeGroup ref="ref"/>

5581

</xsd:complexType>

5582

</xsd:element><xsd:element name="band" id="el.band">

5583

<xsd:annotation>

5584

<xsd:documentation>

5585

<h:div class="summary">A band or Brillouin zone.</h:div>

5586

<h:div class="description">Not yet finalised.</h:div>

5587

<h:div class="example" href="band1.xml"/>

5588

<h:div class="curation">2006-01-21: PMR. added kpointRef and deprecated kpointList.</h:div>

5589

</xsd:documentation>

5590

</xsd:annotation>

5591

5592

<xsd:complexType>

5593

<xsd:sequence>

5594

<xsd:element ref="array" minOccurs="1" maxOccurs="1">

5595

<xsd:annotation>

5596

<xsd:documentation>

5597

<h:div class="summary">Band energies associated with this kpoint.</h:div>

5598

<h:div class="description">The energy units must be given.</h:div>

5599

</xsd:documentation>

5600

</xsd:annotation>

5601

</xsd:element>

5602

</xsd:sequence>

5603

<xsd:attributeGroup ref="kpoint">

5604

<xsd:annotation>

5605

<xsd:documentation>

5606

<h:div class="deprecated">kpoints should be described in

5607

kpointList and referenced.</h:div>

5608

</xsd:documentation>

5609

</xsd:annotation>

5610

</xsd:attributeGroup>

5611

<xsd:attributeGroup ref="kpointRef"/>

5612

<xsd:attributeGroup ref="weight"/>

5613

<xsd:attributeGroup ref="label"/>

5614

<xsd:attributeGroup ref="title"/>

5615

<xsd:attributeGroup ref="id"/>

5616

<xsd:attributeGroup ref="convention"/>

5617

<xsd:attributeGroup ref="dictRef"/>

5618

</xsd:complexType>

5619

</xsd:element><xsd:element name="bandList" id="el.bandList">

5620

<xsd:annotation>

5621

<xsd:documentation>

5622

<h:div class="summary">A container for bands.</h:div>

5623

<h:div class="description">Experimental.</h:div>

5624

<h:div class="example" href="band1.xml"/>

5625

</xsd:documentation>

5626

</xsd:annotation>

5627

5628

<xsd:complexType>

5629

<xsd:sequence>

5630

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5631

<xsd:element ref="band"/>

5632

</xsd:choice>

5633

</xsd:sequence>

5634

<xsd:attributeGroup ref="title"/>

5635

<xsd:attributeGroup ref="id"/>

5636

<xsd:attributeGroup ref="convention"/>

5637

<xsd:attributeGroup ref="dictRef"/>

5638

</xsd:complexType>

5639

</xsd:element><xsd:element name="basisSet" id="el.basisSet">

5640

<xsd:annotation>

5641

<xsd:documentation>

5642

<h:div class="summary">A container for one or more atomicBasisFunctions.</h:div>

5643

<h:div class="description">This can contain several orbitals.</h:div>

5644

<h:div class="example" href="basisSet1.xml"/>

5645

</xsd:documentation>

5646

</xsd:annotation>

5647

5648

<xsd:complexType>

5649

<xsd:sequence>

5650

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

5651

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

5652

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5653

<xsd:element ref="atomicBasisFunction"/>

5654

</xsd:choice>

5655

</xsd:sequence>

5656

<xsd:attributeGroup ref="dictRef"/>

5657

<xsd:attributeGroup ref="convention"/>

5658

<xsd:attributeGroup ref="title"/>

5659

<xsd:attributeGroup ref="id"/>

5660

<xsd:attributeGroup ref="ref"/>

5661

<xsd:attributeGroup ref="role"/>

5662

</xsd:complexType>

5663

</xsd:element><xsd:element name="bond" id="el.bond">

5664

<xsd:annotation>

5665

<xsd:documentation>

5666

<h:div class="summary">A bond between atoms, or between atoms and bonds.</h:div>

5667

<h:div class="description">_bond_ is a child of _bondArray_ and contains bond information. Bond must refer to at least two atoms (normally using _atomRefs2_) but may also refer to more for multicentre bonds. Bond is often EMPTY but may contain _electron_, _length_ or _bondStereo_ elements.</h:div>

5668

<h:div class="example" href="bond1.xml"/>

5669

<!--

5670

<h:div class="example" href="bond2.xml"></h:div>

5671

-->

5672

</xsd:documentation>

5673

<xsd:documentation>

5674

<h:div class="validation" href="cmlCore.val.bond.xml"/>

5675

</xsd:documentation>

5676

<xsd:appinfo>

5677

<comment xmlns="">Validate Bonds</comment>

5678

5679

5680

5681

5682

<comment>Are atoms distinct?</comment>

5683

5684

<call-template name="error">

5685

<with-param name="error">BOND (<value-of select="@id"/>): ATOMS not distinct: <value-of select="$at1"/>

5686

</with-param>

5687

</call-template>

5688

</if>

5689

<comment>Do both atoms exist in current molecule context?</comment>

5690

5691

<call-template name="error">

5692

<with-param name="error">BOND (<value-of select="@id"/>): ATOMREF not found: <value-of select="$at1"/>

5693

</with-param>

5694

</call-template>

5695

</if>

5696

5697

<call-template name="error">

5698

<with-param name="error">BOND (<value-of select="@id"/>): ATOMREF not found: <value-of select="$at2"/>

5699

</with-param>

5700

</call-template>

5701

</if>

5702

</template>

5703

</xsd:appinfo>

5704

</xsd:annotation>

5705

<xsd:complexType id="bond.content.id">

5706

<xsd:choice>

5707

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5708

<xsd:element ref="bondType"/>

5709

<xsd:element ref="electron">

5710

<xsd:annotation>

5711

<xsd:documentation>

5712

<h:div class="summary">One or more electrons associated with the bond.</h:div>

5713

<h:div class="description">The _bondRef_ on the _electron_ should point to the id on the bond. We may relax this later and allow reference by context.</h:div>

5714

</xsd:documentation>

5715

</xsd:annotation>

5716

</xsd:element>

5717

<xsd:element ref="bondStereo">

5718

<xsd:annotation>

5719

<xsd:documentation>

5720

<h:div class="summary">The stereo convention for the bond.</h:div>

5721

<h:div class="general">only one convention allowed.</h:div>

5722

</xsd:documentation>

5723

</xsd:annotation>

5724

</xsd:element>

5725

</xsd:choice>

5726

</xsd:choice>

5727

5728

<xsd:attributeGroup ref="title"/>

5729

<xsd:attributeGroup ref="id"/>

5730

<xsd:attributeGroup ref="convention"/>

5731

<xsd:attributeGroup ref="dictRef"/>

5732

<xsd:attributeGroup ref="ref"/>

5733

<xsd:attributeGroup ref="atomRefs2"/>

5734

<xsd:attributeGroup ref="atomRefs">

5735

<xsd:annotation>

5736

<xsd:documentation>

5737

<h:div class="specific">This is designed for multicentre bonds (as in delocalised systems or electron-deficient centres. The semantics are experimental at this stage. As an example, a B-H-B bond might be described as

5738

5739

</xsd:documentation>

5740

</xsd:annotation>

5741

</xsd:attributeGroup>

5742

<xsd:attributeGroup ref="bondRefs">

5743

<xsd:annotation>

5744

<xsd:documentation>

5745

<h:div class="specific">This is designed for pi-bonds and other systems where formal valence bonds are not drawn to atoms. The semantics are experimental at this stage. As an example, a Pt-|| bond (as the Pt-ethene bond in Zeise's salt) might be described as <bond atomRefs="pt1" bondRefs="b32"/.</h:div>

5746

</xsd:documentation>

5747

</xsd:annotation>

5748

</xsd:attributeGroup>

5749

<xsd:attributeGroup ref="order"/>

5750

5751

</xsd:complexType>

5752

</xsd:element><xsd:element name="bondArray" id="el.bondArray">

5753

<xsd:annotation>

5754

<xsd:documentation>

5755

<h:div class="summary">A container for a number of bonds.</h:div>

5756

<h:div class="description">_bondArray_ is a child of _molecule_ and contains _bond_ information. There are two strategies:

5757

<h:ul>

5758

<h:li>Create individual <h:tt>bond</h:tt> elements under <h:tt>bondArray</h:tt>

5759

(in any order). This gives the greatest flexibility but is the most verbose.</h:li>

5760

<h:li>Create <h:tt>*Array</h:tt> attributes (e.g. of <h:tt>orderArrayType</h:tt> under

5761

<h:tt>bondArray</h:tt>. This requires all arrays to be of identical lengths with explicit values for all bonds in every array. This is NOT suitable for complexType bond children such as _bondStereo_ nor can IDs be added to bonds.. It also cannot be checked as easily by schema- and schematron validation. The _atomRef1Array_ and _atomRef2Array_ attributes are then mandatory. It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_

5762

</h:li>

5763

</h:ul>

5764

<h:p>The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info.</h:p></h:div>

5765

<h:div class="example" href="bondArray1.xml">

5766

<h:p>Example - these are exactly equivalent representations</h:p></h:div>

5767

</xsd:documentation>

5768

</xsd:annotation>

5769

<xsd:complexType>

5770

<xsd:choice>

5771

<xsd:element ref="bond" maxOccurs="unbounded"/>

5772

<xsd:element ref="array" minOccurs="0" maxOccurs="unbounded"/>

5773

</xsd:choice>

5774

5775

<xsd:attributeGroup ref="title"/>

5776

<xsd:attributeGroup ref="id"/>

5777

<xsd:attributeGroup ref="convention"/>

5778

<xsd:attributeGroup ref="dictRef"/>

5779

<xsd:attributeGroup ref="bondIDArray"/>

5780

<xsd:attributeGroup ref="atomRef1Array"/>

5781

<xsd:attributeGroup ref="atomRef2Array"/>

5782

<xsd:attributeGroup ref="orderArray"/>

5783

</xsd:complexType>

5784

</xsd:element><xsd:element name="bondSet" id="el.bondSet">

5785

<xsd:annotation>

5786

<xsd:documentation>

5787

<h:div class="summary">A set of references to bonds.</h:div>

5788

<h:div class="description">An bondSet consists of a number of unique references to bonds throught their ids. bondSets need not be related to molecules (which are generally created by aggregation of explicit bonds). Two or more bondSets may reference the same bond, and bondSets may be empty.

5789

<h:p>bondSets have many potential uses such as:

5790

<h:ul>

5791

<h:li>identifying functional groups</h:li>

5792

<h:li>results of substructure matching</h:li>

5793

<h:li>identifying bonds with particular roles in a calculation</h:li>

5794

</h:ul>

5795

</h:p>

5796

<h:p>The bondSet may be referenced from elsewhere in the document and you are encouraged to use locally unique id attributes on bondSets.

5797

</h:p></h:div>

5798

<h:div class="example" href="bondSet1.xml"/>

5799

</xsd:documentation>

5800

</xsd:annotation>

5801

<xsd:complexType>

5802

<xsd:simpleContent>

5803

<xsd:extension base="bondRefArrayType">

5804

<xsd:attributeGroup ref="title"/>

5805

<xsd:attributeGroup ref="id"/>

5806

<xsd:attributeGroup ref="convention"/>

5807

<xsd:attributeGroup ref="dictRef"/>

5808

<xsd:attributeGroup ref="size"/>

5809

</xsd:extension>

5810

</xsd:simpleContent>

5811

</xsd:complexType>

5812

</xsd:element><xsd:element name="bondStereo" id="el.bondStereo">

5813

<xsd:annotation>

5814

<xsd:documentation>

5815

<h:div class="summary">A container supporting cis trans wedge hatch and other stereochemistry.</h:div>

5816

<h:div class="description">

5817

<h:p>An explict list of atomRefs must be given, or it must be a child of <h:tt>bond</h:tt>. There are no implicit conventions such as E/Z. This will be extended to other types of stereochemistry.</h:p>

5818

<h:p>At present the following are supported:</h:p>

5819

<h:ul>

5820

<h:li>No atomRefs attribute. <h:b>Deprecated, but probably unavoidable</h:b>.

5821

This must be a child of <h:tt>bond</h:tt> where it picks up the two atomRefs

5822

in the <h:tt>atomRefs2</h:tt> attribute. Possible values are C/T (which only makes sense

5823

if there is exactly one ligand at each end of the bond) and W/H. The latter

5824

should be raplaced by <h:tt>atomParity</h:tt> wherever possible. Note that W/H makes

5825

no sense without 2D atom coordinates.</h:li>

5826

<h:li>

5827

<h:b>atomRefs4 attribute</h:b>. The 4 atoms represent a cis or trans configuration.

5828

This may or may not be a child of <h:tt>bond</h:tt>; if so the second and third atomRefs

5829

should be identical with the two atomRefs in the bond. This structure can be used

5830

to guide processors in processing stereochemistry and is recommended, since there is

5831

general agreement on the semantics. The semantics of <h:tt>bondStereo</h:tt> not related to

5832

bonds is less clear (e.g. cumulenes, substituted ring nuclei) etc.It is

5833

currently an error to have more than one <h:tt>bondStereo</h:tt> referring to the same ordered

5834

4-atom list</h:li>

5835

<h:li>

5836

<h:b>atomRefs attribute</h:b>. There are other stereochemical conventions such as cis/trans

5837

for metal complexes which require a variable number of reference atoms. This allows

5838

users to create their own - at present we do not see CML creating exhaustive tables.

5839

For example cis/trans square-planar complexes might require 4 (or 5) atoms for their

5840

definition, octahedral 6 or 7, etc. In principle this is very powerful and could

5841

supplement or replace the use of <h:i>cis-</h:i>, <h:i>mer-</h:i>, etc.</h:li>

5842

</h:ul>

5843

<h:p>the <h:tt>atomRefs</h:tt> and <h:tt>atomRefs4</h:tt> attributes cannot be used

5844

simultaneously.</h:p></h:div>

5845

<h:div class="example" href="bondStereo1.xml"/>

5846

</xsd:documentation>

5847

</xsd:annotation>

5848

<xsd:complexType>

5849

<xsd:simpleContent>

5850

<xsd:extension base="stereoType">

5851

<xsd:attributeGroup ref="atomRefs4"/>

5852

<xsd:attributeGroup ref="atomRefArray"/>

5853

<xsd:attributeGroup ref="title"/>

5854

<xsd:attributeGroup ref="id"/>

5855

<xsd:attributeGroup ref="convention"/>

5856

<xsd:attributeGroup ref="dictRef"/>

5857

<xsd:attributeGroup ref="conventionValue"/>

5858

</xsd:extension>

5859

</xsd:simpleContent>

5860

</xsd:complexType>

5861

</xsd:element><xsd:element name="bondType" id="el.bondType">

5862

<xsd:annotation>

5863

<xsd:documentation>

5864

<h:div class="summary">The type of a bond.</h:div>

5865

<h:div class="description">Bond types are used to describe the behaviour

5866

of bonds in forcefields, functional groups, reactions and many other

5867

domains. They are not as well formalised as atomTypes and we provide

5868

less semantic support. BondTypes are referred to by their mandatory

5869

_name_ attribute.</h:div>

5870

<h:div class="example" href="bondType1.xml"/>

5871

</xsd:documentation>

5872

</xsd:annotation>

5873

5874

<xsd:complexType>

5875

<xsd:sequence>

5876

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5877

<xsd:element ref="molecule"/>

5878

<xsd:element ref="bond"/>

5879

<xsd:element ref="label"/>

5880

</xsd:choice>

5881

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5882

<xsd:element ref="scalar"/>

5883

<xsd:element ref="array"/>

5884

<xsd:element ref="matrix"/>

5885

<xsd:element ref="property"/>

5886

</xsd:choice>

5887

</xsd:sequence>

5888

<xsd:attributeGroup ref="name">

5889

<xsd:annotation>

5890

<xsd:documentation>

5891

<h:div class="specific">The bondType name. The name will usually be namespaced as 'gulp:si', 'tripos:c.3', etc. It must occur except when the ref attribute is give.</h:div>

5892

</xsd:documentation>

5893

</xsd:annotation>

5894

</xsd:attributeGroup>

5895

<xsd:attributeGroup ref="ref"/>

5896

<xsd:attributeGroup ref="title"/>

5897

<xsd:attributeGroup ref="id"/>

5898

<xsd:attributeGroup ref="convention"/>

5899

<xsd:attributeGroup ref="dictRef"/>

5900

</xsd:complexType>

5901

</xsd:element><xsd:element name="bondTypeList" id="el.bondTypeList">

5902

<xsd:annotation>

5903

<xsd:documentation>

5904

<h:div class="summary">A container for one or more bondTypes.</h:div>

5905

<h:div class="description">_bondTypeList_ can contain several bondTypes.</h:div>

5906

<h:div class="example" href="bondTypeList1.xml"/>

5907

</xsd:documentation>

5908

</xsd:annotation>

5909

5910

<xsd:complexType>

5911

<xsd:sequence>

5912

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

5913

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

5914

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5915

<xsd:element ref="bondType"/>

5916

</xsd:choice>

5917

</xsd:sequence>

5918

<xsd:attributeGroup ref="dictRef"/>

5919

<xsd:attributeGroup ref="convention"/>

5920

<xsd:attributeGroup ref="title"/>

5921

<xsd:attributeGroup ref="id"/>

5922

<xsd:attributeGroup ref="ref"/>

5923

</xsd:complexType>

5924

</xsd:element><xsd:element name="cml" id="el.cml">

5925

<xsd:annotation>

5926

<xsd:documentation>

5927

<h:div class="summary">A general container for CML elements.</h:div>

5928

<h:div class="description">Often the root of the CML (sub)document.

5929

Has no explicit function but can serve to hold the dictionary and

5930

namespace information, and is a useful tag to alert CML processors

5931

and search/XMLQuery tools that there is chemistry in the document.

5932

Can contain any content, but usually a list of molecules and other

5933

CML components. The fileId attribute can be used to preserve the origin

5934

of the information, though metadat should also be used. Can be nested.</h:div>

5935

<h:div class="example" href="cml1.xml"/>

5936

</xsd:documentation>

5937

</xsd:annotation>

5938

<xsd:complexType>

5939

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

5940

<xsd:annotation>

5941

<xsd:documentation>

5942

<h:div class="description">No specific restrictions..</h:div>

5943

</xsd:documentation>

5944

</xsd:annotation>

5945

<xsd:any processContents="lax"/>

5946

</xsd:sequence>

5947

<xsd:attributeGroup ref="title"/>

5948

<xsd:attributeGroup ref="id"/>

5949

<xsd:attributeGroup ref="convention"/>

5950

<xsd:attributeGroup ref="dictRef"/>

5951

<xsd:attributeGroup ref="fileId"/>

5952

</xsd:complexType>

5953

</xsd:element><xsd:element name="complexObject" id="el.complexObject">

5954

<xsd:annotation>

5955

<xsd:documentation>

5956

<h:div class="summary">An element to hold any combination of heterogeneous element children</h:div>

5957

<h:div class="description">complexObject can be used as it stands but will often be extended by

5958

schema definitions in dictionary entries.</h:div>

5959

<h:div class="example" href="complexObject1.xml"/>

5960

</xsd:documentation>

5961

</xsd:annotation>

5962

5963

<xsd:complexType>

5964

<xsd:sequence>

5965

<xsd:any processContents="lax" minOccurs="0" maxOccurs="unbounded"/>

5966

</xsd:sequence>

5967

<xsd:attributeGroup ref="title"/>

5968

<xsd:attributeGroup ref="id"/>

5969

<xsd:attributeGroup ref="convention"/>

5970

<xsd:attributeGroup ref="dictRef"/>

5971

</xsd:complexType>

5972

5973

</xsd:element><xsd:element name="conditionList" id="el.conditionList">

5974

<xsd:annotation>

5975

<xsd:documentation>

5976

<h:div class="summary">A container for one or more experimental conditions.</h:div>

5977

<h:div class="description">This can contain several conditions. These include

5978

(but are not limited to) intensive physical properties (temperature, pressure, etc.),

5979

apparatus (test-tube, rotary evaporator, etc.).

5980

Actions can be represented elsewhere by actionList and solvents or other

5981

substances by substanceList.</h:div>

5982

<h:div class="example" href="conditionList1.xml"/>

5983

</xsd:documentation>

5984

</xsd:annotation>

5985

5986

<xsd:complexType>

5987

<xsd:sequence>

5988

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

5989

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

5990

<xsd:choice minOccurs="0" maxOccurs="unbounded">

5991

<xsd:element ref="scalar"/>

5992

<xsd:element ref="list"/>

5993

</xsd:choice>

5994

5995

</xsd:sequence>

5996

<xsd:attributeGroup ref="dictRef"/>

5997

<xsd:attributeGroup ref="convention"/>

5998

<xsd:attributeGroup ref="title"/>

5999

<xsd:attributeGroup ref="id"/>

6000

<xsd:attributeGroup ref="ref"/>

6001

<xsd:attributeGroup ref="role"/>

6002

</xsd:complexType>

6003

</xsd:element><xsd:element name="crystal" id="el.crystal">

6004

<xsd:annotation>

6005

<xsd:documentation>

6006

<h:div class="summary">A crystallographic cell.</h:div>

6007

<h:div class="description">Required if fractional coordinates are provided for a molecule. There are precisely SIX child <h:tt>scalar</h:tt>s to represent the cell lengths and angles in that order. There are no default values; the spacegroup is also included.</h:div>

6008

<h:div class="example" href="crystal1.xml"/>

6009

</xsd:documentation>

6010

</xsd:annotation>

6011

<xsd:complexType>

6012

<xsd:sequence>

6013

<xsd:annotation>

6014

<xsd:documentation>

6015

<h:div class="summary">All 6 cell parameters must be given, even where angles are fixed by symmetry. The order is fixed as a,b,c,alpha,gamma,beta and software can neglect any title or dictRef attributes. Error estimates can be given if required. Any units can be used, but the defaults are Angstrom (10^-10 m) and degrees.</h:div>

6016

</xsd:documentation>

6017

</xsd:annotation>

6018

<xsd:element ref="scalar" minOccurs="6" maxOccurs="6"/>

6019

<xsd:element ref="symmetry" minOccurs="0"/>

6020

</xsd:sequence>

6021

6022

<xsd:attributeGroup ref="z"/>

6023

<xsd:attributeGroup ref="title"/>

6024

<xsd:attributeGroup ref="id"/>

6025

<xsd:attributeGroup ref="convention"/>

6026

<xsd:attributeGroup ref="dictRef"/>

6027

</xsd:complexType>

6028

</xsd:element><xsd:element name="definition" id="el.definition">

6029

<xsd:annotation>

6030

<xsd:documentation>

6031

<h:div class="summary">The definition for an entry.</h:div>

6032

<h:div class="description">The definition should be a short nounal phrase defining the subject of the entry. Definitions should not include commentary, implementations, equations or formulae (unless the subject is one of these) or examples.

6033

<h:p>The definition can be in any markup language, but normally XHTML will be used,

6034

perhaps with links to other XML namespaces such as CML for chemistry.</h:p></h:div>

6035

6036

<h:div class="example" href="definition1.xml">

6037

<h:em>From the IUPAC Dictionary of Medicinal Chemistry</h:em>

6038

<h:br/></h:div>

6039

</xsd:documentation>

6040

</xsd:annotation>

6041

<xsd:complexType mixed="true">

6042

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

6043

<xsd:any processContents="lax"/>

6044

</xsd:sequence>

6045

</xsd:complexType>

6046

6047

</xsd:element><xsd:element name="description" id="el.description">

6048

<xsd:annotation>

6049

<xsd:documentation>

6050

<h:div class="summary">Descriptive information.</h:div>

6051

<h:div class="description">This can occur in objects which require textual comment such as entry.

6052

<h:p>Entries should have at least one separate <h:a href="el.definition">definition</h:a>s.

6053

<h:tt>description</h:tt> is then used for most of the other information, including

6054

examples. The <h:tt>class</h:tt> attribute has an uncontrolled vocabulary and

6055

can be used to clarify the purposes of the <h:tt>description</h:tt>

6056

elements.</h:p></h:div>

6057

<h:div class="example" href="description1.xml"/>

6058

</xsd:documentation>

6059

</xsd:annotation>

6060

6061

<xsd:complexType mixed="true">

6062

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

6063

<xsd:any processContents="lax"/>

6064

</xsd:sequence>

6065

6066

<xsd:attributeGroup ref="convention"/>

6067

<xsd:attributeGroup ref="id"/>

6068

<xsd:attributeGroup ref="title"/>

6069

<xsd:attributeGroup ref="dictRef"/>

6070

<xsd:attributeGroup ref="objectClass"/>

6071

</xsd:complexType>

6072

6073

</xsd:element><xsd:element name="dictionary" id="el.dictionary">

6074

<xsd:annotation>

6075

<xsd:documentation>

6076

<h:div class="summary">A dictionary.</h:div>

6077

<h:div class="description">A dictionary is a container for _entry_ elements.

6078

Dictionaries can also contain unit-related information.

6079

The dictRef attribute on a dictionary element sets a

6080

namespace-like prefix allowing the dictionary to be referenced

6081

from within the document. In general dictionaries are referenced

6082

from an element using the __dictRef__ attribute.</h:div>

6083

<h:div class="example" href="dictionary1.xml"/>

6084

<!--

6085

<h:div class="example" href="dictionary2.xml">

6086

<h:p>

6087

<h:tt>dictionary</h:tt> can be used in an instance

6088

document to reference the dictionary used. Example:</h:p></h:div>

6089

-->

6090

<h:div class="curation">2005-12-15. PMR. added namespace

6091

and dictionaryPrefix.</h:div>

6092

</xsd:documentation>

6093

</xsd:annotation>

6094

6095

<xsd:complexType>

6096

<xsd:sequence>

6097

<xsd:element ref="unitList" minOccurs="0" maxOccurs="unbounded"/>

6098

<xsd:element ref="annotation" minOccurs="0" maxOccurs="unbounded"/>

6099

<xsd:element ref="description" minOccurs="0" maxOccurs="unbounded"/>

6100

<xsd:element ref="entry" minOccurs="0" maxOccurs="unbounded"/>

6101

</xsd:sequence>

6102

<xsd:attributeGroup ref="title"/>

6103

<xsd:attributeGroup ref="id"/>

6104

<xsd:attributeGroup ref="convention"/>

6105

<xsd:attributeGroup ref="dictRef"/>

6106

<xsd:attributeGroup ref="href"/>

6107

<xsd:attributeGroup ref="namespace"/>

6108

<xsd:attributeGroup ref="dictionaryPrefix"/>

6109

</xsd:complexType>

6110

</xsd:element><xsd:element name="dimension" id="el.dimension">

6111

<xsd:annotation>

6112

<xsd:documentation>

6113

<h:div class="summary">A dimension supporting scientific unit.</h:div>

6114

<h:div class="description">This will be primarily used within the definition of units.

6115

Two dimensions are of the same type if their 'name' attributes are (case-sensitive)

6116

identical. Dimensions of the same typecan be algebraically combined using the 'power' attributes.

6117

Normally dimensions will be aggregated and cancelled algebraically, but the 'preserve'

6118

attribute can be used to prevent this. Thus a velocity gradient over length can be

6119

defined as:

6120

<h:pre>

6121

6122

6123

6124

6125

</unitType>

6126

</h:pre>

6127

whereas cancelling the dimensions would give:

6128

<h:pre>

6129

6130

6131

</unitType>

6132

</h:pre>

6133

</h:div>

6134

<h:div class="example" href="dimension1.xml"/>

6135

<h:div class="example" href="dimension2.xml"/>

6136

</xsd:documentation>

6137

</xsd:annotation>

6138

6139

<xsd:complexType>

6140

<xsd:sequence/>

6141

<xsd:attributeGroup ref="dimensionBasis"/>

6142

<xsd:attributeGroup ref="id"/>

6143

<xsd:attributeGroup ref="name"/>

6144

<xsd:attributeGroup ref="power"/>

6145

<xsd:attributeGroup ref="preserve"/>

6146

</xsd:complexType>

6147

</xsd:element><xsd:element name="documentation" id="el.documentation">

6148

<xsd:annotation>

6149

<xsd:documentation>

6150

<h:div class="summary">Documentation in the annotation of an entry.</h:div>

6151

<h:div class="description">

6152

<h:p>A container similar to <h:tt>documentation</h:tt> in XML Schema. This is NOT part of the textual content of an entry but is designed to support the transformation of dictionary entrys into schemas for validation. This is experimental and should only be used for dictionaries, units, etc. One approach is to convert these into XML Schemas when the <h:tt>documentation</h:tt> and <h:tt>appinfo</h:tt> children will emerge in their correct position in the derived schema.</h:p>

6153

<h:p>Do NOT confuse documentation with the description or the definition which are part of the content

6154

of the dictionary</h:p>

6155

<h:p>If will probably only be used when there is significant appinfo

6156

in the entry or where the entry defines an XSD-like datatype of an element in the document.</h:p></h:div>

6157

6158

<h:div class="example" href="documentation1.xml"/>

6159

</xsd:documentation>

6160

</xsd:annotation>

6161

6162

<xsd:complexType mixed="true">

6163

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

6164

<xsd:any processContents="lax"/>

6165

</xsd:sequence>

6166

<xsd:attributeGroup ref="id"/>

6167

<xsd:attributeGroup ref="title"/>

6168

</xsd:complexType>

6169

6170

</xsd:element><xsd:element name="eigen" id="el.eigen">

6171

<xsd:annotation>

6172

<xsd:documentation>

6173

<h:div class="summary">An element to hold eigenstuff.</h:div>

6174

<h:div class="description">Holds an array of eigenvalues and a matrix of eigenvectors.</h:div>

6175

<h:div class="example" href="eigen1.xml"/>

6176

</xsd:documentation>

6177

</xsd:annotation>

6178

6179

<xsd:complexType>

6180

<xsd:sequence>

6181

<xsd:element ref="array" minOccurs="0"/>

6182

<xsd:element ref="matrix" minOccurs="0"/>

6183

</xsd:sequence>

6184

<xsd:attributeGroup ref="units"/>

6185

<xsd:attributeGroup ref="title"/>

6186

<xsd:attributeGroup ref="id"/>

6187

<xsd:attributeGroup ref="convention"/>

6188

<xsd:attributeGroup ref="dictRef"/>

6189

<xsd:attributeGroup ref="type">

6190

<xsd:annotation>

6191

<xsd:documentation>

6192

<h:div class="summary">No current semantics.</h:div>

6193

<h:div class="description">Suggest it is developed

6194

for the chemical/physical role, e.g. "molecular obitals", "inertial

6195

matrix", "vibrational modes", "phonons", etc.</h:div>

6196

</xsd:documentation>

6197

</xsd:annotation>

6198

</xsd:attributeGroup>

6199

<xsd:attributeGroup ref="eigenOrientation"/>

6200

</xsd:complexType>

6201

</xsd:element><xsd:element name="electron" id="el.electron">

6202

<xsd:annotation>

6203

<xsd:documentation>

6204

<h:div class="summary">An electron.</h:div>

6205

<h:div class="description">Since there is very little use of electrons in current chemical information this is a fluid concept. I expect it to be used for electron counting, input and output of theochem operations, descriptions of orbitals, spin states, oxidation states, etc. Electrons can be associated with atoms, bonds and combinations of these. At present there is no hardcoded semantics. However, _atomRef_ and similar attributes can be used to associate electrons with atoms or bond.</h:div>

6206

<h:div class="example" href="electron1.xml"/>

6207

</xsd:documentation>

6208

</xsd:annotation>

6209

<xsd:complexType>

6210

<xsd:sequence/>

6211

<xsd:attributeGroup ref="title"/>

6212

<xsd:attributeGroup ref="id"/>

6213

<xsd:attributeGroup ref="convention"/>

6214

<xsd:attributeGroup ref="dictRef"/>

6215

<xsd:attributeGroup ref="atomRef"/>

6216

<xsd:attributeGroup ref="atomRefs"/>

6217

<xsd:attributeGroup ref="bondRef"/>

6218

<xsd:attributeGroup ref="bondRefs"/>

6219

<xsd:attributeGroup ref="count"/>

6220

<xsd:attributeGroup ref="ref"/>

6221

</xsd:complexType>

6222

</xsd:element><xsd:element name="entry" id="el.entry">

6223

<xsd:annotation>

6224

<xsd:documentation>

6225

<h:div class="summary">A dictionary entry.</h:div>

6226

<h:div class="desacription">The original design for validation with attribute-based constraints is ponderous and fragile. In future constraints will be added through <h:tt>appinfo</h:tt> in <h:tt>annotation</h:tt>. We shall develop this further in the near future.</h:div>

6227

<h:div class="curation">2003-03-30: added metadataList to content mode.</h:div>

6228

<h:div class="example" href="entry1.xml"/>

6229

<!--

6230

<h:div class="example" href="entry2.xml"></h:div>

6231

-->

6232

</xsd:documentation>

6233

</xsd:annotation>

6234

6235

<xsd:complexType>

6236

<xsd:sequence>

6237

<xsd:choice minOccurs="0" maxOccurs="unbounded">

6238

<xsd:element ref="metadataList"/>

6239

<xsd:element ref="alternative"/>

6240

<xsd:element ref="annotation"/>

6241

<xsd:element ref="definition"/>

6242

<xsd:element ref="description"/>

6243

<xsd:element ref="enumeration"/>

6244

<xsd:element ref="relatedEntry"/>

6245

</xsd:choice>

6246

</xsd:sequence>

6247

<xsd:attributeGroup ref="title"/>

6248

<xsd:attributeGroup ref="id"/>

6249

<xsd:attributeGroup ref="convention"/>

6250

<xsd:attributeGroup ref="dataType"/>

6251

<xsd:attributeGroup ref="rows"/>

6252

<xsd:attributeGroup ref="columns"/>

6253

<xsd:attributeGroup ref="unitType"/>

6254

<xsd:attributeGroup ref="minExclusive"/>

6255

<xsd:attributeGroup ref="minInclusive"/>

6256

<xsd:attributeGroup ref="maxExclusive"/>

6257

<xsd:attributeGroup ref="maxInclusive"/>

6258

<xsd:attributeGroup ref="totalDigits"/>

6259

<xsd:attributeGroup ref="fractionDigits"/>

6260

<xsd:attributeGroup ref="length"/>

6261

<xsd:attributeGroup ref="minLength"/>

6262

<xsd:attributeGroup ref="maxLength"/>

6263

<xsd:attributeGroup ref="units"/>

6264

<xsd:attributeGroup ref="whiteSpace"/>

6265

<xsd:attributeGroup ref="pattern"/>

6266

<xsd:attributeGroup ref="term"/>

6267

</xsd:complexType>

6268

</xsd:element><xsd:element name="enumeration" id="el.enumeration">

6269

<xsd:annotation>

6270

<xsd:documentation>

6271

<h:div class="summary">An enumeration of value.</h:div>

6272

<h:div class="description">An enumeration of string values. Used where a dictionary entry constrains the possible values in a document instance. The dataTypes (if any) must all be identical and are defined by the dataType of the containing element.</h:div>

6273

6274

<h:div class="example" href="enumeration1.xml"/>

6275

6276

</xsd:documentation>

6277

</xsd:annotation>

6278

6279

<xsd:complexType>

6280

<xsd:sequence>

6281

<xsd:element ref="annotation" minOccurs="0"/>

6282

</xsd:sequence>

6283

<xsd:attributeGroup ref="value"/>

6284

<xsd:attributeGroup ref="id"/>

6285

<xsd:attributeGroup ref="dictRef"/>

6286

<xsd:attributeGroup ref="default"/>

6287

</xsd:complexType>

6288

</xsd:element><xsd:element name="expression" id="el.expression">

6289

<xsd:annotation>

6290

<xsd:documentation>

6291

<h:div class="summary">An expression that can be evaluated.</h:div>

6292

<h:div class="description">Experimental. This is essentially a mathematical function, expressed currently in reverse Polish notation but we expect to move to MathML.</h:div>

6293

<h:div class="example" href="potential1.xml"/>

6294

</xsd:documentation>

6295

</xsd:annotation>

6296

6297

<xsd:complexType>

6298

<xsd:sequence>

6299

<xsd:choice minOccurs="0" maxOccurs="unbounded">

6300

<xsd:element ref="parameter"/>

6301

<xsd:element ref="operator"/>

6302

</xsd:choice>

6303

</xsd:sequence>

6304

<xsd:attributeGroup ref="title"/>

6305

<xsd:attributeGroup ref="id"/>

6306

<xsd:attributeGroup ref="convention"/>

6307

<xsd:attributeGroup ref="dictRef"/>

6308

<xsd:attributeGroup ref="dataType"/>

6309

</xsd:complexType>

6310

</xsd:element><xsd:element name="float" id="el.float">

6311

<xsd:annotation>

6312

<xsd:documentation>

6313

<h:div class="summary">CML-1 dataType DEPRECATED.</h:div>

6314

<h:div class="description"/>

6315

<h:div class="example" href="../../examples/cmlone.xml"/>

6316

</xsd:documentation>

6317

</xsd:annotation>

6318

<xsd:complexType>

6319

<xsd:simpleContent>

6320

<xsd:extension base="xsd:double">

6321

<xsd:attributeGroup ref="builtin"/>

6322

<xsd:attributeGroup ref="convention"/>

6323

<xsd:attributeGroup ref="dictRef"/>

6324

<xsd:attributeGroup ref="id"/>

6325

<xsd:attributeGroup ref="title"/>

6326

<xsd:attributeGroup ref="min"/>

6327

<xsd:attributeGroup ref="max"/>

6328

<xsd:attributeGroup ref="units"/>

6329

<xsd:attributeGroup ref="unitsRef"/>

6330

</xsd:extension>

6331

</xsd:simpleContent>

6332

</xsd:complexType>

6333

</xsd:element><xsd:element name="floatArray" id="el.floatArray">

6334

<xsd:annotation>

6335

<xsd:documentation>

6336

<h:div class="summary">CML-1 dataType DEPRECATED.</h:div>

6337

<h:div class="description"/>

6338

<h:div class="example" href="../../examples/cmlone.xml"/>

6339

</xsd:documentation>

6340

</xsd:annotation>

6341

<xsd:complexType>

6342

<xsd:simpleContent>

6343

<xsd:extension base="xsd:string">

6344

<xsd:attributeGroup ref="builtin"/>

6345

<xsd:attributeGroup ref="convention"/>

6346

<xsd:attributeGroup ref="dictRef"/>

6347

<xsd:attributeGroup ref="id"/>

6348

<xsd:attributeGroup ref="title"/>

6349

<xsd:attributeGroup ref="min"/>

6350

<xsd:attributeGroup ref="max"/>

6351

<xsd:attributeGroup ref="size"/>

6352

<xsd:attributeGroup ref="units"/>

6353

<xsd:attributeGroup ref="unitsRef"/>

6354

</xsd:extension>

6355

</xsd:simpleContent>

6356

</xsd:complexType>

6357

</xsd:element><xsd:element name="formula" id="el.formula">

6358

<xsd:annotation>

6359

<xsd:documentation>

6360

<h:div class="summary">A molecular formula.</h:div>

6361

<h:div class="description">

6362

<h:p>It is

6363

defined by <h:tt>atomArray</h:tt>s each with a list of elementTypes and their

6364

counts (or default=1). All other information in the <h:tt>atomArray</h:tt>

6365

is ignored. <h:tt>formula</h:tt> are nestable so that aggregates (e.g. hydrates,

6366

salts, etc.) can be described. CML does not require that formula information

6367

is consistent with (say) crystallographic information; this allows for

6368

experimental variance.</h:p>

6369

<h:p>An alternative briefer representation is also available through the

6370

<h:tt>concise</h:tt>. This must include whitespace round all elements and

6371

their counts, which must be explicit. </h:p>

6372

<h:p>2005-10-16. The semantics are now the following. A formula must have one or both:

6373

<h:ul>

6374

<h:li>A concise attribute

6375

</h:li>A single atomArray child, using array format.

6376

</h:ul>

6377

it must also have a formalCharge attribute if atomArray is used and the charge is non-zero.

6378

</h:p>

6379

<h:p>

6380

The concise, formalCharge and atomArrary information must always be consistent and software should

6381

throw an error if not.

6382

</h:p>

6383

<h:p>

6384

Until now there was no way of holding inline formula other than concise (although JUMBO5.0 is

6385

capable of reading them). We now extend formula.xsd to incorporate this through the attribute

6386

"inline" which requires the use of the "convention" attribute. The contents of inline are

6387

purely textual. It can be used with or without atomArray or concise but there is no

6388

guarantee that it can be interpreted as a meaningful chemical formula or that there is consistency.

6389

In some cases a document supplies several formula representations (e.g. the IUCr's CIF). In this

6390

case a molecule (or crystal) element might contain several formula children. The semantics of which

6391

to use are application dependent.

6392

</h:p>

6393

</h:div>

6394

<h:div class="example" href="formula1.xml"/>

6395

</xsd:documentation>

6396

</xsd:annotation>

6397

<xsd:complexType>

6398

<xsd:choice>

6399

<xsd:choice minOccurs="0" maxOccurs="unbounded">

6400

<xsd:element ref="formula"/>

6401

<xsd:element ref="atomArray"/>

6402

</xsd:choice>

6403

</xsd:choice>

6404

<xsd:attributeGroup ref="title"/>

6405

<xsd:attributeGroup ref="id"/>

6406

<xsd:attributeGroup ref="convention"/>

6407

<xsd:attributeGroup ref="dictRef"/>

6408

<xsd:attributeGroup ref="count">

6409

<xsd:annotation>

6410

<xsd:documentation>

6411

<h:div class="specific">Allows for fractional components.</h:div>

6412

</xsd:documentation>

6413

</xsd:annotation>

6414

</xsd:attributeGroup>

6415

<xsd:attributeGroup ref="formalCharge">

6416

<xsd:annotation>

6417

<xsd:documentation>

6418

<h:div class="specific">The charge on the formula. Mandatory if non-zero

6419

(i.e. cannot rely on concise)</h:div>

6420

</xsd:documentation>

6421

</xsd:annotation>

6422

</xsd:attributeGroup>

6423

<xsd:attributeGroup ref="concise"/>

6424

<xsd:attributeGroup ref="inline">

6425

<xsd:annotation>

6426

<xsd:documentation>

6427

<h:div class="specific">An inline representation of the formula.

6428

There are no controlled semantics and it need not be compatible with concise

6429

or atomArray.</h:div>

6430

</xsd:documentation>

6431

</xsd:annotation>

6432

</xsd:attributeGroup>

6433

</xsd:complexType>

6434

</xsd:element><xsd:element name="gradient" id="el.gradient">

6435

<xsd:annotation>

6436

<xsd:documentation>

6437

<h:div class="summary">A gradient.</h:div>

6438

<h:div class="description">A container for a quantity or quantities representing the

6439

gradient of other quantities. At present just takes a scalar child.</h:div>

6440

<h:div class="example" href="gradient1.xml"/>

6441

</xsd:documentation>

6442

</xsd:annotation>

6443

6444

<xsd:complexType>

6445

<xsd:sequence>

6446

<xsd:choice minOccurs="0" maxOccurs="unbounded">

6447

<xsd:element ref="scalar"/>

6448

<xsd:element ref="array"/>

6449

<xsd:element ref="matrix"/>

6450

<xsd:element ref="property"/>

6451

</xsd:choice>

6452

</xsd:sequence>

6453

<xsd:attributeGroup ref="title"/>

6454

<xsd:attributeGroup ref="id"/>

6455

<xsd:attributeGroup ref="convention"/>

6456

<xsd:attributeGroup ref="dictRef"/>

6457

</xsd:complexType>

6458

</xsd:element><xsd:element name="identifier" id="el.identifier">

6459

<xsd:annotation>

6460

<xsd:documentation>

6461

<h:div class="summary">A structured identifier.</h:div>

6462

<h:div class="description">

6463

<h:p>Supports compund identifiers such as IChI. At present uses the V0.9 IChI XML representation verbatim but will almost certainly change with future IChIs. </h:p>

6464

<h:p>The inclusion of elements from other namespaces causes problems with validation. The content model is deliberately LAX but the actual elements in IChI will fail the validation as they are not declared in CML.</h:p>

6465

For simple scalar values the value attribute can be used with empty content. Where an identifier has several components a series of label elements can be used.</h:div>

6466

<h:div class="curation">2003-07-10: Fixed count on identifier children..</h:div>

6467

<h:div class="curation">2003-03-12: Added isotopic and atoms..</h:div>

6468

<h:div class="example" href="identifier1.xml"/>

6469

</xsd:documentation>

6470

</xsd:annotation>

6471

<xsd:complexType>

6472

6473

6474

<xsd:sequence maxOccurs="unbounded" minOccurs="0">

6475

<xsd:any processContents="lax"/>

6476

</xsd:sequence>

6477

<xsd:attributeGroup ref="value"/>

6478

<xsd:attributeGroup ref="version"/>

6479

<xsd:attributeGroup ref="title"/>

6480

<xsd:attributeGroup ref="id"/>

6481

<xsd:attributeGroup ref="convention"/>

6482

<xsd:attributeGroup ref="dictRef"/>

6483

<xsd:attributeGroup ref="tautomeric"/>

6484

</xsd:complexType>

6485

</xsd:element><xsd:element name="integer" id="el.integer">

6486

<xsd:annotation>

6487

<xsd:documentation>

6488

<h:div class="summary">CML-1 dataType DEPRECATED.</h:div>

6489

<h:div class="description"/>

6490

<h:div class="example" href="../../examples/cmlone.xml"/>

6491

</xsd:documentation>

6492

</xsd:annotation>

6493

<xsd:complexType>

6494

<xsd:simpleContent>

6495

<xsd:extension base="xsd:integer">

6496

<xsd:attributeGroup ref="builtin"/>

6497

<xsd:attributeGroup ref="convention"/>

6498

<xsd:attributeGroup ref="dictRef"/>

6499

<xsd:attributeGroup ref="id"/>

6500

<xsd:attributeGroup ref="title"/>

6501

<xsd:attributeGroup ref="min"/>

6502

<xsd:attributeGroup ref="max"/>

6503

<xsd:attributeGroup ref="units"/>

6504

<xsd:attributeGroup ref="unitsRef"/>

6505

</xsd:extension>

6506

</xsd:simpleContent>

6507

</xsd:complexType>

6508

</xsd:element><xsd:element name="integerArray" id="el.integerArray">

6509

<xsd:annotation>

6510

<xsd:documentation>

6511

<h:div class="summary">CML-1 dataType DEPRECATED.</h:div>

6512

<h:div class="description"/>

6513

<h:div class="example" href="../../examples/cmlone.xml"/>

6514

</xsd:documentation>

6515

</xsd:annotation>

6516

<xsd:complexType>

6517

<xsd:simpleContent>

6518

<xsd:extension base="xsd:string">

6519

<xsd:attributeGroup ref="builtin"/>

6520

<xsd:attributeGroup ref="convention"/>

6521

<xsd:attributeGroup ref="dictRef"/>

6522

<xsd:attributeGroup ref="id"/>

6523

<xsd:attributeGroup ref="title"/>

6524

<xsd:attributeGroup ref="min"/>

6525

<xsd:attributeGroup ref="max"/>

6526

<xsd:attributeGroup ref="size"/>

6527

<xsd:attributeGroup ref="units"/>

6528

<xsd:attributeGroup ref="unitsRef"/>

6529

</xsd:extension>

6530

</xsd:simpleContent>

6531

</xsd:complexType>

6532

</xsd:element><xsd:element name="isotope" id="el.isotope">

6533

<xsd:annotation>

6534

<xsd:documentation>

6535

<h:div class="summary">A specific isotope.</h:div>

6536

<h:div class="description">Defines an isotope in terms of exact mass and spin. Differentiate from isotopeList which defines a mixture of isotope.</h:div>

6537

<h:div class="example" href="isotope1.xml"/>

6538

</xsd:documentation>

6539

</xsd:annotation>

6540

<xsd:complexType>

6541

<xsd:sequence>

6542

<xsd:element ref="abundance" minOccurs="0" maxOccurs="1"/>

6543

</xsd:sequence>

6544

<xsd:attributeGroup ref="title"/>

6545

<xsd:attributeGroup ref="id"/>

6546

<xsd:attributeGroup ref="convention"/>

6547

<xsd:attributeGroup ref="dictRef"/>

6548

<xsd:attributeGroup ref="number"/>

6549

<xsd:attributeGroup ref="spin"/>

6550

<xsd:attributeGroup ref="elementType"/>

6551

<xsd:attributeGroup ref="ref"/>

6552

</xsd:complexType>

6553

</xsd:element><xsd:element name="isotopeList" id="el.isotopeList">

6554

<xsd:annotation>

6555

<xsd:documentation>

6556

<h:div class="summary">A container for one or more isotopes.</h:div>

6557

<h:div class="description">Can contain several isotopes. These may be related in several ways. This allows the definition of natural abundance and averged enrichment.</h:div>

6558

<h:div class="example" href="isotopeList1.xml"/>

6559

</xsd:documentation>

6560

</xsd:annotation>

6561

6562

<xsd:complexType>

6563

<xsd:sequence>

6564

<xsd:element ref="isotope" minOccurs="0" maxOccurs="unbounded"/>

6565

</xsd:sequence>

6566

<xsd:attributeGroup ref="dictRef"/>

6567

<xsd:attributeGroup ref="convention"/>

6568

<xsd:attributeGroup ref="title"/>

6569

<xsd:attributeGroup ref="id"/>

6570

<xsd:attributeGroup ref="ref"/>

6571

</xsd:complexType>

6572

</xsd:element><xsd:element name="kpoint" id="el.kpoint">

6573

<xsd:annotation>

6574

<xsd:documentation>

6575

<h:div class="summary">A kpoint.</h:div>

6576

<h:div class="description">Not yet finalised.</h:div>

6577

<h:div class="example" href="kpoint1.xml"/>

6578

<h:div class="curation">2006-01-21: PMR. Created</h:div>

6579

</xsd:documentation>

6580

</xsd:annotation>

6581

6582

<xsd:complexType>

6583

<xsd:simpleContent>

6584

<xsd:extension base="vector3Type">

6585

<xsd:attributeGroup ref="weight"/>

6586

<xsd:attributeGroup ref="label"/>

6587

<xsd:attributeGroup ref="title"/>

6588

<xsd:attributeGroup ref="id"/>

6589

<xsd:attributeGroup ref="convention"/>

6590

<xsd:attributeGroup ref="dictRef"/>

6591

</xsd:extension>

6592

</xsd:simpleContent>

6593

</xsd:complexType>

6594

</xsd:element><xsd:element name="kpointList" id="el.kpointList">

6595

<xsd:annotation>

6596

<xsd:documentation>

6597

<h:div class="summary">A container for kpoints.</h:div>

6598

<h:div class="description">Experimental.</h:div>

6599

<h:div class="example" href="kpoint1.xml"/>

6600

</xsd:documentation>

6601

</xsd:annotation>

6602

6603

<xsd:complexType>

6604

<xsd:sequence>

6605

<xsd:choice minOccurs="0" maxOccurs="unbounded">

6606

<xsd:element ref="kpoint"/>

6607

</xsd:choice>

6608

</xsd:sequence>

6609

<xsd:attributeGroup ref="title"/>

6610

<xsd:attributeGroup ref="id"/>

6611

<xsd:attributeGroup ref="convention"/>

6612

<xsd:attributeGroup ref="dictRef"/>

6613

</xsd:complexType>

6614

</xsd:element><xsd:element name="label" id="el.label">

6615

<xsd:annotation>

6616

<xsd:documentation>

6617

<h:div class="summary">A text string qualifying an object.</h:div>

6618

<h:div class="description">A label can be used to identify or distinguish elements, add keywords or classifications and similar processes. It is usually interpretable by domain-aware humans (e.g. C3'-endo, but not a34561). It is usually either built in a semantically rich fashion (e.g. C2'-alpha-H) or belongs to a controlled vocabulary. It is possibly accessed by software in a domain-specific manner. It differs from <h:tt>description</h:tt> which is free text. The distinction between titles, names and labels is fuzzy, but we think this is worth making. Labels may be necesssary to identify objects within programs, while names are more likely to be reserved for database searches. Titles are likely to be freer text and not recommended for precise object retrieval.</h:div>

6619

<h:div class="note">Labels should not contain whitespace. Punctuation marks are often necessary, but should not be gratuitously used. Punctuation clashing with XML character entities should be avoided; if this is not possible it should be escaped.</h:div>

6620

6621

<h:div class="example" href="label1.xml">

6622

<h:em>From IUPAC Dictionary of Medicinal Chemistry</h:em></h:div>

6623

</xsd:documentation>

6624

</xsd:annotation>

6625

6626

<xsd:complexType>

6627

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

6628

<xsd:any processContents="lax"/>

6629

</xsd:sequence>

6630

<xsd:attributeGroup ref="id"/>

6631

<xsd:attributeGroup ref="dictRef"/>

6632

<xsd:attributeGroup ref="value"/>

6633

<xsd:attributeGroup ref="objectClass"/>

6634

</xsd:complexType>

6635

6636

</xsd:element><xsd:element name="lattice" id="el.lattice">

6637

<xsd:annotation>

6638

<xsd:documentation>

6639

<h:div class="summary">A lattice of dimension 3 or less.</h:div>

6640

<h:div class="description">Lattice is a general approach to describing periodic systems.

6641

It can have variable dimensionality or periodicity, and could be finite.</h:div>

6642

<h:div class="note">

6643

_lattice_ is more general than _crystal_ in cmlCore which is used primarily for reporting

6644

crystallographic experiments.`A lattice can be described by latticeVectors, cell axes

6645

and angles, or metric tensors, etc. (only axes/angles are allowed under <h:tt>crystal</h:tt>). The dimensionality is enforced through a _system_ parent element.</h:div>

6646

<h:div class="example" href="lattice3.xml"/>

6647

</xsd:documentation>

6648

</xsd:annotation>

6649

<xsd:complexType>

6650

<xsd:sequence>

6651

<xsd:choice>

6652

<xsd:element ref="scalar" minOccurs="3" maxOccurs="6">

6653

<xsd:annotation>

6654

<xsd:documentation>

6655

<h:div class="summary">All appropriate cell parameters must be given, even

6656

where angles are fixed by symmetry. The order is fixed as a,b,c,alpha,beta,gamma

6657

and software can neglect any title or dictRef attributes. Error estimates

6658

can be given if required. Any units can be used, but the defaults are

6659

Angstrom (10^-10 m) and degrees. To be developed for lower dimensionality.</h:div>

6660

</xsd:documentation>

6661

</xsd:annotation>

6662

</xsd:element>

6663

<xsd:element ref="latticeVector" minOccurs="1" maxOccurs="3">

6664

<!--

6665

<h:div class="summary">A number of lattice vectors equal to the dimensionality. Note that some vectors may give rise to periodicty while others do not. Thus a surface can be described by two vector in the plane of the surface and one perpendicular to them.</h:div>

6666

--></xsd:element>

6667

<xsd:element ref="matrix" minOccurs="1" maxOccurs="1">

6668

<!--

6669

<h:div class="summary">The metric tensor (normally for 3 dimensions).</h:div>

6670

--></xsd:element>

6671

</xsd:choice>

6672

<xsd:element ref="symmetry" minOccurs="0"/>

6673

</xsd:sequence>

6674

6675

<xsd:attributeGroup ref="title"/>

6676

<xsd:attributeGroup ref="id"/>

6677

<xsd:attributeGroup ref="convention"/>

6678

<xsd:attributeGroup ref="dictRef"/>

6679

<xsd:attributeGroup ref="latticeType"/>

6680

<xsd:attributeGroup ref="spaceType"/>

6681

</xsd:complexType>

6682

</xsd:element><xsd:element name="latticeVector" id="el.latticeVector">

6683

<xsd:annotation>

6684

<xsd:documentation>

6685

<h:div class="summary">A vector3 representing a lattice axis.</h:div>

6686

<h:div class="description">a <h:tt>lattice</h:tt> can be represented by 1-3 non-linearly

6687

dependent latticeVectors. If the dimensionality is less than 3 latticeVectors are the

6688

preferred method. Similarly, if the axes show a mixture of periodicity and non-periodicity

6689

latticeVectors can support this. The number of periodic vectors must correspond with

6690

the periodicity attribute on a <h:tt>system</h:tt> element.

6691

<h:p>The vector must not be zero and units must be given. (Zero vectors must not be

6692

used to reduce dimensionality). </h:p>

6693

<h:p>A lattice vector defaults to periodic.</h:p>.</h:div>

6694

<h:div class="description">Any or all of the axes may be periodic or aperiodic. An example

6695

could be a surface where 2 periodic axes (not necessarily orthogonal) are used to describe

6696

the coordinates in the surface, perhaps representing lattice vectors of a 3D crystal or

6697

2D layer. The third vector is orthogonal and represents coordinates normal to the surface.

6698

In this case only the direction, not the magnitude of the vector is important.</h:div>

6699

<h:div class="example" href="latticeVector1.xml"/>

6700

</xsd:documentation>

6701

</xsd:annotation>

6702

<xsd:complexType>

6703

<xsd:simpleContent>

6704

<xsd:extension base="vector3Type">

6705

<xsd:attributeGroup ref="convention"/>

6706

<xsd:attributeGroup ref="dictRef"/>

6707

<xsd:attributeGroup ref="id"/>

6708

<xsd:attributeGroup ref="title"/>

6709

<xsd:attributeGroup ref="units"/>

6710

<xsd:attributeGroup ref="periodic"/>

6711

</xsd:extension>

6712

</xsd:simpleContent>

6713

</xsd:complexType>

6714

</xsd:element><xsd:element name="length" id="el.length">

6715

<xsd:annotation>

6716

<xsd:documentation>

6717

<h:div class="summary">A length between two atoms.</h:div>

6718

<h:div class="general">This is either an experimental measurement or used to build up internal coordinates (as in a z-matrix) (only one allowed). We expect to move length as a child of _molecule_ and remove it from here.</h:div>

6719

<h:div class="example" href="length1.xml"/>

6720

</xsd:documentation>

6721

</xsd:annotation>

6722

<xsd:complexType>

6723

<xsd:simpleContent>

6724

<xsd:extension base="xsd:double">

6725

<xsd:attributeGroup ref="title"/>

6726

<xsd:attributeGroup ref="id"/>

6727

<xsd:attributeGroup ref="convention"/>

6728

<xsd:attributeGroup ref="dictRef"/>

6729

<xsd:attributeGroup ref="atomRefs2"/>

6730

<xsd:attributeGroup ref="units"/>

6731

<xsd:attributeGroup ref="errorValue"/>

6732

<xsd:attributeGroup ref="errorBasis"/>

6733

<xsd:attributeGroup ref="min"/>

6734

<xsd:attributeGroup ref="max"/>

6735

<xsd:attributeGroup ref="ref"/>

6736

</xsd:extension>

6737

</xsd:simpleContent>

6738

</xsd:complexType>

6739

</xsd:element><xsd:element name="line3" id="el.line3">

6740

<xsd:annotation>

6741

<xsd:documentation>

6742

<h:div class="summary">A line in 3-space.</h:div>

6743

<h:div class="description">A line characterised by one or two endpoints.</h:div>

6744

<h:div class="curation">2006-01-02: the 6-number content has caused much confusion and

6745

will be obsoleted in favour of the point3 and vector3 attributes</h:div>

6746

</xsd:documentation>

6747

</xsd:annotation>

6748

<xsd:complexType>

6749

<xsd:simpleContent>

6750

<xsd:extension base="line3Type">

6751

<xsd:attributeGroup ref="convention"/>

6752

<xsd:attributeGroup ref="dictRef"/>

6753

<xsd:attributeGroup ref="id"/>

6754

<xsd:attributeGroup ref="title"/>

6755

<xsd:attributeGroup ref="units"/>

6756

<xsd:attributeGroup ref="point3"/>

6757

<xsd:attributeGroup ref="vector3"/>

6758

</xsd:extension>

6759

</xsd:simpleContent>

6760

</xsd:complexType>

6761

</xsd:element><xsd:element name="link" id="el.link">

6762

<xsd:annotation>

6763

<xsd:documentation>

6764

<h:div class="summary">An internal or external link to other objects.</h:div>

6765

<h:div class="description">

6766

<h:p>

6767

<h:b>Semantics are similar to XLink, but simpler and only a subset is implemented.</h:b>

6768

This is intended to make the instances easy to create and read, and software

6769

relatively easy to implement. The architecture is:</h:p>

6770

<h:ul>

6771

<h:li>

6772

<h:b>A single element (<h:tt>link</h:tt>) used for all linking purposes.</h:b></h:li>

6773

<h:li>

6774

<h:b>The link types are determined by the <h:tt>type</h:tt> attribute and can be:</h:b>.

6775

<h:ul>

6776

<h:li><h:b>locator</h:b>. This points to a single target and must carry either a <h:tt>ref</h:tt> or <h:tt>href</h:tt> attribute.

6777

<h:tt>locator</h:tt> links are usually children of an extended link.

6778

<h:li><h:b>arc</h:b>. This is a 1:1 link with both ends (<h:tt>from</h:tt> and <h:tt>to</h:tt>) defined.</h:li>

6779

<h:li>

6780

<h:b>extended</h:b>. This is usually a parent of several locator links and serves

6781

to create a grouping of link ends (i.e. a list of references in documents).</h:li>

6782

Many-many links can be built up from arcs linking extended elements</h:li>

6783

</h:ul>

6784

<h:p>All links can have optional <h:tt>role</h:tt> attributes. The semantics of this are not defined;

6785

you are encouraged to use a URI as described in the XLink specification.</h:p>

6786

<h:p>There are two address spaces: </h:p>

6787

<h:ul>

6788

<h:li>The <h:tt>href</h:tt> attribute on locators behaves in the same way as <h:tt>href</h:tt> in

6789

HTML and is of type <h:tt>xsd:anyURI</h:tt>. Its primary use is to use XPointer to reference

6790

elements outside the document.</h:li>

6791

<h:li>The <h:tt>ref</h:tt> attribute on locators and the <h:tt>from</h:tt> and <h:tt>to</h:tt>

6792

attributes on <h:tt>arc</h:tt>s refer to IDs (<h:em>without</h:em> the '#' syntax).</h:li>

6793

</h:ul>

6794

6795

<h:p>Note: several other specific linking mechanisms are defined elsewhere in STM. <h:a href="el.relatedEntry">relatedEntry</h:a> should be used in dictionaries, and <h:a href="st.dictRef">dictRef</h:a>

6796

should be used to link to dictionaries. There are no required uses of <h:tt>link</h:tt> in STMML

6797

but we have used it to map atoms, electrons and bonds in reactions in CML</h:p>

6798

</h:li>

6799

</h:ul>

6800

<h:p>

6801

<h:b>Relation to XLink</h:b>.

6802

At present (2002) we are not aware of generic XLink

6803

processors from which we would benefit, so the complete implementation brings little

6804

extra value.

6805

Among the simplifications from Xlink are:</h:p>

6806

<h:ul>

6807

<h:li>

6808

<h:tt>type</h:tt> supports only <h:tt>extended</h:tt>, <h:tt>locator</h:tt> and <h:tt>arc</h:tt>

6809

</h:li>

6810

<h:li>

6811

<h:tt>label</h:tt> is not supported and <h:tt>id</h:tt>s are used as targets of links.</h:li>

6812

<h:li>

6813

<h:tt>show</h:tt> and <h:tt>actuate</h:tt> are not supported.</h:li>

6814

<h:li>

6815

<h:tt>xlink:title</h:tt> is not supported (all STM elements can have a <h:tt>title</h:tt>

6816

attribute).</h:li>

6817

<h:li>

6818

<h:tt>xlink:role</h:tt> supports any string (i.e. does not have to be a namespaced resource).

6819

This mechanism can, of course, still be used and we shall promote it where STM

6820

benefits from it</h:li>

6821

<h:li>The <h:tt>to</h:tt> and <h:tt>from</h:tt> attributes point to IDs rather than labels</h:li>

6822

<h:li>The xlink namespace is not used</h:li>

6823

<h:li>It is not intended to create independent linkbases, although some collections of

6824

links may have this property and stand outside the documents they link to</h:li>

6825

</h:ul></h:div>

6826

</xsd:documentation>

6827

</xsd:annotation>

6828

<xsd:complexType>

6829

<xsd:sequence>

6830

<xsd:any minOccurs="0" maxOccurs="unbounded"/>

6831

</xsd:sequence>

6832

<xsd:attributeGroup ref="title"/>

6833

<xsd:attributeGroup ref="id"/>

6834

<xsd:attributeGroup ref="convention"/>

6835

<xsd:attributeGroup ref="dictRef"/>

6836

<xsd:attributeGroup ref="from"/>

6837

<xsd:attributeGroup ref="to"/>

6838

<xsd:attributeGroup ref="ref"/>

6839

<xsd:attributeGroup ref="fromType">

6840

<xsd:annotation>

6841

<xsd:documentation>

6842

<h:div class="specific">The type of the object/element in the 'from' attributes. Requires the objects referenced by the 'from' attributes to have a given elementType. Can be overridden by 'from' attributes in individual links. 2005-06-18: created</h:div>

6843

</xsd:documentation>

6844

</xsd:annotation>

6845

</xsd:attributeGroup>

6846

<xsd:attributeGroup ref="toType">

6847

<xsd:annotation>

6848

<xsd:documentation>

6849

<h:div class="specific">The type of the object/element in the 'to' attributes. Requires the objects referenced by the 'to' attributes to have a given elementType. Can be overridden by 'to' attributes in individual links. 2005-06-18: created</h:div>

6850

</xsd:documentation>

6851

</xsd:annotation>

6852

</xsd:attributeGroup>

6853

<xsd:attributeGroup ref="fromSet">

6854

<xsd:annotation>

6855

<xsd:documentation>

6856

<h:div class="specific">The set of ids in the base of the link. 2005-06-18: created</h:div>

6857

</xsd:documentation>

6858

</xsd:annotation>

6859

</xsd:attributeGroup>

6860

<xsd:attributeGroup ref="toSet">

6861

<xsd:annotation>

6862

<xsd:documentation>

6863

<h:div class="specific">The set of ids in the target of the link. 2005-06-18: created</h:div>

6864

</xsd:documentation>

6865

</xsd:annotation>

6866

</xsd:attributeGroup>

6867

<xsd:attributeGroup ref="fromContext">

6868

<xsd:annotation>

6869

<xsd:documentation>

6870

<h:div class="specific">The id of the ancestral element of objects referenced by 'from' attributes. Provides a context for uniquifying the references in the 'from' attributes. Thus atoms referenced by ids should be unique within a given molecule and the id of this could be the 'fromContext'. 2005-06-18: created</h:div>

6871

</xsd:documentation>

6872

</xsd:annotation>

6873

</xsd:attributeGroup>

6874

<xsd:attributeGroup ref="toContext">

6875

<xsd:annotation>

6876

<xsd:documentation>

6877

<h:div class="specific">The id of the ancestral element of objects referenced by 'to' attributes. Provides a context for uniquifying the references in the 'to' attributes. Thus atoms referenced by ids should be unique within a given molecule and the id of this could be the 'toContext'. 2005-06-18: created</h:div>

6878

</xsd:documentation>

6879

</xsd:annotation>

6880

</xsd:attributeGroup>

6881

<xsd:attributeGroup ref="role">

6882

<xsd:annotation>

6883

<xsd:documentation>

6884

<h:div class="specific">The role of the link. Xlink adds semantics through a

6885

URI; we shall not be this strict. We shall not normally use this mechanism

6886

and use dictionaries instead.</h:div>

6887

</xsd:documentation>

6888

</xsd:annotation>

6889

</xsd:attributeGroup>

6890

<xsd:attributeGroup ref="href">

6891

<xsd:annotation>

6892

<xsd:documentation>

6893

<h:div class="specific">The target of the (locator) link, outside the document.</h:div>

6894

</xsd:documentation>

6895

</xsd:annotation>

6896

</xsd:attributeGroup>

6897

<xsd:attributeGroup ref="linkType"/>

6898

</xsd:complexType>

6899

</xsd:element><xsd:element name="list" id="el.list">

6900

<xsd:annotation>

6901

<xsd:documentation>

6902

<h:div class="summary">A generic container with no implied semantics.</h:div>

6903

<h:div class="description">A generic container with no implied semantics. It just contains things and can have attributes which bind conventions to it. It could often act as the root element in an STM document.</h:div>

6904

<h:div class="example" href="list1.xml"/>

6905

</xsd:documentation>

6906

</xsd:annotation>

6907

<xsd:complexType>

6908

<xsd:sequence>

6909

<xsd:any minOccurs="0" maxOccurs="unbounded" processContents="lax"/>

6910

</xsd:sequence>

6911

<xsd:attributeGroup ref="title"/>

6912

<xsd:attributeGroup ref="id"/>

6913

<xsd:attributeGroup ref="convention"/>

6914

<xsd:attributeGroup ref="dictRef"/>

6915

<xsd:attributeGroup ref="type"/>

6916

</xsd:complexType>

6917

</xsd:element><xsd:element name="map" id="el.map">

6918

<xsd:annotation>

6919

<xsd:documentation>

6920

<h:div class="summary">A container for links</h:div>

6921

<h:div class="description"><h:p>Usage is now standardized with map as the container and link as the individual links. The links are often effectively typed pointers to other parts of the document. The type can be set for all links by the 'fromType' and 'toType' attributes, either in the map, which then applied to all links by default, or in individual links, when it overrides the map setting. Since ids may not be unique within a document the refs can be given context with the 'fromRef' and 'toRef' attributes in the map element. If more than one context is used it may be better to use multiple maps. The role of map, and its relationship to RDF is still being developed.

6922

</h:p>

6923

<h:p>

6924

Currently (2005) map has primarily been used to map atoms between reactants and products, but we also expect shortly to extend it to peak assignments and several otherr areas. A map consists of a number of links, which can be directional, relating two elements through their ids. Reference is through the mandatory 'to' and 'from' attributes which must point to existing id attributes on elements. The type of the dereferenced element can be specified in 'toType' and 'fromType' which, while redundant, is an aid to software and acts as a check on referential type integrity.

6925

</h:p>

6926

<h:p>

6927

In principle any element can be linked to any other, with 1:1, 1:n, and n:m topology. We expect maps to be used for precise chemical concepts such as reactions, peak assignments, electron management, molecular superpositions, etc. and that these are supported by bespoke code. For other links, especially with complex topology, users should consider whether RDF may be more appropriate.

6928

</h:p>

6929

<h:p>In some cases partial mapping is known (e.g. one set of atoms maps to another set), but the precise links are unknown. (This is not the same as n:m mapping where n*m precise links would be expected). In some cases there may be objects such as atomSets or peakGroups which could be linked to support this. Alternatively the 'fromSet' and 'toSet' attributes can be used to hold a list of ids. Thus from='a1 a2' to='b3 b4' might imply that there were two precise links (either {a1=>b3, a2=>b4} or {a1=>b4, a2=>b3}). This is most likely to be used in intermediate documents where more precise semantics can be added later. The ids must all refer to elements of the same type. Note that a 'to' link referencing a single atomSet (toType='atomSet') is not the same as a 'toSet' of toType='atom' with multiple atomIds. The first would require an 'atomSet' element in the document; the second would not. The precise semantics such as the order of ids are application-dependent. If the order is known in both the toSet and fromSet then individual links should be used rather than adding the burden of deconstruction on the implementer.

6930

</h:p>

6931

</h:div>

6932

<h:div class="curation">2005-06-18: added typing and role and updated docs.</h:div>

6933

</xsd:documentation>

6934

</xsd:annotation>

6935

<xsd:complexType>

6936

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

6937

<xsd:element ref="link"/>

6938

</xsd:sequence>

6939

<xsd:attributeGroup ref="title"/>

6940

<xsd:attributeGroup ref="id"/>

6941

<xsd:attributeGroup ref="convention"/>

6942

<xsd:attributeGroup ref="dictRef"/>

6943

<xsd:attributeGroup ref="fromType">

6944

<xsd:annotation>

6945

<xsd:documentation>

6946

6947

</xsd:documentation>

6948

</xsd:annotation>

6949

</xsd:attributeGroup>

6950

<xsd:attributeGroup ref="toType">

6951

<xsd:annotation>

6952

<xsd:documentation>

6953

6954

</xsd:documentation>

6955

</xsd:annotation>

6956

</xsd:attributeGroup>

6957

<xsd:attributeGroup ref="fromContext">

6958

<xsd:annotation>

6959

<xsd:documentation>

6960

6961

</xsd:documentation>

6962

</xsd:annotation>

6963

</xsd:attributeGroup>

6964

<xsd:attributeGroup ref="toContext">

6965

<xsd:annotation>

6966

<xsd:documentation>

6967

6968

</xsd:documentation>

6969

</xsd:annotation>

6970

</xsd:attributeGroup>

6971

<xsd:attributeGroup ref="role">

6972

<xsd:annotation>

6973

<xsd:documentation>

6974

<h:div class="specific">The role of the map. Semantics are undefined, and can be used to provide a small semi-controlled vocabulary for identifying maps of different types. 2005-06-18: created</h:div>

6975

</xsd:documentation>

6976

</xsd:annotation>

6977

</xsd:attributeGroup>

6978

</xsd:complexType>

6979

</xsd:element><xsd:element name="matrix" id="el.matrix">

6980

<xsd:annotation>

6981

<xsd:documentation>

6982

<h:div class="summary">A rectangular matrix of any quantities.</h:div>

6983

<h:div class="description">

6984

<h:p>By default <h:tt>matrix</h:tt> represents

6985

a rectangular matrix of any quantities

6986

representable as XSD or STMML dataTypes. It consists of

6987

<h:tt>rows*columns</h:tt> elements, where <h:tt>columns</h:tt> is the

6988

fasting moving index. Assuming the elements are counted from 1 they are

6989

ordered <h:tt>V[1,1],V[1,2],...V[1,columns],V[2,1],V[2,2],...V[2,columns],

6990

...V[rows,1],V[rows,2],...V[rows,columns]</h:tt>

6991

</h:p>

6992

<h:p>By default whitespace is used to separate matrix elements; see

6993

<h:a href="el.array">array</h:a> for details. There are NO characters or markup

6994

delimiting the end of rows; authors must be careful!. The <h:tt>columns</h:tt>

6995

and <h:tt>rows</h:tt> attributes have no default values; a row vector requires

6996

a <h:tt>rows</h:tt> attribute of 1.</h:p>

6997

<h:p>

6998

<h:tt>matrix</h:tt> also supports many types of square matrix, but at present we

6999

require all elements to be given, even if the matrix is symmetric, antisymmetric

7000

or banded diagonal. The <h:tt>matrixType</h:tt> attribute allows software to

7001

validate and process the type of matrix.</h:p></h:div>

7002

<h:div class="example" href="matrix1.xml"/>

7003

</xsd:documentation>

7004

</xsd:annotation>

7005

7006

<xsd:complexType>

7007

<xsd:simpleContent>

7008

<xsd:extension base="xsd:string">

7009

<xsd:attributeGroup ref="dataType"/>

7010

<xsd:attributeGroup ref="delimiter"/>

7011

<xsd:attributeGroup ref="rows"/>

7012

<xsd:attributeGroup ref="columns"/>

7013

<xsd:attributeGroup ref="units"/>

7014

<xsd:attributeGroup ref="title"/>

7015

<xsd:attributeGroup ref="id"/>

7016

<xsd:attributeGroup ref="convention"/>

7017

<xsd:attributeGroup ref="dictRef"/>

7018

<xsd:attributeGroup ref="matrixType"/>

7019

<xsd:attributeGroup ref="errorValueArray"/>

7020

<xsd:attributeGroup ref="errorBasis"/>

7021

<xsd:attributeGroup ref="minValueArray"/>

7022

<xsd:attributeGroup ref="maxValueArray"/>

7023

7024

</xsd:extension>

7025

</xsd:simpleContent>

7026

</xsd:complexType>

7027

</xsd:element><xsd:element name="mechanism" id="el.mechanism">

7028

<xsd:annotation>

7029

<xsd:documentation>

7030

<h:div class="summary">The mechanism of a reaction.</h:div>

7031

<h:div class="description">

7032

<h:p>In some cases this may be a simple textual description or reference within a controlled vocabulary. In others it may describe the complete progress of the reaction, including topological or cartesian movement of atoms, bonds and electrons and annotation with varying quantities (e.g. energies). </h:p>

7033

<h:p>

7034

For named reaction mechanisms ("Diels-Alder", "ping-pong", "Claisen rearrangement", etc.) the <h:tt>name</h:tt> element should be used. For classification (e.g. "hydrolysis"), the <h:tt>label</h:tt> may be more appropriate.

7035

</h:p>

7036

<h:p>In more detailed cases the mechanism refers to components of the <h:tt>reaction</h:tt> element. Thus bond23 might be cleaved while bond19 is transformed (mapped) to bond99. The <h:tt>mechanismComponent</h:tt> can be used to refer to components and add annotation. This is still experimental.</h:p></h:div>

7037

<h:div class="description">

7038

<h:p>IUPAC Compendium of Chemical Terminology 2nd Edition (1997) describes a mechanism as:

7039

7040

<h:blockquote>A detailed description of the process leading from the reactants to the

7041

products of a reaction, including a characterization as complete as possible

7042

of the composition, structure, energy and other properties of reaction

7043

intermediates, products and transition states. An acceptable mechanism of

7044

a specified reaction (and there may be a number of such alternative mechanisms

7045

not excluded by the evidence) must be consistent with the reaction

7046

stoichiometry, the rate law and with all other available experimental data,

7047

such as the stereochemical course of the reaction. Inferences concerning

7048

the electronic motions which dynamically interconvert successive species

7049

along the reaction path (as represented by curved arrows, for example) are

7050

often included in the description of a mechanism.

7051

It should be noted that for many reactions all this information is not

7052

available and the suggested mechanism is based on incomplete experimental

7053

data. It is not appropriate to use the term mechanism to describe a

7054

statement of the probable sequence in a set of stepwise reactions. That

7055

should be referred to as a reaction sequence, and not a mechanism.</h:blockquote>

7056

</h:p>

7057

<h:p>CMLReact provides reactionScheme and annotions to describe the reaction sequence and both it and <h:tt>mechanism</h:tt> could co-occur within a reactionScheme container.</h:p></h:div>

7058

<h:div class="example" href="mechanism1.xml"/>

7059

</xsd:documentation>

7060

</xsd:annotation>

7061

7062

<xsd:complexType>

7063

<xsd:sequence>

7064

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

7065

<xsd:element ref="label" minOccurs="0" maxOccurs="unbounded"/>

7066

<xsd:element ref="description" minOccurs="0" maxOccurs="unbounded"/>

7067

<xsd:element ref="mechanismComponent" minOccurs="0" maxOccurs="unbounded"/>

7068

</xsd:sequence>

7069

<xsd:attributeGroup ref="title"/>

7070

<xsd:attributeGroup ref="id"/>

7071

<xsd:attributeGroup ref="convention"/>

7072

<xsd:attributeGroup ref="dictRef"/>

7073

</xsd:complexType>

7074

</xsd:element><xsd:element name="mechanismComponent" id="el.mechanismComponent">

7075

<xsd:annotation>

7076

<xsd:documentation>

7077

<h:div class="summary">An information component within a reaction mechanism.</h:div>

7078

<h:div class="description">

7079

<h:p>Information components can represent both physical constituents of the reaction or abstract concepts (types of bond cleavage, thermodynamics, etc.). There are several ways that components of the reaction can be annotated and/or quantified. One approach will be to refer to specific bonds and atoms through their ids and use mechanismComponent to describe their role, properties, etc. Another is to use mechanismComponent to identify types of bond formed/broken without reference to actual atoms and bonds (initially through the <h:tt>name</h:tt> element). Yet another will be to include information on the reaction profile.</h:p>

7080

<h:p> This is still experimental.</h:p></h:div>

7081

<h:div class="example" href="mechanismComponent1.xml"/>

7082

</xsd:documentation>

7083

</xsd:annotation>

7084

7085

<xsd:complexType>

7086

<xsd:sequence>

7087

<xsd:any processContents="lax" minOccurs="0" maxOccurs="unbounded"/>

7088

</xsd:sequence>

7089

<xsd:attributeGroup ref="title"/>

7090

<xsd:attributeGroup ref="id"/>

7091

<xsd:attributeGroup ref="convention"/>

7092

<xsd:attributeGroup ref="dictRef"/>

7093

</xsd:complexType>

7094

7095

</xsd:element><xsd:element name="metadata" id="el.metadata">

7096

<xsd:annotation>

7097

<xsd:documentation>

7098

<h:div class="summary">A general container for metadata.</h:div>

7099

<h:div class="description">

7100

<h:p>A general container for metadata, including at least

7101

Dublin Core (DC) and CML-specific metadata</h:p>

7102

<h:p>In its simple form each element provides a name and content in a similar

7103

fashion to the <h:tt>meta</h:tt> element in HTML. <h:tt>metadata</h:tt> may have simpleContent

7104

(i.e. a string for adding further information - this is not controlled).</h:p></h:div>

7105

<h:div class="example" href="metadata1.xml"/>

7106

</xsd:documentation>

7107

</xsd:annotation>

7108

<xsd:complexType>

7109

<xsd:simpleContent>

7110

<xsd:extension base="xsd:string">

7111

<xsd:attributeGroup ref="content"/>

7112

<xsd:attributeGroup ref="convention"/>

7113

<xsd:attributeGroup ref="dictRef"/>

7114

<xsd:attributeGroup ref="id"/>

7115

7116

<xsd:attributeGroup ref="metadataType"/>

7117

<xsd:attributeGroup ref="title"/>

7118

</xsd:extension>

7119

</xsd:simpleContent>

7120

</xsd:complexType>

7121

</xsd:element><xsd:element name="metadataList" id="el.metadataList">

7122

<xsd:annotation>

7123

<xsd:documentation>

7124

<h:div class="summary">A general container for metadata elements.</h:div>

7125

<h:div class="description">MetadataLists can have local roles (e.g. a bibliographic reference could be a single meteadatList with, say, 3-6 components). The role attribute is used in an uncontrolled manner for this. MetadataLists can also be nested, but metadata and metadataList children should not occur on the same level of the hierarchy.</h:div>

7126

<h:div class="example" href="metadata1.xml"/>

7127

</xsd:documentation>

7128

</xsd:annotation>

7129

7130

<xsd:complexType>

7131

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7132

<xsd:element ref="metadataList"/>

7133

<xsd:element ref="metadata"/>

7134

</xsd:choice>

7135

<xsd:attributeGroup ref="id"/>

7136

<xsd:attributeGroup ref="title"/>

7137

<xsd:attributeGroup ref="convention"/>

7138

<xsd:attributeGroup ref="dictRef"/>

7139

<xsd:attributeGroup ref="name"/>

7140

<xsd:attributeGroup ref="role"/>

7141

</xsd:complexType>

7142

</xsd:element><xsd:element name="module" id="el.module">

7143

<xsd:annotation>

7144

<xsd:documentation>

7145

<h:div class="summary">A module in a calculation.</h:div>

7146

<h:div class="description">

7147

<h:p>Many programs are based on discrete modules which produce chunks of output. There are also conceptual chunks such as initialisation, calculation and summary/final which often have finer submodules such as cycle, iteration, snapshot, etc. There is no controlled vocabulary but a typical structure is shown in the example. One of the challenges of CCML is to find communality between different programs and to use agreed abstractions for the modules.

7148

</h:p></h:div>

7149

<h:div class="example" href="module1.xml"/>

7150

</xsd:documentation>

7151

</xsd:annotation>

7152

7153

<xsd:complexType>

7154

<xsd:sequence>

7155

<xsd:any minOccurs="0" maxOccurs="unbounded" processContents="lax"/>

7156

</xsd:sequence>

7157

<xsd:attributeGroup ref="serial"/>

7158

<xsd:attributeGroup ref="title"/>

7159

<xsd:attributeGroup ref="id"/>

7160

<xsd:attributeGroup ref="convention"/>

7161

<xsd:attributeGroup ref="dictRef"/>

7162

<xsd:attributeGroup ref="role">

7163

<xsd:annotation>

7164

<xsd:documentation>

7165

<h:div class="specific">The module can have a program-specific name through its title or dictRef (e.g. "MINIM", "l201") and a generic role ("dynamicsCalculation", "equilibration", etc.). In general role will be controlled by CCML.</h:div>

7166

</xsd:documentation>

7167

</xsd:annotation>

7168

</xsd:attributeGroup>

7169

</xsd:complexType>

7170

</xsd:element><xsd:element name="molecule" id="el.molecule">

7171

<xsd:annotation>

7172

<xsd:documentation>

7173

<h:div class="summary">A container for atoms, bonds and submolecules.</h:div>

7174

<h:div class="description">

7175

<h:p>

7176

<h:tt>molecule</h:tt> is a container for atoms, bonds and submolecules along

7177

with properties such as crystal and non-builtin properties. It should either

7178

contain <h:tt>molecule</h:tt> or *Array for atoms and bonds. A molecule

7179

can be empty (e.g. we just know its name, id, etc.)</h:p>

7180

<h:p>"Molecule" need not represent a chemically meaningful molecule. It

7181

can contain atoms with bonds (as in the solid-sate) and it could

7182

simply carry a name (e.g. "taxol") without formal representation

7183

of the structure. It can contain "sub molecules", which are often

7184

discrete subcomponents (e.g. guest-host).</h:p>

7185

<h:p>Molecule can contain a <list> element to contain data

7186

related to the molecule.

7187

Within this can be string/float/integer and other nested lists</h:p></h:div>

7188

<h:div class="example" href="molecule1.xml"/>

7189

</xsd:documentation>

7190

<xsd:documentation>

7191

<h:div class="curation">Revised content model to allow any order of lengths, angles, torsions 2003-01-01..</h:div>

7192

</xsd:documentation>

7193

<xsd:documentation>

7194

<h:div class="curation">Added role attribute 2003-03-19..</h:div>

7195

</xsd:documentation>

7196

</xsd:annotation>

7197

7198

7199

<xsd:complexType>

7200

<xsd:annotation>

7201

<xsd:documentation>

7202

<h:div class="summary">The float|integer|string children are for compatibility with CML-1 and are deprecated. scalar|array|matrix should be used instead.</h:div>

7203

</xsd:documentation>

7204

</xsd:annotation>

7205

7206

<xsd:sequence>

7207

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

7208

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7209

<xsd:element ref="formula"/>

7210

<xsd:element ref="name"/>

7211

<xsd:element ref="label"/>

7212

<xsd:element ref="identifier"/>

7213

<xsd:element ref="symmetry"/>

7214

</xsd:choice>

7215

<xsd:element ref="crystal" minOccurs="0"/>

7216

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7217

<xsd:element ref="molecule" minOccurs="0" maxOccurs="unbounded"/>

7218

<xsd:sequence>

7219

<xsd:element ref="atomArray"/>

7220

<xsd:element ref="bondArray" minOccurs="0"/>

7221

<xsd:element ref="electron" minOccurs="0" maxOccurs="unbounded"/>

7222

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7223

<xsd:element ref="zMatrix"/>

7224

<xsd:element ref="length"/>

7225

<xsd:element ref="angle"/>

7226

<xsd:element ref="torsion"/>

7227

</xsd:choice>

7228

</xsd:sequence>

7229

</xsd:choice>

7230

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7231

<xsd:element ref="scalar"/>

7232

<xsd:element ref="array"/>

7233

<xsd:element ref="matrix"/>

7234

<xsd:element ref="list"/>

7235

<xsd:element ref="propertyList"/>

7236

</xsd:choice>

7237

</xsd:sequence>

7238

7239

<xsd:attributeGroup ref="dictRef"/>

7240

<xsd:attributeGroup ref="convention"/>

7241

<xsd:attributeGroup ref="title"/>

7242

<xsd:attributeGroup ref="id"/>

7243

<xsd:attributeGroup ref="ref"/>

7244

<xsd:attributeGroup ref="formula"/>

7245

<xsd:attributeGroup ref="count"/>

7246

<xsd:attributeGroup ref="chirality"/>

7247

<xsd:attributeGroup ref="formalCharge"/>

7248

<xsd:attributeGroup ref="spinMultiplicity"/>

7249

<xsd:attributeGroup ref="symmetryOriented"/>

7250

<xsd:attributeGroup ref="role">

7251

<xsd:annotation>

7252

<xsd:documentation>

7253

<h:div class="specific">

7254

<h:p>No formal semantics (yet). The role describes the purpose of the molecule element at this stage in the information. Examples can be "conformation", "dynamicsStep", "vibration", "valenceBondIsomer", etc. This attribute may be used by applications to determine how to present a set of molecule elements.</h:p></h:div>

7255

</xsd:documentation>

7256

</xsd:annotation>

7257

</xsd:attributeGroup>

7258

</xsd:complexType>

7259

</xsd:element><xsd:element name="name" id="el.name">

7260

<xsd:annotation>

7261

<xsd:documentation>

7262

<h:div class="summary">A string identifying a object.</h:div>

7263

<h:div class="description">

7264

<h:tt>name</h:tt> is used for chemical names (formal and trivial) for molecules and also for identifiers such as CAS registry and RTECS. It can also be used for labelling atoms. It should be used in preference to the <h:tt>title</h:tt> attribute because it is repeatable and can be linked to a dictionary.

7265

<h:p>Constraining patterns can be described in the dictionary and used to validate <h:tt>name</h:tt>s.</h:p></h:div>

7266

<h:div class="example" href="name1.xml"/>

7267

</xsd:documentation>

7268

</xsd:annotation>

7269

<xsd:complexType>

7270

<xsd:simpleContent>

7271

<xsd:extension base="xsd:string">

7272

<xsd:attributeGroup ref="id"/>

7273

<xsd:attributeGroup ref="convention"/>

7274

<xsd:attributeGroup ref="dictRef"/>

7275

</xsd:extension>

7276

</xsd:simpleContent>

7277

</xsd:complexType>

7278

</xsd:element><xsd:element name="object" id="el.object">

7279

<xsd:annotation>

7280

<xsd:documentation>

7281

<h:div class="summary">An object which might occur in scientific data or narrative.</h:div>

7282

<h:div class="description">Deliberately vague. Thus an instrument might be built from sub component objects, or a program could be composed of smaller modules (objects). <h:tt>object</h:tt> could be used to encapsulate graphical primitives (e.g. in reaction schemes, drawings of apparatus, etc.). Unrestricted content model.</h:div>

7283

<h:div class="example" href="object1.xml"/>

7284

</xsd:documentation>

7285

</xsd:annotation>

7286

<xsd:complexType mixed="true">

7287

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

7288

<xsd:any processContents="lax"/>

7289

</xsd:sequence>

7290

<xsd:attributeGroup ref="title"/>

7291

<xsd:attributeGroup ref="id"/>

7292

<xsd:attributeGroup ref="convention"/>

7293

<xsd:attributeGroup ref="dictRef"/>

7294

<xsd:attributeGroup ref="name"/>

7295

<xsd:attributeGroup ref="type"/>

7296

<xsd:attributeGroup ref="count"/>

7297

</xsd:complexType>

7298

7299

</xsd:element><xsd:element name="observation" id="el.observation">

7300

<xsd:annotation>

7301

<xsd:documentation>

7302

<h:div class="summary">An observation or occurrence.</h:div>

7303

<h:div class="description">A container for any events that need to be recorded, whether planned or not. They can include notes, measurements, conditions that may be referenced elsewhere, etc. There are no controlled semantics.</h:div>

7304

<h:div class="example" href="observation1.xml"/>

7305

</xsd:documentation>

7306

</xsd:annotation>

7307

<xsd:complexType mixed="true">

7308

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

7309

<xsd:any processContents="lax"/>

7310

</xsd:sequence>

7311

<xsd:attributeGroup ref="title"/>

7312

<xsd:attributeGroup ref="id"/>

7313

<xsd:attributeGroup ref="convention"/>

7314

<xsd:attributeGroup ref="dictRef"/>

7315

<xsd:attributeGroup ref="type"/>

7316

<xsd:attributeGroup ref="count"/>

7317

</xsd:complexType>

7318

7319

</xsd:element><xsd:element name="operator" id="el.operator">

7320

<xsd:annotation>

7321

<xsd:documentation>

7322

<h:div class="summary">An operator within an expression.</h:div>

7323

<h:div class="description">Experimental. An operator acts on one or more arguments (at present the number is fixed by the type). The formulation is reverse Polish so the result (with its dataType) is put on a stack for further use.</h:div>

7324

<h:div class="example" href="potential1.xml"/>

7325

</xsd:documentation>

7326

</xsd:annotation>

7327

7328

<xsd:complexType>

7329

<xsd:sequence>

7330

<xsd:choice minOccurs="0" maxOccurs="unbounded"/>

7331

</xsd:sequence>

7332

<xsd:attributeGroup ref="title"/>

7333

<xsd:attributeGroup ref="id"/>

7334

<xsd:attributeGroup ref="convention"/>

7335

<xsd:attributeGroup ref="dictRef"/>

7336

<xsd:attributeGroup ref="type"/>

7337

</xsd:complexType>

7338

</xsd:element><xsd:element name="parameter" id="el.parameter">

7339

<xsd:annotation>

7340

<xsd:documentation>

7341

<h:div class="summary">A parameter describing the computation.</h:div>

7342

<h:div class="description">

7343

<h:p>A parameter is a broad concept and can describe numeric quantities, objects,

7344

keywords, etc. The distinction between keywords and parameters is often fuzzy.

7345

("MINIM" might mean "minimize", while "MINIM=3" might require three iterations

7346

to be run. It may help to think of control keywords as boolean parameters. </h:p>

7347

<h:p>Numeric parameters can describe values in molecules, forcefields or other

7348

objects. Often the parameters will be refined or otherwise varied during the

7349

calculation. Some parameters may be fixed at particular values or relaxed at different

7350

stages in the calculation. Parameters can have errors, gradients and other indications

7351

of uncertainty.</h:p>

7352

<h:p>String/character parameters are often abbreviated in program input, and this

7353

is supported through the <h:tt>regex</h:tt> and <h:tt>ignoreCase</h:tt> attributes. ?????</h:p>

7354

<h:p>Parameters will usually be defined separately from the objects and use the

7355

<h:tt>ref</h:tt> attribute to reference them.</h:p>

7356

<h:p>Parameters can be used to describe additional constraints. This will probably

7357

require the development of a microlanguage and until then may use program-specific

7358

mechanisms. A common approach will be to use an array of values (or objects) to

7359

represent different input values for (parts of) the calculation. Thus a conformational

7360

change could be specified by an array of several torsion angles.</h:p>

7361

<h:p>A parameter will frequently have a <h:tt>dictRef</h:tt> pointing to a dictionary

7362

which may have more information about how the parameter is to be used or the values

7363

it can take. </h:p>

7364

<h:p>The allowable content of <h:tt>parameter</h:tt>s may be shown by a "template"

7365

in the <h:tt>appinfo</h:tt>; this is stil experimental.</h:p></h:div>

7366

<h:div class="example" href="parameter1.xml"/>

7367

</xsd:documentation>

7368

</xsd:annotation>

7369

7370

<xsd:complexType>

7371

<xsd:sequence>

7372

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7373

<xsd:element ref="scalar"/>

7374

<xsd:element ref="array"/>

7375

<xsd:element ref="matrix"/>

7376

<xsd:element ref="property"/>

7377

<xsd:element ref="expression"/>

7378

</xsd:choice>

7379

<xsd:choice minOccurs="0" maxOccurs="1">

7380

<xsd:element ref="gradient"/>

7381

</xsd:choice>

7382

</xsd:sequence>

7383

7384

<xsd:attributeGroup ref="ref"/>

7385

7386

<xsd:attributeGroup ref="title"/>

7387

<xsd:attributeGroup ref="id"/>

7388

<xsd:attributeGroup ref="convention"/>

7389

<xsd:attributeGroup ref="dictRef"/>

7390

<xsd:attributeGroup ref="value">

7391

<xsd:annotation>

7392

<xsd:documentation>

7393

<h:div class="specific">This is a shorthand for a single scalar value of the

7394

parameter. It should only be used with the <h:tt>ref</h:tt> attribute as it inherits all the dataTyping of the referenced element. It must not be used for defining new parameters as it has no mechanism for units and dataTyping. [This may change?].</h:div>

7395

</xsd:documentation>

7396

</xsd:annotation>

7397

</xsd:attributeGroup>

7398

7399

<xsd:attributeGroup ref="constraint"/>

7400

<xsd:attributeGroup ref="name"/>

7401

7402

<xsd:attributeGroup ref="role">

7403

<xsd:annotation>

7404

<xsd:documentation>

7405

<h:div class="specific">

7406

<h:p>Used to define concepts such as independent and dependent

7407

variables</h:p></h:div>

7408

</xsd:documentation>

7409

</xsd:annotation>

7410

</xsd:attributeGroup>

7411

7412

</xsd:complexType>

7413

</xsd:element><xsd:element name="parameterList" id="el.parameterList">

7414

<xsd:annotation>

7415

<xsd:documentation>

7416

<h:div class="summary">A container for one or more parameters.</h:div>

7417

<h:div class="description">parameterList can contain several parameters.</h:div>

7418

<h:div class="example" href="parameterList1.xml"/>

7419

</xsd:documentation>

7420

</xsd:annotation>

7421

7422

<xsd:complexType>

7423

<xsd:sequence>

7424

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

7425

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

7426

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7427

<xsd:element ref="parameter"/>

7428

<xsd:element ref="parameterList"/>

7429

<xsd:any processContents="lax" minOccurs="0" maxOccurs="unbounded"/>

7430

</xsd:choice>

7431

</xsd:sequence>

7432

<xsd:attributeGroup ref="dictRef"/>

7433

<xsd:attributeGroup ref="convention"/>

7434

<xsd:attributeGroup ref="title"/>

7435

<xsd:attributeGroup ref="id"/>

7436

<xsd:attributeGroup ref="ref"/>

7437

<xsd:attributeGroup ref="role"/>

7438

</xsd:complexType>

7439

</xsd:element><xsd:element name="particle" id="el.particle">

7440

<xsd:annotation>

7441

<xsd:documentation>

7442

<h:div class="summary">An object in space carrying a set of properties.</h:div>

7443

<h:div class="description">

7444

<h:tt>particles</h:tt> have many of the characteristics of <h:tt>atom</h:tt>s

7445

but without an atomic nucleus. It does not have an elementType and cannot be

7446

involved in bonding, etc. It has coordinates, may carry charge and might have a

7447

mass. It represents some aspect of a computational model and should not be used

7448

for purely geometrical concepts such as centroid. Examples of particles are

7449

"shells" (e.g. in GULP) which are linked to atoms for modelling polarizability

7450

or lonepairs and approximations to multipoles. Properties such as charge, mass

7451

should be scalar/array/matrix children.</h:div>

7452

<!--

7453

<h:div class="example" href="particle1.xml"></h:div>

7454

-->

7455

</xsd:documentation>

7456

</xsd:annotation>

7457

7458

<xsd:complexType>

7459

<xsd:sequence>

7460

<xsd:any minOccurs="0" maxOccurs="unbounded" processContents="lax"/>

7461

</xsd:sequence>

7462

<xsd:attributeGroup ref="title"/>

7463

<xsd:attributeGroup ref="id"/>

7464

<xsd:attributeGroup ref="convention"/>

7465

<xsd:attributeGroup ref="dictRef"/>

7466

<xsd:attributeGroup ref="type">

7467

<xsd:annotation>

7468

<xsd:documentation>

7469

<h:div class="specific">Used in a similar manner to <h:tt>atomType</h:tt>. Examples

7470

might be "lonePair", "polarizable Oxygen", etc.</h:div>

7471

</xsd:documentation>

7472

</xsd:annotation>

7473

</xsd:attributeGroup>

7474

<xsd:attributeGroup ref="x3"/>

7475

<xsd:attributeGroup ref="y3"/>

7476

<xsd:attributeGroup ref="z3"/>

7477

</xsd:complexType>

7478

</xsd:element><xsd:element name="peak" id="el.peak">

7479

<xsd:annotation>

7480

<xsd:documentation>

7481

<h:div class="summary">A peak; annotated by human or machine.</h:div>

7482

<h:div class="description">

7483

<h:p>A <h:tt>peak</h:tt> can describe:

7484

<h:ul>

7485

<h:li>A single point in a spectrum. Usually a maximum but could be a shoulder, inflexion or indeed any point of interest.</h:li>

7486

<h:li>A continuous range of values within a spectrum, defined by maximum and minimum values on either/both axes</h:li>

7487

</h:ul>

7488

</h:p>

7489

The finer structure of the peak can be given with one or more peakStructure

7490

children</h:div>

7491

<h:div class="description">The units should always be given. (The raw spectral data may unfortunately use different units and no assumptions should be made).</h:div>

7492

<h:div class="description">The content model includes atom, bond, molecule, but these

7493

are deprecated and should be replaced by atomRefs, etc.</h:div>

7494

<h:div class="curation">2005-11-22: PMR. Added moleculeRefs</h:div>

7495

<h:div class="example" href="peak1.xml"/>

7496

</xsd:documentation>

7497

</xsd:annotation>

7498

7499

7500

<xsd:complexType>

7501

<xsd:sequence>

7502

<xsd:element ref="metadataList" minOccurs="0">

7503

<xsd:annotation>

7504

<xsd:documentation>

7505

<h:div class="summary">Allows <h:i>inter alia</h:i> the provenance of the peak assignment to be recorde.</h:div>

7506

</xsd:documentation>

7507

</xsd:annotation>

7508

</xsd:element>

7509

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7510

<xsd:element ref="atom">

7511

<xsd:annotation>

7512

<xsd:documentation>

7513

<h:div class="curation">2005-11-9. DEPRECATED; use atomRefs</h:div>

7514

</xsd:documentation>

7515

</xsd:annotation>

7516

</xsd:element>

7517

<xsd:element ref="bond">

7518

<xsd:annotation>

7519

<xsd:documentation>

7520

<h:div class="curation">2005-11-9. DEPRECATED; use bondRefs</h:div>

7521

</xsd:documentation>

7522

</xsd:annotation>

7523

</xsd:element>

7524

<xsd:element ref="molecule">

7525

<xsd:annotation>

7526

<xsd:documentation>

7527

<h:div class="curation">2005-11-9. DEPRECATED; use moleculeRefs

7528

when developed</h:div>

7529

</xsd:documentation>

7530

</xsd:annotation>

7531

</xsd:element>

7532

<xsd:element ref="peakStructure">

7533

<xsd:annotation>

7534

<xsd:documentation>

7535

<h:div class="curation">2005-11-9. PMR, added</h:div>

7536

</xsd:documentation>

7537

</xsd:annotation>

7538

</xsd:element>

7539

</xsd:choice>

7540

</xsd:sequence>

7541

7542

<xsd:attributeGroup ref="dictRef"/>

7543

<xsd:attributeGroup ref="convention"/>

7544

<xsd:attributeGroup ref="title"/>

7545

<xsd:attributeGroup ref="id"/>

7546

<xsd:attributeGroup ref="ref"/>

7547

7548

<xsd:attributeGroup ref="peakHeight"/>

7549

<xsd:attributeGroup ref="peakMultiplicity"/>

7550

<xsd:attributeGroup ref="peakShape"/>

7551

<xsd:attributeGroup ref="integral"/>

7552

<xsd:attributeGroup ref="peakUnits"/>

7553

7554

<xsd:attributeGroup ref="xMin"/>

7555

<xsd:attributeGroup ref="xMax"/>

7556

<xsd:attributeGroup ref="xValue"/>

7557

<xsd:attributeGroup ref="xWidth"/>

7558

<xsd:attributeGroup ref="xUnits"/>

7559

7560

<xsd:attributeGroup ref="yMin"/>

7561

<xsd:attributeGroup ref="yMax"/>

7562

<xsd:attributeGroup ref="yValue"/>

7563

<xsd:attributeGroup ref="yWidth"/>

7564

<xsd:attributeGroup ref="yUnits"/>

7565

7566

<xsd:attributeGroup ref="atomRefs">

7567

<xsd:annotation>

7568

<xsd:documentation>

7569

<h:div class="summary">Atoms contributing to this peak</h:div>

7570

<h:div class="description">The primary set of atoms responsible for

7571

the peak such as an NMR peak. Coupling constants and similar splitting

7572

should not use this but peakStructure. At present there is no substructure to this

7573

attribute or concept and only one attribute is allowed. It may be

7574

combined with bondRefs. Even single atoms should use atomRefs, not atomRef.

7575

</h:div>

7576

</xsd:documentation>

7577

</xsd:annotation>

7578

</xsd:attributeGroup>

7579

<xsd:attributeGroup ref="bondRefs">

7580

<xsd:annotation>

7581

<xsd:documentation>

7582

<h:div class="summary">Bonds contributing to this peak</h:div>

7583

<h:div class="description">The primary set of bonds responsible for

7584

the peak such as an IR frequency. At present there is no substructure to this

7585

attribute or concept and only one attribute is allowed. It may be

7586

combined with atomRefs.</h:div>

7587

</xsd:documentation>

7588

</xsd:annotation>

7589

</xsd:attributeGroup>

7590

<xsd:attributeGroup ref="moleculeRefs">

7591

<xsd:annotation>

7592

<xsd:documentation>

7593

<h:div class="summary">Molecule(s) contributing to this peak</h:div>

7594

<h:div class="description">The molecule or molecule responsible for

7595

the peak. At present there is no substructure to this

7596

attribute or concept and only one attribute is allowed. This might, for example,

7597

be used to manage a mass spectrum or chromatogram</h:div>

7598

</xsd:documentation>

7599

</xsd:annotation>

7600

</xsd:attributeGroup>

7601

7602

7603

</xsd:complexType>

7604

</xsd:element><xsd:element name="peakGroup" id="el.peakGroup">

7605

<xsd:annotation>

7606

<xsd:documentation>

7607

<h:div class="summary">A list of closely related peaks or peakGroups.</h:div>

7608

<h:div class="description">Distinguish between <h:tt>peakList</h:tt> (primarily a navigational container) and <h:tt>peakGroup</h:tt> where the peaks (or groups) have some close relation not shared by all peaks. All descendants must use consistent units.</h:div>

7609

<h:div class="curation">2005-11-22. added atomRefs, bondRefs and moleculeRefs and deprecated

7610

atom, bond, molecule children</h:div>

7611

<h:div class="example" href="peakGroup1.xml"/>

7612

</xsd:documentation>

7613

</xsd:annotation>

7614

7615

<xsd:complexType>

7616

<xsd:sequence>

7617

<xsd:element ref="metadataList" minOccurs="0">

7618

<xsd:annotation>

7619

<xsd:documentation>

7620

<h:div class="summary">Allows <h:i>inter alia</h:i> the provenance of the peak assignment to be recorde.</h:div>

7621

</xsd:documentation>

7622

</xsd:annotation>

7623

</xsd:element>

7624

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7625

<xsd:element ref="peak"/>

7626

<xsd:element ref="peakGroup"/>

7627

<xsd:element ref="atom">

7628

<xsd:annotation>

7629

<xsd:documentation>

7630

<h:div class="curation">2005-11-22. DEPRECATED; use atomRefs</h:div>

7631

</xsd:documentation>

7632

</xsd:annotation>

7633

</xsd:element>

7634

<xsd:element ref="bond">

7635

<xsd:annotation>

7636

<xsd:documentation>

7637

<h:div class="curation">2005-11-22. DEPRECATED; use bondRefs</h:div>

7638

</xsd:documentation>

7639

</xsd:annotation>

7640

</xsd:element>

7641

<xsd:element ref="molecule">

7642

<xsd:annotation>

7643

<xsd:documentation>

7644

<h:div class="curation">2005-11-22. DEPRECATED; use moleculeRefs</h:div>

7645

</xsd:documentation>

7646

</xsd:annotation>

7647

</xsd:element>

7648

</xsd:choice>

7649

</xsd:sequence>

7650

<xsd:attributeGroup ref="dictRef"/>

7651

<xsd:attributeGroup ref="convention"/>

7652

<xsd:attributeGroup ref="title"/>

7653

<xsd:attributeGroup ref="id"/>

7654

<xsd:attributeGroup ref="ref"/>

7655

7656

<xsd:attributeGroup ref="peakHeight"/>

7657

<xsd:attributeGroup ref="peakMultiplicity"/>

7658

<xsd:attributeGroup ref="peakShape"/>

7659

<xsd:attributeGroup ref="integral"/>

7660

<xsd:attributeGroup ref="peakUnits"/>

7661

7662

<xsd:attributeGroup ref="xMin"/>

7663

<xsd:attributeGroup ref="xMax"/>

7664

<xsd:attributeGroup ref="xValue"/>

7665

<xsd:attributeGroup ref="xWidth"/>

7666

<xsd:attributeGroup ref="xUnits"/>

7667

7668

<xsd:attributeGroup ref="yMin"/>

7669

<xsd:attributeGroup ref="yMax"/>

7670

<xsd:attributeGroup ref="yValue"/>

7671

<xsd:attributeGroup ref="yWidth"/>

7672

<xsd:attributeGroup ref="yUnits"/>

7673

7674

<xsd:attributeGroup ref="atomRefs">

7675

<xsd:annotation>

7676

<xsd:documentation>

7677

<h:div class="summary">Atoms contributing to this peak</h:div>

7678

<h:div class="description">The primary set of atoms responsible for

7679

the peak such as an NMR peak. Coupling constants and similar splitting

7680

should not use this but peakStructure. At present there is no substructure to this

7681

attribute or concept and only one attribute is allowed. It may be

7682

combined with bondRefs. Even single atoms should use atomRefs, not atomRef.

7683

</h:div>

7684

</xsd:documentation>

7685

</xsd:annotation>

7686

</xsd:attributeGroup>

7687

<xsd:attributeGroup ref="bondRefs">

7688

<xsd:annotation>

7689

<xsd:documentation>

7690

<h:div class="summary">Bonds contributing to this peak</h:div>

7691

<h:div class="description">The primary set of bonds responsible for

7692

the peak such as an IR frequency. At present there is no substructure to this

7693

attribute or concept and only one attribute is allowed. It may be

7694

combined with atomRefs.</h:div>

7695

</xsd:documentation>

7696

</xsd:annotation>

7697

</xsd:attributeGroup>

7698

<xsd:attributeGroup ref="moleculeRefs">

7699

<xsd:annotation>

7700

<xsd:documentation>

7701

<h:div class="summary">Molecule(s) contributing to this peak</h:div>

7702

<h:div class="description">The molecule or molecule responsible for

7703

the peak. At present there is no substructure to this

7704

attribute or concept and only one attribute is allowed. This might, for example,

7705

be used to manage a mass spectrum or chromatogram</h:div>

7706

</xsd:documentation>

7707

</xsd:annotation>

7708

</xsd:attributeGroup>

7709

7710

</xsd:complexType>

7711

</xsd:element><xsd:element name="peakList" id="el.peakList">

7712

<xsd:annotation>

7713

<xsd:documentation>

7714

<h:div class="summary">A list of peaks or peakGroups.</h:div>

7715

7716

<h:div class="example" href="peakList1.xml"/>

7717

</xsd:documentation>

7718

</xsd:annotation>

7719

7720

<xsd:complexType>

7721

<xsd:sequence>

7722

<xsd:element ref="metadataList" minOccurs="0">

7723

<xsd:annotation>

7724

<xsd:documentation>

7725

<h:div class="summary">Allows <h:i>inter alia</h:i> the provenance of the peak assignment to be recorde.</h:div>

7726

</xsd:documentation>

7727

</xsd:annotation>

7728

</xsd:element>

7729

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7730

<xsd:element ref="peak"/>

7731

<xsd:element ref="peakGroup"/>

7732

</xsd:choice>

7733

</xsd:sequence>

7734

<xsd:attributeGroup ref="dictRef"/>

7735

<xsd:attributeGroup ref="convention"/>

7736

<xsd:attributeGroup ref="title"/>

7737

<xsd:attributeGroup ref="id"/>

7738

<xsd:attributeGroup ref="ref"/>

7739

</xsd:complexType>

7740

</xsd:element><xsd:element name="peakStructure" id="el.peakStructure">

7741

<xsd:annotation>

7742

<xsd:documentation>

7743

<h:div class="summary">The structure of a peak.</h:div>

7744

<h:div class="description">Primarily to record couplings and other fine

7745

structure. At present we have tested this on HNMR spectra, C13 NMR and

7746

simple IR. We believe that other types of spectroscopy (ESR, NQR, etc) can be

7747

represented to some extent, but there may be systems beyond the current

7748

expressive power.</h:div>

7749

<h:div>For molecules without symmetry we believe that most of the important

7750

types of NMR coupling can be represented. Thus an atom which gives rise to

7751

two couplings can have two child PeakStructures, and this is shown

7752

in example1.

7753

<h:pre>

7754

7755

7756

7757

7758

7759

7760

</atom>

7761

7762

7763

</atom>

7764

7765

7766

</atom>

7767

7768

7769

</atom>

7770

</atomArray>

7771

</molecule>

7772

7773

7774

<peak id="p1" title="Ha" atomRefs="a1"

7775

peakShape="sharp" xUnits="unit:ppm" xValue="6.0">

7776

<peakStructure type="coupling" peakMultiplicity="doublet11"

7777

value="12" units="unit:hertz" atomRefs="a2"/>

7778

</peak>

7779

<peak id="p2" title="Hb" atomRefs="a2"

7780

peakShape="sharp" xUnits="unit:ppm" xValue="7.0">

7781

<peakStructure type="coupling" peakMultiplicity="doublet11"

7782

value="12" units="unit:hertz" atomRefs="a1"/>

7783

<peakStructure type="coupling" peakMultiplicity="triplet121"

7784

value="15" units="unit:hertz" atomRefs="a3 a4"/>

7785

</peak>

7786

<peak id="p3" title="Hc" atomRefs="a3 a4"

7787

peakShape="sharp" xUnits="unit:ppm" xValue="8.0">

7788

<peakStructure type="coupling" peakMultiplicity="doublet11"

7789

value="15" units="unit:hertz" atomRefs="a2"/>

7790

</peak>

7791

</peakList>

7792

</spectrum>

7793

</cml>

7794

</h:pre>

7795

Where a peak is due to symmetry-related atoms there are

7796

different couplings to symmetrical atoms. Thus in an AA'BB' system there

7797

can be two couplings to the A atoms and we need nested peakStructures to

7798

represent these. In this case the order of the atoms in the peak@atomRefs

7799

maps to the order of the grandchildren. See example2.

7800

<h:pre>

7801

<!-- AA'BB' where there are 2 Ha and 2 Hb with two couplings

7802

J1 Ha ... Hb and Ha' ... Hb'

7803

J2 Ha ... Hb' and Ha' ... Hb

7804

-->

7805

7806

7807

7808

7809

</atom>

7810

7811

7812

</atom>

7813

7814

7815

</atom>

7816

7817

7818

</atom>

7819

</atomArray>

7820

</molecule>

7821

7822

7823

<!-- the ORDER of a1 and a2 is linked to the ORDER of the

7824

grandchildren elements, i.e. a1 couples to atoms in ps11 and ps21

7825

while a2 relates to atoms is ps21 and ps22

7826

-->

7827

<peak id="p1" title="Ha" atomRefs="a1, a2"

7828

peakShape="sharp" xUnits="unit:ppm" xValue="6.0">

7829

<peakStructure id="ps1" type="coupling" peakMultiplicity="doublet"

7830

value="10" units="unit:hertz">

7831

7832

7833

</peakStructure>

7834

<peakStructure id="ps2" type="coupling" peakMultiplicity="doublet"

7835

value="2" units="unit:hertz">

7836

7837

7838

</peakStructure>

7839

</peak>

7840

</peakList>

7841

</spectrum>

7842

</cml>

7843

</h:pre>

7844

</h:div>

7845

<h:div class="example" href="peakStructure1.xml"/>

7846

<h:div class="example" href="peakStructure2.xml"/>

7847

7848

</xsd:documentation>

7849

</xsd:annotation>

7850

7851

<xsd:complexType>

7852

<xsd:sequence>

7853

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded">

7854

<xsd:annotation>

7855

<xsd:documentation>

7856

<h:div class="summary">Allows <h:i>inter alia</h:i> the provenance of the peakStructure assignment to be recorded.</h:div>

7857

</xsd:documentation>

7858

</xsd:annotation>

7859

</xsd:element>

7860

<xsd:element ref="peakStructure" minOccurs="0" maxOccurs="unbounded">

7861

<xsd:annotation>

7862

<xsd:documentation>

7863

<h:div class="summary">Allows identification of couplings in symmetric systems. May also

7864

be usable for other complicated systems.</h:div>

7865

</xsd:documentation>

7866

</xsd:annotation>

7867

</xsd:element>

7868

</xsd:sequence>

7869

7870

<xsd:attributeGroup ref="dictRef"/>

7871

<xsd:attributeGroup ref="convention"/>

7872

<xsd:attributeGroup ref="title"/>

7873

<xsd:attributeGroup ref="id"/>

7874

<xsd:attributeGroup ref="ref"/>

7875

7876

<xsd:attributeGroup ref="peakMultiplicity"/>

7877

<xsd:attributeGroup ref="peakStructureType"/>

7878

<xsd:attributeGroup ref="peakShape"/>

7879

7880

<xsd:attributeGroup ref="value"/>

7881

<xsd:attributeGroup ref="units"/>

7882

7883

<xsd:attributeGroup ref="atomRefs">

7884

<xsd:annotation>

7885

<xsd:documentation>

7886

<h:div class="summary">The atoms to which the peakStructure refers.</h:div>

7887

<h:div class="description">Allows identification of the atoms to which the

7888

peak is coupled (not the atoms contributing to the primnary reference for

7889

which <tt xmlns="">peak</tt> should be used). It may be

7890

combined with bondRefs. Even single atoms should use atomRefs, not atomRef.

7891

</h:div>

7892

</xsd:documentation>

7893

</xsd:annotation>

7894

</xsd:attributeGroup>

7895

7896

<xsd:attributeGroup ref="bondRefs">

7897

<xsd:annotation>

7898

<xsd:documentation>

7899

<h:div class="summary">Bonds contributing to this peakStructure</h:div>

7900

<h:div class="description">Even a single bond should use bondRefs, not bondRef</h:div>

7901

</xsd:documentation>

7902

</xsd:annotation>

7903

</xsd:attributeGroup>

7904

7905

</xsd:complexType>

7906

</xsd:element><xsd:element name="plane3" id="el.plane3">

7907

<xsd:annotation>

7908

<xsd:documentation>

7909

<h:div class="summary">A plane in 3-space.</h:div>

7910

<h:div class="description">An oriented plane of indefinite extent.</h:div>

7911

</xsd:documentation>

7912

</xsd:annotation>

7913

<xsd:complexType>

7914

<xsd:simpleContent>

7915

<xsd:extension base="plane3Type">

7916

<xsd:attributeGroup ref="convention"/>

7917

<xsd:attributeGroup ref="dictRef"/>

7918

<xsd:attributeGroup ref="id"/>

7919

<xsd:attributeGroup ref="title"/>

7920

<xsd:attributeGroup ref="units"/>

7921

</xsd:extension>

7922

</xsd:simpleContent>

7923

</xsd:complexType>

7924

</xsd:element><xsd:element name="point3" id="el.point3">

7925

<xsd:annotation>

7926

<xsd:documentation>

7927

<h:div class="summary">A point in 3-space.</h:div>

7928

<h:div class="description"/>

7929

</xsd:documentation>

7930

</xsd:annotation>

7931

<xsd:complexType>

7932

<xsd:simpleContent>

7933

<xsd:extension base="point3Type">

7934

<xsd:attributeGroup ref="convention"/>

7935

<xsd:attributeGroup ref="dictRef"/>

7936

<xsd:attributeGroup ref="id"/>

7937

<xsd:attributeGroup ref="title"/>

7938

<xsd:attributeGroup ref="units"/>

7939

</xsd:extension>

7940

</xsd:simpleContent>

7941

</xsd:complexType>

7942

</xsd:element><xsd:element name="potential" id="el.potential">

7943

<xsd:annotation>

7944

<xsd:documentation>

7945

<h:div class="summary">An explicit potential.</h:div>

7946

<h:div class="description">This represents the actual function for the potential (i.e. with explicit values) rather than the functional form, which will normally be referenced from this.</h:div>

7947

<h:div class="example" href="potential1.xml"/>

7948

</xsd:documentation>

7949

</xsd:annotation>

7950

7951

<xsd:complexType>

7952

<xsd:sequence>

7953

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7954

<xsd:element ref="arg"/>

7955

</xsd:choice>

7956

</xsd:sequence>

7957

<xsd:attributeGroup ref="title"/>

7958

<xsd:attributeGroup ref="id"/>

7959

<xsd:attributeGroup ref="convention"/>

7960

<xsd:attributeGroup ref="dictRef"/>

7961

<xsd:attributeGroup ref="form"/>

7962

</xsd:complexType>

7963

</xsd:element><xsd:element name="potentialForm" id="el.potentialForm">

7964

<xsd:annotation>

7965

<xsd:documentation>

7966

<h:div class="summary">The functional form of a potential.</h:div>

7967

<h:div class="description">This has generic arguments and parameters rather than explicit ones. It is essentially a mathematical function, expressed currently in reverse Polish notation.</h:div>

7968

<h:div class="example" href="potential1.xml"/>

7969

</xsd:documentation>

7970

</xsd:annotation>

7971

7972

<xsd:complexType>

7973

<xsd:sequence>

7974

<!--

7975

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7976

<xsd:element ref="annotation"/>

7977

</xsd:choice>

7978

-->

7979

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7980

<xsd:element ref="arg"/>

7981

</xsd:choice>

7982

<xsd:choice minOccurs="0" maxOccurs="unbounded">

7983

<xsd:element ref="parameter"/>

7984

</xsd:choice>

7985

<xsd:choice minOccurs="0" maxOccurs="1">

7986

<xsd:element ref="expression"/>

7987

</xsd:choice>

7988

</xsd:sequence>

7989

<xsd:attributeGroup ref="title"/>

7990

<xsd:attributeGroup ref="id"/>

7991

<xsd:attributeGroup ref="convention"/>

7992

<xsd:attributeGroup ref="dictRef"/>

7993

<xsd:attributeGroup ref="name"/>

7994

</xsd:complexType>

7995

</xsd:element><xsd:element name="potentialList" id="el.potentialList">

7996

<xsd:annotation>

7997

<xsd:documentation>

7998

<h:div class="summary">A container for explicit potentials.</h:div>

7999

<h:div class="description">Experimental.</h:div>

8000

<h:div class="example" href="potential1.xml"/>

8001

</xsd:documentation>

8002

</xsd:annotation>

8003

8004

<xsd:complexType>

8005

<xsd:sequence>

8006

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8007

<xsd:element ref="potential"/>

8008

</xsd:choice>

8009

</xsd:sequence>

8010

<xsd:attributeGroup ref="title"/>

8011

<xsd:attributeGroup ref="id"/>

8012

<xsd:attributeGroup ref="convention"/>

8013

<xsd:attributeGroup ref="dictRef"/>

8014

</xsd:complexType>

8015

</xsd:element><xsd:element name="product" id="el.product">

8016

<xsd:annotation>

8017

<xsd:documentation>

8018

<h:div class="summary">A product within a productList.</h:div>

8019

<h:div class="description"><h:tt>product</h:tt> describes a product species which is produced in a reaction. See <h:tt>reactant</h:tt> for discussion of catalysis and solvents.</h:div>

8020

<h:div class="example" href="product1.xml"/>

8021

</xsd:documentation>

8022

</xsd:annotation>

8023

8024

<xsd:complexType>

8025

<xsd:annotation>

8026

<xsd:documentation>

8027

<h:div class="description">

8028

<h:p>A product will normally be identified by name(s), formula, or molecule and at least one of these should normally be given. Amount(s) of product can be given after this identification and can describe mass, volume, percent yield, etc. but not stoichiometry</h:p></h:div>

8029

</xsd:documentation>

8030

</xsd:annotation>

8031

<xsd:sequence>

8032

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8033

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8034

<xsd:element ref="identifier" minOccurs="0"/>

8035

<xsd:element ref="label" minOccurs="0"/>

8036

<xsd:element ref="name" minOccurs="0"/>

8037

</xsd:choice>

8038

<xsd:element ref="molecule" minOccurs="0" maxOccurs="1"/>

8039

<xsd:element ref="electron" minOccurs="0" maxOccurs="1"/>

8040

<xsd:element ref="substance" minOccurs="0" maxOccurs="1"/>

8041

<xsd:element ref="substanceList" minOccurs="0" maxOccurs="1"/>

8042

<xsd:element ref="formula" minOccurs="0" maxOccurs="1"/>

8043

<xsd:element ref="amount" minOccurs="0" maxOccurs="unbounded"/>

8044

</xsd:sequence>

8045

<xsd:attributeGroup ref="dictRef"/>

8046

<xsd:attributeGroup ref="convention"/>

8047

<xsd:attributeGroup ref="title"/>

8048

<xsd:attributeGroup ref="id"/>

8049

<xsd:attributeGroup ref="ref"/>

8050

<xsd:attributeGroup ref="role"/>

8051

<xsd:attributeGroup ref="count"/>

8052

<xsd:attributeGroup ref="state"/>

8053

8054

</xsd:complexType>

8055

</xsd:element><xsd:element name="productList" id="el.productList">

8056

<xsd:annotation>

8057

<xsd:documentation>

8058

<h:div class="summary">A container for one or more products.</h:div>

8059

<h:div class="description">

8060

<h:p>

8061

<h:tt>productList</h:tt> can contain several products. These may be related in several ways, including

8062

<h:ul>

8063

<h:li>single list of products</h:li>

8064

<h:li>grouping of products of parallel reactions</h:li>

8065

</h:ul>.

8066

A productList can contain nested productLists. The semantics of this are currently undefined.

8067

</h:p></h:div>

8068

<h:div class="example" href="productList1.xml"/>

8069

</xsd:documentation>

8070

</xsd:annotation>

8071

8072

<xsd:complexType>

8073

<xsd:sequence>

8074

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8075

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

8076

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8077

<xsd:element ref="productList"/>

8078

<xsd:element ref="product"/>

8079

</xsd:choice>

8080

</xsd:sequence>

8081

<xsd:attributeGroup ref="dictRef"/>

8082

<xsd:attributeGroup ref="convention"/>

8083

<xsd:attributeGroup ref="title"/>

8084

<xsd:attributeGroup ref="id"/>

8085

<xsd:attributeGroup ref="ref"/>

8086

<xsd:attributeGroup ref="role"/>

8087

<xsd:attributeGroup ref="count">

8088

<xsd:annotation>

8089

<xsd:documentation>

8090

<h:div class="specific">The number of copies of the productList involved in the stoichiometric reaction. Probably not useful for simple reactions but could be used for parallel reactions.</h:div>

8091

</xsd:documentation>

8092

</xsd:annotation>

8093

</xsd:attributeGroup>

8094

</xsd:complexType>

8095

</xsd:element><xsd:element name="property" id="el.property">

8096

<xsd:annotation>

8097

<xsd:documentation>

8098

<h:div class="summary">A container for a property.</h:div>

8099

<h:div class="description">

8100

<h:tt>property</h:tt> can contain one or more children, usually <h:tt>scalar</h:tt>,

8101

<h:tt>array</h:tt> or <h:tt>matrix</h:tt>. The <h:tt>dictRef</h:tt> attribute is

8102

required, even if there is a single scalar child with the same dictRef. The

8103

property may have a different dictRef from the child, thus providing an extension

8104

mechanism.

8105

<h:p>Properties may have a <h:tt>state</h:tt> attribute to distinguish the state of

8106

matter</h:p></h:div>

8107

<h:div class="example" href="property1.xml"/>

8108

</xsd:documentation>

8109

</xsd:annotation>

8110

8111

<xsd:complexType>

8112

<xsd:sequence>

8113

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8114

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

8115

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8116

<xsd:element ref="scalar"/>

8117

<xsd:element ref="array"/>

8118

<xsd:element ref="matrix"/>

8119

</xsd:choice>

8120

</xsd:sequence>

8121

<xsd:attributeGroup ref="dictRef"/>

8122

<xsd:attributeGroup ref="convention"/>

8123

<xsd:attributeGroup ref="title"/>

8124

<xsd:attributeGroup ref="id"/>

8125

<xsd:attributeGroup ref="ref"/>

8126

<xsd:attributeGroup ref="role">

8127

<xsd:annotation>

8128

<xsd:documentation>

8129

<h:div class="specific">Semantics are not yet controlled but could include

8130

thermochemistry, kinetics or other common properties.</h:div>

8131

</xsd:documentation>

8132

</xsd:annotation>

8133

</xsd:attributeGroup>

8134

<xsd:attributeGroup ref="state"/>

8135

</xsd:complexType>

8136

</xsd:element><xsd:element name="propertyList" id="el.propertyList">

8137

<xsd:annotation>

8138

<xsd:documentation>

8139

<h:div class="summary">A container for one or more properties.</h:div>

8140

<h:div class="description"><h:tt>propertyList</h:tt> can contain several properties.

8141

These include (but are not limited to) observations, or numeric quantities.</h:div>

8142

<h:div class="example" href="propertyList1.xml"/>

8143

</xsd:documentation>

8144

</xsd:annotation>

8145

8146

<xsd:complexType>

8147

<xsd:sequence>

8148

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8149

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

8150

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8151

<xsd:element ref="property"/>

8152

<xsd:element ref="observation"/>

8153

</xsd:choice>

8154

8155

</xsd:sequence>

8156

<xsd:attributeGroup ref="dictRef"/>

8157

<xsd:attributeGroup ref="convention"/>

8158

<xsd:attributeGroup ref="title"/>

8159

<xsd:attributeGroup ref="id"/>

8160

<xsd:attributeGroup ref="ref"/>

8161

<xsd:attributeGroup ref="role"/>

8162

</xsd:complexType>

8163

</xsd:element><xsd:element name="reactant" id="el.reactant">

8164

<xsd:annotation>

8165

<xsd:documentation>

8166

<h:div class="summary">A reactant within a reactantList.</h:div>

8167

<h:div class="description">

8168

<h:tt>reactant</h:tt> describes a reactant species which takes part in a reaction. Catalysts and supports are not normally classified as reactants, but this is subjective. Enzymes (or parts of enzymes) may well be reactants, as could be substances which underwent chemical change but were restored to their original state. <h:tt>reactant</h:tt> is a powerful concept as it can support stoichiometry (atom and molecule counting), mapping (for mechanisms), etc. Solvents are best contained within substanceList.</h:div>

8169

<h:div class="example" href="reactant1.xml"/>

8170

</xsd:documentation>

8171

</xsd:annotation>

8172

8173

<xsd:complexType>

8174

<xsd:annotation>

8175

<xsd:documentation>

8176

<h:div>A reactant will normally be identified by name(s), formula, or molecule and at least one of these should normally be given. Amount(s) of reactant can be given after this identification and can describe mass, volume, etc. but not stoichiometr.</h:div>

8177

</xsd:documentation>

8178

</xsd:annotation>

8179

<xsd:sequence>

8180

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8181

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8182

<xsd:element ref="identifier"/>

8183

<xsd:element ref="label"/>

8184

<xsd:element ref="name"/>

8185

</xsd:choice>

8186

<xsd:element ref="molecule" minOccurs="0" maxOccurs="1"/>

8187

<xsd:element ref="electron" minOccurs="0" maxOccurs="1"/>

8188

<xsd:element ref="substance" minOccurs="0" maxOccurs="1"/>

8189

<xsd:element ref="substanceList" minOccurs="0" maxOccurs="1"/>

8190

<xsd:element ref="formula" minOccurs="0" maxOccurs="1"/>

8191

<xsd:element ref="amount" minOccurs="0" maxOccurs="unbounded"/>

8192

</xsd:sequence>

8193

<xsd:attributeGroup ref="dictRef"/>

8194

<xsd:attributeGroup ref="convention"/>

8195

<xsd:attributeGroup ref="title"/>

8196

<xsd:attributeGroup ref="id"/>

8197

<xsd:attributeGroup ref="ref"/>

8198

<xsd:attributeGroup ref="role">

8199

<xsd:annotation>

8200

<xsd:documentation>

8201

<h:div class="specific">The role of the reactant within a reactantList. Semantics are not yet controlled but could be limiting, oxidant, etc. TODO: a reactant might have multiple roles so this may have to become an element.</h:div>

8202

</xsd:documentation>

8203

</xsd:annotation>

8204

</xsd:attributeGroup>

8205

<xsd:attributeGroup ref="count">

8206

<xsd:annotation>

8207

<xsd:documentation>

8208

<h:div class="specific">The number of copies of the reactant involved in the stoichiometric reaction. Could be non-integer but should not be used for actual ratios of materials added (for which amount should be used).</h:div>

8209

</xsd:documentation>

8210

</xsd:annotation>

8211

</xsd:attributeGroup>

8212

<xsd:attributeGroup ref="state"/>

8213

</xsd:complexType>

8214

</xsd:element><xsd:element name="reactantList" id="el.reactantList">

8215

<xsd:annotation>

8216

<xsd:documentation>

8217

<h:div class="summary">A container for one or more reactants.</h:div>

8218

<h:div class="description">

8219

<h:p>

8220

<h:tt>reactantList</h:tt> can contain several reactants. These may be related in several ways, including

8221

<h:ul>

8222

<h:li>lists of related reactants</h:li>

8223

<h:li>reactant schemes</h:li>

8224

<h:li>multi-step reactants</h:li>

8225

<h:li>parallel and/or coupled reactants</h:li>

8226

</h:ul>.

8227

A reactantList can contain nested reactantLists. The semantics of this are currently undefined.

8228

</h:p></h:div>

8229

<h:div class="example" href="reactantList1.xml"/>

8230

</xsd:documentation>

8231

</xsd:annotation>

8232

8233

<xsd:complexType>

8234

<xsd:sequence>

8235

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8236

<xsd:element ref="name" minOccurs="0" maxOccurs="1"/>

8237

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8238

<xsd:element ref="reactantList"/>

8239

<xsd:element ref="reactant"/>

8240

</xsd:choice>

8241

</xsd:sequence>

8242

<xsd:attributeGroup ref="dictRef"/>

8243

<xsd:attributeGroup ref="convention"/>

8244

<xsd:attributeGroup ref="title"/>

8245

<xsd:attributeGroup ref="id"/>

8246

<xsd:attributeGroup ref="ref"/>

8247

<xsd:attributeGroup ref="role"/>

8248

<xsd:attributeGroup ref="count"/>

8249

</xsd:complexType>

8250

</xsd:element><xsd:element name="reaction" id="el.reaction">

8251

<xsd:annotation>

8252

<xsd:documentation>

8253

<h:div class="summary">A chemical reaction or reaction step.</h:div>

8254

<h:div class="description">

8255

<h:p>

8256

<h:tt>reaction</h:tt> is a container for reactants, products, conditions, properties and possibly other information relating to the reaction, often within a reactionList. Partial semantics exist:

8257

<h:ul>

8258

<h:li><h:b>name</h:b> the name(s) of the reaction</h:li>

8259

<h:li>

8260

<h:b>reactantList</h:b> (normally only one) the grouped reactants</h:li>

8261

<h:li>

8262

<h:b>spectatorList</h:b> substances with well-defined chemistry which are involved in the reaction but do not change. Examples are side groups in proteins, cofactors, etc. The division between specattor and substance is subjective.</h:li>

8263

<h:li>

8264

<h:b>substance</h:b> or <h:b>substanceList</h:b> substances present in the reaction but not classified as reactants. Examples might be enzymes, catalysts, solvents, supports, workup, etc. </h:li>

8265

<h:li>

8266

<h:b>condition</h:b> conditions of the reaction. These may be text strings, but ideally will have clearer semantics such as scalars for temperature, etc.</h:li>

8267

<h:li>

8268

<h:b>productList</h:b> the grouped products. This allows for parallel reactions or other semantics.</h:li>

8269

<h:li>

8270

<h:b>property</h:b> properties (often physical) associated with the reaction. Examples might be heat of formation, kinetics or equilibrium constant.</h:li>

8271

</h:ul>

8272

</h:p></h:div>

8273

<h:div>

8274

<h:p>Reaction normally refers to an overall reaction or a step within a reactionList. For a complex "reaction", such as in enzymes or chain reactions, it may be best to use <h:tt>reactionScheme</h:tt> to hold the overall <h:tt>reaction</h:tt> and a <h:tt>reactionList</h:tt> of the individual <h:tt>reaction</h:tt> steps.</h:p></h:div>

8275

<h:div class="example" href="reaction1.xml"/>

8276

<h:div class="example" href="reaction9a.xml"/>

8277

<h:div class="example" href="reaction9b.xml"/>

8278

<h:div class="example" href="reaction10a.xml"/>

8279

<h:div class="example" href="reaction10b.xml"/>

8280

<h:div class="example" href="reaction11.xml"/>

8281

</xsd:documentation>

8282

</xsd:annotation>

8283

8284

<xsd:complexType>

8285

<xsd:annotation>

8286

<xsd:documentation>

8287

<h:div>

8288

<h:p>The semantics of the content model are</h:p>

8289

<h:ul>

8290

<h:li>metadataList for general metadata</h:li>

8291

<h:li>label for classifying or describing the reaction (e.g. "hydrolysis")</h:li>

8292

<h:li>identifier for unique identification. This could be a classification such as EC (enzyme commission) or an IChI-like string generated from the components.</h:li>

8293

<h:li>these are followed by the possible components of the reaction and/or a reactionList of further details.</h:li>

8294

</h:ul>.</h:div>

8295

8296

</xsd:documentation>

8297

</xsd:annotation>

8298

8299

<xsd:sequence>

8300

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8301

<xsd:element ref="label" minOccurs="0" maxOccurs="unbounded"/>

8302

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8303

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

8304

<xsd:element ref="identifier" minOccurs="0" maxOccurs="unbounded"/>

8305

</xsd:choice>

8306

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

8307

<xsd:element ref="reactiveCentre" minOccurs="0" maxOccurs="unbounded"/>

8308

<xsd:element ref="mechanism" minOccurs="0" maxOccurs="unbounded"/>

8309

<xsd:element ref="reactantList" minOccurs="0" maxOccurs="unbounded"/>

8310

<xsd:element ref="spectatorList" minOccurs="0" maxOccurs="unbounded"/>

8311

<xsd:element ref="substanceList" minOccurs="0" maxOccurs="unbounded"/>

8312

<xsd:element ref="conditionList" minOccurs="0" maxOccurs="unbounded"/>

8313

<xsd:element ref="transitionState" minOccurs="0" maxOccurs="unbounded"/>

8314

<xsd:element ref="productList" minOccurs="0" maxOccurs="unbounded"/>

8315

<xsd:element ref="propertyList" minOccurs="0" maxOccurs="unbounded"/>

8316

<xsd:element ref="map" minOccurs="0" maxOccurs="unbounded"/>

8317

<xsd:element ref="object" minOccurs="0" maxOccurs="unbounded">

8318

<xsd:annotation>

8319

<xsd:documentation>

8320

<h:div>This allows any objects to be attached to the reaction, but particularly graphical primitives such as lines, arrows, etc. These should be provided as elements where possible (e.g. SVG) and should have references to the chemical objects they interact with (i.e. not simply relying on geometry). Markers with IDs can be included as part of the graphics object and their ids linked to the chemical elements using <h:tt>link</h:tt>.</h:div>

8321

</xsd:documentation>

8322

</xsd:annotation>

8323

</xsd:element>

8324

</xsd:sequence>

8325

</xsd:sequence>

8326

<xsd:attributeGroup ref="dictRef"/>

8327

<xsd:attributeGroup ref="convention"/>

8328

<xsd:attributeGroup ref="title"/>

8329

<xsd:attributeGroup ref="id"/>

8330

<xsd:attributeGroup ref="reactionFormat"/>

8331

<xsd:attributeGroup ref="ref"/>

8332

<xsd:attributeGroup ref="reactionRole"/>

8333

<xsd:attributeGroup ref="reactionType"/>

8334

<xsd:attributeGroup ref="state"/>

8335

<xsd:attributeGroup ref="atomMap"/>

8336

<xsd:attributeGroup ref="electronMap"/>

8337

<xsd:attributeGroup ref="bondMap"/>

8338

<xsd:attributeGroup ref="yield">

8339

<xsd:annotation>

8340

<xsd:documentation>

8341

<h:div class="specific">

8342

<h:p>The yield of the reaction. Note that this lies in the range 0-1.</h:p>

8343

</h:div>

8344

8345

</xsd:documentation>

8346

</xsd:annotation>

8347

</xsd:attributeGroup>

8348

8349

</xsd:complexType>

8350

</xsd:element><xsd:element name="reactionList" id="el.reactionList">

8351

<xsd:annotation>

8352

<xsd:documentation>

8353

<h:div class="summary">A container for one or more reactions or reactionSchemes with no interrelations.</h:div>

8354

<h:div class="description">A reactionList aggregates reactions and reactionSchemes but implies no semantics. The most common uses are to create small collections of reactions (e.g. databases or publications).</h:div>

8355

<h:div class="example" href="reactionList1.xml"/>

8356

</xsd:documentation>

8357

</xsd:annotation>

8358

8359

<xsd:complexType>

8360

<xsd:annotation>

8361

<xsd:documentation>

8362

<h:div/>

8363

</xsd:documentation>

8364

</xsd:annotation>

8365

<xsd:sequence>

8366

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8367

<xsd:choice>

8368

<xsd:element ref="reactionScheme" minOccurs="0" maxOccurs="unbounded"/>

8369

<xsd:element ref="reaction" minOccurs="0" maxOccurs="unbounded"/>

8370

</xsd:choice>

8371

</xsd:sequence>

8372

<xsd:attributeGroup ref="dictRef"/>

8373

<xsd:attributeGroup ref="convention"/>

8374

<xsd:attributeGroup ref="title"/>

8375

<xsd:attributeGroup ref="id"/>

8376

<xsd:attributeGroup ref="name"/>

8377

<xsd:attributeGroup ref="ref"/>

8378

</xsd:complexType>

8379

</xsd:element><xsd:element name="reactionScheme" id="el.reactionScheme">

8380

<xsd:annotation>

8381

<xsd:documentation>

8382

<h:div class="summary">A container for two or more related reactions and their relationships.</h:div>

8383

<h:div class="description">

8384

Where reactions are closely related (and often formally dependent on each other) they should be contained within the reactionStepList of a reactionScheme. The semantics which have informed this design include:

8385

<h:ul>

8386

<h:li>Steps within an organic synthesis.</h:li>

8387

<h:li>Two or more individual (primitive) steps provding the detailed mechanism for an overall reaction.</h:li>

8388

<h:li>Coupled or sequential reactions within biochemical pathways.</h:li>

8389

</h:ul>

8390

<h:p>This design is general because "reaction" is used in several ways. A biochemical pathway (e.g. oxidation of glucose to CO2 and water) involves many coupled enzyme reactions proceeding both in parallel and in sequence. Each of these steps ("reactions" in their own right) is itself complex and can include several mechanistics steps which are themselves reactions with products, reactants, etc. <h:tt>reactionScheme</h:tt> can therefore include reactionStepLists (with more reactionScheme children) which provide a more detailed view of the individual components.</h:p>

8391

<h:p>Where a set of reactions are primitives...</h:p>

8392

</h:div>

8393

<h:div class="example" href="reactionScheme1.xml"/>

8394

<h:div class="example" href="reactionScheme3.xml"/>

8395

<h:div class="example" href="reactionScheme4a.xml"/>

8396

<h:div class="example" href="reactionScheme4b.xml"/>

8397

</xsd:documentation>

8398

</xsd:annotation>

8399

8400

<xsd:complexType>

8401

<xsd:annotation>

8402

<xsd:documentation>

8403

<h:div class="description">

8404

<h:p>The semantics of the content model are</h:p>

8405

<h:ul>

8406

<h:li>metadataList for general metadata</h:li>

8407

<h:li>label for classifying or describing the reaction (e.g. "hydrolysis")</h:li>

8408

<h:li>identifier for unique identification. This could be a classification such as EC (enzyme commission) or an IChI-like string generated from the components.</h:li>

8409

<h:li>these are followed by the possible components of the reaction and/or a reactionList of further details.</h:li>

8410

</h:ul>

8411

</h:div>

8412

8413

</xsd:documentation>

8414

</xsd:annotation>

8415

8416

<xsd:sequence>

8417

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8418

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8419

<xsd:element ref="label"/>

8420

<xsd:element ref="name"/>

8421

<xsd:element ref="identifier"/>

8422

</xsd:choice>

8423

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8424

<xsd:element ref="reaction"/>

8425

<xsd:element ref="reactionStepList"/>

8426

<xsd:element ref="reactionScheme"/>

8427

</xsd:choice>

8428

</xsd:sequence>

8429

<xsd:attributeGroup ref="dictRef"/>

8430

<xsd:attributeGroup ref="convention"/>

8431

<xsd:attributeGroup ref="title"/>

8432

<xsd:attributeGroup ref="id"/>

8433

<xsd:attributeGroup ref="ref"/>

8434

<xsd:attributeGroup ref="reactionRole"/>

8435

<xsd:attributeGroup ref="reactionType"/>

8436

<xsd:attributeGroup ref="state"/>

8437

<xsd:attributeGroup ref="reactionFormat"/>

8438

8439

</xsd:complexType>

8440

</xsd:element><xsd:element name="reactionStep" id="el.reactionStep">

8441

<xsd:annotation>

8442

<xsd:documentation>

8443

<h:div class="summary">A child of reactionStepList and a container for reaction or reactionScheme.</h:div>

8444

<h:div class="description">

8445

<h:p>

8446

<h:tt>reactionStep</h:tt> is always contained within reactionStepList and is designed to manage "sub-reactions" which have close relationships. These will often involve reactions which, taken together, describe a higher level reaction or reaction type. Examples are:

8447

<h:ul>

8448

<h:li>biochemical pathways</h:li>

8449

<h:li>synthetic reaction schemes</h:li>

8450

<h:li>multi-step reactions</h:li>

8451

<h:li>parallel and/or coupled reactions</h:li>

8452

</h:ul>.

8453

A reactionStep normally contains a single reaction or reactionScheme. It can have attributes such as yield and ratio which can be used by the parent reactionStepList.

8454

</h:p>

8455

</h:div>

8456

<h:div class="example" href="reactionStepList4.xml"/>

8457

<h:div class="example" href="reactionStepList5a.xml"/>

8458

<h:div class="example" href="reactionStepList5b.xml"/>

8459

</xsd:documentation>

8460

</xsd:annotation>

8461

8462

<xsd:complexType>

8463

<xsd:annotation>

8464

<xsd:documentation>

8465

<h:div>

8466

<h:p>

8467

The <h:tt>name</h:tt> applies to the overall schema of reactions. <h:tt>label</h:tt> is for additional textual information and classification. <h:tt>reactionStepList</h:tt> normally contains <h:tt>reaction</h:tt>s but we make provision for nested reactionSchemes if required. </h:p></h:div>

8468

</xsd:documentation>

8469

</xsd:annotation>

8470

<xsd:sequence>

8471

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8472

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8473

<xsd:element ref="name"/>

8474

<xsd:element ref="label"/>

8475

</xsd:choice>

8476

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8477

<xsd:element ref="reactionScheme"/>

8478

<xsd:element ref="reaction"/>

8479

</xsd:choice>

8480

</xsd:sequence>

8481

<xsd:attributeGroup ref="dictRef"/>

8482

<xsd:attributeGroup ref="convention"/>

8483

<xsd:attributeGroup ref="title"/>

8484

<xsd:attributeGroup ref="id"/>

8485

<xsd:attributeGroup ref="ref"/>

8486

<xsd:attributeGroup ref="yield">

8487

<xsd:annotation>

8488

<xsd:documentation>

8489

<h:div class="specific">

8490

<h:p>The yield of the reactionStep. Note that this lies in the range 0-1.</h:p>

8491

</h:div>

8492

8493

</xsd:documentation>

8494

</xsd:annotation>

8495

</xsd:attributeGroup>

8496

<xsd:attributeGroup ref="ratio">

8497

<xsd:annotation>

8498

<xsd:documentation>

8499

<h:div class="specific">

8500

<h:p>The ratio of this step to one or more sibling steps. Note that this lies in the range 0-1. It is meaningless to use this unless there are siblings, in which case it refers to the relative molar fluxes through each. The "percentage yields" will need to be transformed to this range. There is no requirement that the sum of fluxes through a group of siblings sum to 1.0, though they should not sum to more.</h:p>

8501

</h:div>

8502

8503

</xsd:documentation>

8504

</xsd:annotation>

8505

</xsd:attributeGroup>

8506

8507

</xsd:complexType>

8508

</xsd:element><xsd:element name="reactionStepList" id="el.reactionStepList">

8509

<xsd:annotation>

8510

<xsd:documentation>

8511

<h:div class="summary">A container for one or more related reactionSteps.</h:div>

8512

<h:div class="description">

8513

<h:p>

8514

<h:tt>reactionStepList</h:tt> is always contained within reactionScheme and is designed to manage "sub-reactions" which have close relationships. These will often involve reactions which, taken together, describe a higher level reaction or reaction type. Examples are:

8515

<h:ul>

8516

<h:li>biochemical pathways</h:li>

8517

<h:li>synthetic reaction schemes</h:li>

8518

<h:li>multi-step reactions</h:li>

8519

<h:li>parallel and/or coupled reactions</h:li>

8520

</h:ul>.

8521

A reactionStepList contains reactionSteps (each of which contains reactions and/or reactionSchemes (e.g. where part of the process is known in greater detail)). It may not directly contain child reactionStepLists.

8522

</h:p>

8523

<h:p>The child reactionSteps can have attributes such as yield and ratio which describe the relationship of the component steps.</h:p>

8524

<h:p>Guidance on use: <h:ul>

8525

<h:li>reactionScheme describes a complex of reactions with metadata, one (or more) overall reactions and a reactionStepList with the overall component reactions.</h:li>

8526

<h:li> reactionStepList aggregates and structures the individual subreactions.

8527

</h:li>

8528

<h:li>reactionList is a container for reactions and reactionSchemes with no semantics (e.g. a book or database of selected reactions).

8529

</h:li>

8530

</h:ul>

8531

</h:p></h:div>

8532

<h:div class="example" href="reactionStepList1.xml"/>

8533

<h:div class="example" href="reactionStepList3.xml"/>

8534

</xsd:documentation>

8535

</xsd:annotation>

8536

8537

<xsd:complexType>

8538

<xsd:annotation>

8539

<xsd:documentation>

8540

<h:div>

8541

<h:p>

8542

8543

</xsd:documentation>

8544

</xsd:annotation>

8545

<xsd:sequence>

8546

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8547

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8548

<xsd:element ref="name"/>

8549

<xsd:element ref="label"/>

8550

</xsd:choice>

8551

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

8552

<xsd:element ref="reactionStep"/>

8553

</xsd:sequence>

8554

</xsd:sequence>

8555

<xsd:attributeGroup ref="dictRef"/>

8556

<xsd:attributeGroup ref="convention"/>

8557

<xsd:attributeGroup ref="title"/>

8558

<xsd:attributeGroup ref="id"/>

8559

<xsd:attributeGroup ref="ref"/>

8560

<xsd:attributeGroup ref="type"/>

8561

<xsd:attributeGroup ref="reactionFormat"/>

8562

</xsd:complexType>

8563

</xsd:element><xsd:element name="reactiveCentre" id="el.reactiveCentre">

8564

<xsd:annotation>

8565

<xsd:documentation>

8566

<h:div class="summary">The reactiveCentre in a reaction.</h:div>

8567

<h:div class="description">This describes the set(s) of bonds and atoms involved in the reaction. The semantics are flexible, but a common usage would be to create atomSet(s) and bondSet(s) mapping to groups which undergo changes.</h:div>

8568

<h:div class="example" href="reactiveCentre1.xml"/>

8569

</xsd:documentation>

8570

</xsd:annotation>

8571

8572

<xsd:complexType>

8573

<xsd:sequence>

8574

<xsd:element ref="description" minOccurs="0"/>

8575

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8576

<xsd:element ref="atomTypeList"/>

8577

<xsd:element ref="bondTypeList"/>

8578

<xsd:element ref="atomSet"/>

8579

<xsd:element ref="bondSet"/>

8580

</xsd:choice>

8581

</xsd:sequence>

8582

<xsd:attributeGroup ref="title"/>

8583

<xsd:attributeGroup ref="id"/>

8584

<xsd:attributeGroup ref="convention"/>

8585

<xsd:attributeGroup ref="dictRef"/>

8586

</xsd:complexType>

8587

</xsd:element><xsd:element name="region" id="el.region">

8588

<xsd:annotation>

8589

<xsd:documentation>

8590

<h:div class="summary">A region of the system.</h:div>

8591

<h:div class="description">Under development. A subdivision of the system to which special

8592

protocols or properties may be attached. Typical regions could be defined by the

8593

presence of atoms belonging to an atomSet or geometrical boundaries.</h:div>

8594

<h:div class="note">A region element will not always contain other elements,

8595

but may have references from other elements. It may create a protocol, e.g. atoms

8596

within a region might be replaced by a continuum model or be subject to a field.

8597

Semantics yet to be determined.</h:div>

8598

<h:div>Regions can be created by the unions of two or more regions. This allows a region

8599

to be built from a series of (say) spheres or boxes filling space.</h:div>

8600

<h:div class="example" href="region1.xml"/>

8601

</xsd:documentation>

8602

</xsd:annotation>

8603

8604

<xsd:complexType>

8605

<xsd:sequence/>

8606

<xsd:attributeGroup ref="sphere3"/>

8607

<xsd:attributeGroup ref="box3"/>

8608

<xsd:attributeGroup ref="atomSetRef"/>

8609

<xsd:attributeGroup ref="regionRefs"/>

8610

<xsd:attributeGroup ref="title"/>

8611

<xsd:attributeGroup ref="id"/>

8612

<xsd:attributeGroup ref="convention"/>

8613

<xsd:attributeGroup ref="dictRef"/>

8614

</xsd:complexType>

8615

</xsd:element><xsd:element name="relatedEntry" id="el.relatedEntry">

8616

<xsd:annotation>

8617

<xsd:documentation>

8618

<h:div class="summary">An entry related in some way to a dictionary entry.</h:div>

8619

<h:div class="description">The range of relationships is not restricted but should include parents, aggregation, seeAlso and so on. DataCategories from ISO12620 can be referenced through the namespaced mechanism.</h:div>

8620

<h:div class="example" href="relatedEntry1.xml"/>

8621

</xsd:documentation>

8622

</xsd:annotation>

8623

<xsd:complexType mixed="true">

8624

<xsd:attributeGroup ref="relatedEntryType"/>

8625

<xsd:attributeGroup ref="href">

8626

<xsd:annotation>

8627

<xsd:documentation>

8628

<h:div class="specific">The related entry.</h:div>

8629

</xsd:documentation>

8630

</xsd:annotation>

8631

</xsd:attributeGroup>

8632

</xsd:complexType>

8633

</xsd:element><xsd:element name="sample" id="el.sample">

8634

<xsd:annotation>

8635

<xsd:documentation>

8636

<h:div class="summary">An analytical or spectral sample.</h:div>

8637

<h:div class="description">The <h:tt>sample</h:tt> should contain information on what things were in the sample and their roles. It can include <h:tt>molecule</h:tt>, <h:tt>substance</h:tt> and <h:tt>substanceList</h:tt>. Typical rolos include solvent, mulling agents, salt disks, molecular supports, etc. but should not cover apparatus or conditions.</h:div>

8638

<h:div class="example" href="sample1.xml"/>

8639

</xsd:documentation>

8640

</xsd:annotation>

8641

8642

<xsd:complexType>

8643

<xsd:sequence>

8644

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8645

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8646

<xsd:element ref="molecule">

8647

<xsd:annotation>

8648

<xsd:documentation>

8649

<h:div>A molecular description.</h:div>

8650

</xsd:documentation>

8651

</xsd:annotation>

8652

</xsd:element>

8653

<xsd:element ref="substance">

8654

<xsd:annotation>

8655

<xsd:documentation>

8656

<h:div>A substance in the sample.</h:div>

8657

</xsd:documentation>

8658

</xsd:annotation>

8659

</xsd:element>

8660

<xsd:element ref="substanceList">

8661

<xsd:annotation>

8662

<xsd:documentation>

8663

<h:div>A list of substances in the sample.</h:div>

8664

</xsd:documentation>

8665

</xsd:annotation>

8666

</xsd:element>

8667

</xsd:choice>

8668

</xsd:sequence>

8669

<xsd:attributeGroup ref="dictRef"/>

8670

<xsd:attributeGroup ref="convention"/>

8671

<xsd:attributeGroup ref="title"/>

8672

<xsd:attributeGroup ref="id"/>

8673

<xsd:attributeGroup ref="ref"/>

8674

<xsd:attributeGroup ref="state"/>

8675

</xsd:complexType>

8676

</xsd:element><xsd:element name="scalar" id="el.scalar">

8677

<xsd:annotation>

8678

<xsd:documentation>

8679

<h:div class="summary">An element to hold scalar data.</h:div>

8680

<h:div class="description">

8681

<h:tt>scalar</h:tt> holds scalar data under a single

8682

generic container. The semantics are usually resolved by

8683

linking to a dictionary.

8684

<h:b>scalar</h:b> defaults to a scalar string but

8685

has attributes which affect the type.

8686

<h:p>

8687

<h:tt>scalar</h:tt> does not necessarily reflect a physical object (for which

8688

<h:a href="el.object">object</h:a> should be used). It may reflect a property of an object

8689

such as temperature, size, etc. </h:p>

8690

<h:p>Note that normal Schema validation tools cannot validate the data type

8691

of <h:b>scalar</h:b> (it is defined as <h:tt>string</h:tt>), but that a temporary schema

8692

can be constructed from the type and used for validation. Also the type

8693

can be contained in a dictionary and software could decide to retrieve this

8694

and use it for validation.</h:p></h:div>

8695

8696

<h:div class="example" href="scalar1.xml"/>

8697

</xsd:documentation>

8698

</xsd:annotation>

8699

<xsd:complexType>

8700

<xsd:simpleContent>

8701

<xsd:extension base="xsd:string">

8702

<xsd:attributeGroup ref="title"/>

8703

<xsd:attributeGroup ref="id"/>

8704

<xsd:attributeGroup ref="convention"/>

8705

<xsd:attributeGroup ref="dictRef"/>

8706

<xsd:attributeGroup ref="dataType"/>

8707

<xsd:attributeGroup ref="errorValue"/>

8708

<xsd:attributeGroup ref="errorBasis"/>

8709

<xsd:attributeGroup ref="min"/>

8710

<xsd:attributeGroup ref="max"/>

8711

<xsd:attributeGroup ref="ref"/>

8712

<xsd:attributeGroup ref="units"/>

8713

<xsd:attributeGroup ref="constantToSI">

8714

<xsd:annotation>

8715

<xsd:documentation>

8716

<h:div class="specific">Alternative to units</h:div>

8717

<h:div class="description">Must be used in conjunction with unitType</h:div>

8718

<h:div class="curation">2005-10-26: added</h:div>

8719

</xsd:documentation>

8720

</xsd:annotation>

8721

</xsd:attributeGroup>

8722

<xsd:attributeGroup ref="multiplierToSI">

8723

<xsd:annotation>

8724

<xsd:documentation>

8725

<h:div class="specific">Alternative to units</h:div>

8726

<h:div class="description">Must be used in conjunction with unitType</h:div>

8727

<h:div class="curation">2005-10-26: added</h:div>

8728

</xsd:documentation>

8729

</xsd:annotation>

8730

</xsd:attributeGroup>

8731

<xsd:attributeGroup ref="unitType">

8732

<xsd:annotation>

8733

<xsd:documentation>

8734

<h:div class="specific">Alternative to units</h:div>

8735

<h:div class="description">Must be used in conjunction with multiplierToSI and/or constantToSI</h:div>

8736

<h:div class="curation">2005-10-26: added</h:div>

8737

</xsd:documentation>

8738

</xsd:annotation>

8739

</xsd:attributeGroup>

8740

</xsd:extension>

8741

</xsd:simpleContent>

8742

</xsd:complexType>

8743

</xsd:element><xsd:element name="spectator" id="el.spectator">

8744

<xsd:annotation>

8745

<xsd:documentation>

8746

<h:div class="summary">A spectator object in a reaction.</h:div>

8747

<h:div class="description">Objects are often present during a reaction which are not formally involved in bond breaking/formation and which are not modified during the reaction. They may be catalysts, but may also be objects which in some way constrain or help the reaction to take place (surfaces, micelles, groups in enzyme active sites, etc.). In some cases molecules present in a reaction mixture may act as spectators in steps in which they are not transformed.</h:div>

8748

<h:div class="example" href="spectator1.xml"/>

8749

</xsd:documentation>

8750

</xsd:annotation>

8751

8752

<xsd:complexType>

8753

<xsd:sequence>

8754

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8755

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8756

<xsd:element ref="label"/>

8757

<xsd:element ref="molecule"/>

8758

<xsd:element ref="object"/>

8759

</xsd:choice>

8760

</xsd:sequence>

8761

<xsd:attributeGroup ref="title"/>

8762

<xsd:attributeGroup ref="id"/>

8763

<xsd:attributeGroup ref="convention"/>

8764

<xsd:attributeGroup ref="dictRef"/>

8765

<xsd:attributeGroup ref="role">

8766

<xsd:annotation>

8767

<xsd:documentation>

8768

<h:div class="specific">No controlled vocabulary. Examples could be 'host', 'hydrophobic ligand', 'charge-stabilizer', etc..</h:div>

8769

</xsd:documentation>

8770

</xsd:annotation>

8771

</xsd:attributeGroup>

8772

</xsd:complexType>

8773

</xsd:element><xsd:element name="spectatorList" id="el.spectatorList">

8774

<xsd:annotation>

8775

<xsd:documentation>

8776

<h:div class="summary">A container for spectators in a reaction.</h:div>

8777

<h:div class="description"/>

8778

<h:div class="example" href="spectatorList1.xml"/>

8779

</xsd:documentation>

8780

</xsd:annotation>

8781

8782

<xsd:complexType>

8783

<xsd:sequence maxOccurs="unbounded">

8784

<xsd:element ref="spectator"/>

8785

</xsd:sequence>

8786

<xsd:attributeGroup ref="title"/>

8787

<xsd:attributeGroup ref="id"/>

8788

<xsd:attributeGroup ref="convention"/>

8789

<xsd:attributeGroup ref="dictRef"/>

8790

</xsd:complexType>

8791

</xsd:element><xsd:element name="spectrum" id="el.spectrum">

8792

<xsd:annotation>

8793

<xsd:documentation>

8794

<h:div class="summary">A spectrum and relevant data or metadata.</h:div>

8795

<h:div class="description">The <h:tt>spectrum</h:tt> construct can hold <h:tt>metadataList</h:tt>, <h:tt>sample</h:tt> (which can contain molecule), <h:tt>conditionList</h:tt> (mainly for physical/chemical conditions, not instrumental), <h:tt>spectrumData</h:tt> for the actual data and instrumental settings/procedure and <h:tt>peakList</h:tt> for the assigned peaks. This approach puts the spectrum as the primary object of interest. It could also be possible to make <h:tt>spectrum</h:tt> a child of <h:tt>molecule</h:tt> (although a reference using <h:tt>ref</h:tt> might be preferable).</h:div>

8796

<h:div class="example" href="spectrum1.xml"/>

8797

</xsd:documentation>

8798

</xsd:annotation>

8799

8800

<xsd:complexType>

8801

<xsd:choice minOccurs="0" maxOccurs="unbounded">

8802

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8803

<xsd:element ref="sample" minOccurs="0" maxOccurs="unbounded">

8804

<xsd:annotation>

8805

<xsd:documentation>

8806

<h:div>A (complete) description of the thing to which the spectrum relates. May contain <h:tt>molecule</h:tt> or <h:tt>substanceList</h:tt>. Solvents, mulls, etc should be described here.</h:div>

8807

</xsd:documentation>

8808

</xsd:annotation>

8809

</xsd:element>

8810

<xsd:element ref="conditionList" minOccurs="0" maxOccurs="unbounded">

8811

<xsd:annotation>

8812

<xsd:documentation>

8813

<h:div>The conditions relating to the spectrum (complementary to substanceList.</h:div>

8814

</xsd:documentation>

8815

</xsd:annotation>

8816

</xsd:element>

8817

<xsd:element ref="spectrumData" minOccurs="0" maxOccurs="unbounded"/>

8818

<xsd:element ref="peakList" minOccurs="0" maxOccurs="unbounded">

8819

<xsd:annotation>

8820

<xsd:documentation>

8821

<h:div>A list of peaks. This may occur independently of the xaxis/yaxis data.</h:div>

8822

</xsd:documentation>

8823

</xsd:annotation>

8824

</xsd:element>

8825

</xsd:choice>

8826

<xsd:attributeGroup ref="dictRef"/>

8827

<xsd:attributeGroup ref="convention"/>

8828

<xsd:attributeGroup ref="title"/>

8829

<xsd:attributeGroup ref="id"/>

8830

<xsd:attributeGroup ref="ref"/>

8831

<xsd:attributeGroup ref="moleculeRef">

8832

<xsd:annotation>

8833

<xsd:documentation>

8834

<h:div class="specific">The molecule to which the spectrum refers.</h:div>

8835

</xsd:documentation>

8836

</xsd:annotation>

8837

</xsd:attributeGroup>

8838

8839

<xsd:attributeGroup ref="spectrumType"/>

8840

8841

<xsd:attributeGroup ref="format"/>

8842

<xsd:attributeGroup ref="measurement"/>

8843

<xsd:attributeGroup ref="ft"/>

8844

8845

<xsd:attributeGroup ref="state">

8846

<xsd:annotation>

8847

<xsd:documentation>

8848

<h:div class="specific">Although this may also be contained in the <h:tt>sample</h:tt> element it is useful to state it here. No default.</h:div>

8849

</xsd:documentation>

8850

</xsd:annotation>

8851

</xsd:attributeGroup>

8852

8853

</xsd:complexType>

8854

</xsd:element><xsd:element name="spectrumData" id="el.spectrumData">

8855

<xsd:annotation>

8856

<xsd:documentation>

8857

<h:div class="summary">Data for the spectrum.</h:div>

8858

<h:div class="description">This is primarily to record the data in interchangeable format and machine and manufacturers settings and can include other MLs in this area (AniML, SpectroML, etc.). We recommend ASCII representations of data and this is the only format that CMLSpect implementers have to support, but we also allow for the carriage of JCAMP and other data (in ML wrappers such as AniML). All numeric data should carry units and dictionary references if possible to allow for semantic interoperability.</h:div>

8859

8860

<h:div class="example" href="spectrumData1.xml"/>

8861

</xsd:documentation>

8862

</xsd:annotation>

8863

8864

<xsd:complexType>

8865

<xsd:sequence>

8866

<xsd:sequence minOccurs="0" maxOccurs="1">

8867

<xsd:element ref="xaxis">

8868

<xsd:annotation>

8869

<xsd:documentation>

8870

<h:div>The x-axis/es, usually including the list of points at which data are recorded. Mandatory if y-axis data are given. Multiple x-axes are initially reserved for multiple scales rather than different measurements (for which an additional spectrum should be used).</h:div>

8871

</xsd:documentation>

8872

</xsd:annotation>

8873

</xsd:element>

8874

<xsd:element ref="yaxis" maxOccurs="unbounded">

8875

<xsd:annotation>

8876

<xsd:documentation>

8877

<h:div>The y-axis/es, usually including the list of points at which data are recorded. Mandatory if x-axis data are given. Multiple y-axes are initially reserved for multiple scales rather than different measurements (for which an additional spectrum should be used).</h:div>

8878

</xsd:documentation>

8879

</xsd:annotation>

8880

</xsd:element>

8881

</xsd:sequence>

8882

</xsd:sequence>

8883

<xsd:attributeGroup ref="dictRef"/>

8884

<xsd:attributeGroup ref="convention"/>

8885

<xsd:attributeGroup ref="title"/>

8886

<xsd:attributeGroup ref="id"/>

8887

<xsd:attributeGroup ref="ref"/>

8888

8889

</xsd:complexType>

8890

</xsd:element><xsd:element name="spectrumList" id="el.spectrumList">

8891

<xsd:annotation>

8892

<xsd:documentation>

8893

<h:div class="summary">A container for one or more spectra.</h:div>

8894

<h:div class="description">

8895

<h:p>

8896

<h:tt>spectrumList</h:tt> can contain several spectra. These may be related in several ways, including

8897

<h:ul>

8898

<h:li>lists of related spectra</h:li>

8899

<h:li>bundle of common analytical spectra (NMR, IR, UV...)</h:li>

8900

<h:li>repeat measurements</h:li>

8901

</h:ul>.

8902

A spectrumList can contain nested spectrumLists.

8903

</h:p></h:div>

8904

<h:div class="example" href="spectrumList1.xml"/>

8905

</xsd:documentation>

8906

</xsd:annotation>

8907

8908

<xsd:complexType>

8909

<xsd:annotation>

8910

<xsd:documentation>

8911

<h:div><h:tt>metadataList</h:tt> contains <h:tt>metadata</h:tt>. <h:tt>list</h:tt> is for experimental and other data. <h:tt>spectrumList</h:tt> normally contains <h:tt>spectrum</h:tt>s but we make provision for nested spectrumLists if required. The <h:tt>molecule</h:tt>s can be a set of reference molecules which occur in the <h:tt>spectrum</h:tt>s and can be referenced. This makes the spectrums more readable and normalizes data when molecules are used more than once.</h:div>

8912

</xsd:documentation>

8913

</xsd:annotation>

8914

<xsd:sequence>

8915

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

8916

<xsd:element ref="list" minOccurs="0" maxOccurs="unbounded"/>

8917

<xsd:choice>

8918

<xsd:element ref="spectrumList" minOccurs="0" maxOccurs="unbounded"/>

8919

<xsd:element ref="spectrum" minOccurs="0" maxOccurs="unbounded"/>

8920

</xsd:choice>

8921

</xsd:sequence>

8922

<xsd:attributeGroup ref="dictRef"/>

8923

<xsd:attributeGroup ref="convention"/>

8924

<xsd:attributeGroup ref="title"/>

8925

<xsd:attributeGroup ref="id"/>

8926

<xsd:attributeGroup ref="ref"/>

8927

<xsd:attributeGroup ref="moleculeRef"/>

8928

8929

</xsd:complexType>

8930

</xsd:element><xsd:element name="sphere3" id="el.sphere3">

8931

<xsd:annotation>

8932

<xsd:documentation>

8933

<h:div class="summary">A sphere in 3-space.</h:div>

8934

<h:div class="description"/>

8935

</xsd:documentation>

8936

</xsd:annotation>

8937

<xsd:complexType>

8938

<xsd:simpleContent>

8939

<xsd:extension base="sphere3Type">

8940

<xsd:attributeGroup ref="convention"/>

8941

<xsd:attributeGroup ref="dictRef"/>

8942

<xsd:attributeGroup ref="id"/>

8943

<xsd:attributeGroup ref="title"/>

8944

<xsd:attributeGroup ref="units"/>

8945

</xsd:extension>

8946

</xsd:simpleContent>

8947

</xsd:complexType>

8948

</xsd:element><xsd:element name="stmml" id="el.stmml">

8949

<xsd:annotation>

8950

<xsd:documentation>

8951

<h:div class="summary">An element to hold stmml data.</h:div>

8952

<h:div class="description"><h:tt>stmml</h:tt> holds stmml data under a single

8953

generic container. Other namespaces may be present as children.

8954

No semantics implied.</h:div>

8955

<h:div class="example" href="stmml1.xml"/>

8956

<!--

8957

<h:div class="example" href="bad.stmml.xml">

8958

<h:p>Note attribute (mistake) not in schema</h:p></h:div>

8959

<h:div class="example" href="bad.stmml2.xml">

8960

<h:p>Note bad name</h:p></h:div>

8961

-->

8962

</xsd:documentation>

8963

</xsd:annotation>

8964

<xsd:complexType>

8965

<xsd:sequence minOccurs="0" maxOccurs="unbounded">

8966

<xsd:any processContents="lax"/>

8967

</xsd:sequence>

8968

<xsd:attributeGroup ref="title"/>

8969

<xsd:attributeGroup ref="id"/>

8970

<xsd:attributeGroup ref="convention"/>

8971

<xsd:attributeGroup ref="dictRef"/>

8972

</xsd:complexType>

8973

</xsd:element><xsd:element name="string" id="el.string">

8974

<xsd:annotation>

8975

<xsd:documentation>

8976

<h:div class="summary">CML-1 dataType (DEPRECATED).</h:div>

8977

<h:div class="description"/>

8978

<h:div class="example" href="../../examples/cmlone.xml"/>

8979

</xsd:documentation>

8980

</xsd:annotation>

8981

<xsd:complexType>

8982

<xsd:simpleContent>

8983

<xsd:extension base="xsd:string">

8984

<xsd:attributeGroup ref="builtin"/>

8985

<xsd:attributeGroup ref="convention"/>

8986

<xsd:attributeGroup ref="dictRef"/>

8987

<xsd:attributeGroup ref="id"/>

8988

<xsd:attributeGroup ref="title"/>

8989

</xsd:extension>

8990

</xsd:simpleContent>

8991

</xsd:complexType>

8992

</xsd:element><xsd:element name="stringArray" id="el.stringArray">

8993

<xsd:annotation>

8994

<xsd:documentation>

8995

<h:div class="summary">CML-1 dataType DEPRECATED.</h:div>

8996

<h:div class="description"/>

8997

<h:div class="example" href="../../examples/cmlone.xml"/>

8998

</xsd:documentation>

8999

</xsd:annotation>

9000

<xsd:complexType>

9001

<xsd:simpleContent>

9002

<xsd:extension base="xsd:string">

9003

<xsd:attributeGroup ref="builtin"/>

9004

<xsd:attributeGroup ref="convention"/>

9005

<xsd:attributeGroup ref="dictRef"/>

9006

<xsd:attributeGroup ref="id"/>

9007

<xsd:attributeGroup ref="title"/>

9008

<xsd:attributeGroup ref="min"/>

9009

<xsd:attributeGroup ref="max"/>

9010

<xsd:attributeGroup ref="size"/>

9011

<xsd:attributeGroup ref="delimiter"/>

9012

</xsd:extension>

9013

</xsd:simpleContent>

9014

</xsd:complexType>

9015

</xsd:element><xsd:element name="substance" id="el.substance">

9016

<xsd:annotation>

9017

<xsd:documentation>

9018

<h:div class="summary">A chemical substance.</h:div>

9019

<h:div class="description"><h:tt>substance</h:tt> represents a <h:i>chemical substance</h:i> which is deliberately very general. It can represent things that may or may not be molecules, can and cannot be stored in bottles and may or may not be microscopic. Solutions and mixtures can be described by _substanceList_s of substances. The <h:tt>type</h:tt> attribute can be used to give qualitative information characterising the substance ("granular", "90%", etc.) and _role_ to describe the role in process ("desiccant", "support", etc.). There is currently no controlled vocabulary. Note that <h:tt>reaction</h:tt> is likely to have more precise semantics. The amount of a substance is controlled by the optional _amount_ child.</h:div>

9020

<h:div class="example" href="substance1.xml"/>

9021

</xsd:documentation>

9022

<xsd:documentation>

9023

<h:div class="curation">

9024

<h:p>Added property as a child 2002-12-29</h:p></h:div>

9025

</xsd:documentation>

9026

</xsd:annotation>

9027

<xsd:complexType>

9028

<xsd:sequence>

9029

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

9030

<xsd:element ref="amount" minOccurs="0"/>

9031

<xsd:choice>

9032

<xsd:element ref="molecule" minOccurs="0" maxOccurs="unbounded"/>

9033

<xsd:element ref="name" minOccurs="0" maxOccurs="unbounded"/>

9034

<xsd:element ref="property" minOccurs="0" maxOccurs="unbounded"/>

9035

</xsd:choice>

9036

</xsd:sequence>

9037

<xsd:attributeGroup ref="dictRef"/>

9038

<xsd:attributeGroup ref="convention"/>

9039

<xsd:attributeGroup ref="title"/>

9040

<xsd:attributeGroup ref="id"/>

9041

<xsd:attributeGroup ref="type"/>

9042

<xsd:attributeGroup ref="role">

9043

<xsd:annotation>

9044

<xsd:documentation>

9045

<h:div class="specific"><h:tt>role</h:tt> depends on context, and indicates some purpose associated with the substance. It might indicate 'catalyst', 'solvent', 'antoxidant', etc. but is not limited to any vocabulary.</h:div>

9046

</xsd:documentation>

9047

</xsd:annotation>

9048

</xsd:attributeGroup>

9049

<xsd:attributeGroup ref="ref"/>

9050

<xsd:attributeGroup ref="count"/>

9051

<xsd:attributeGroup ref="state"/>

9052

</xsd:complexType>

9053

</xsd:element><xsd:element name="substanceList" id="el.substanceList">

9054

<xsd:annotation>

9055

<xsd:documentation>

9056

<h:div class="summary">A list of chemical substances.</h:div>

9057

<h:div class="description">Deliberately very general - see substance. substanceList is designed to manage solutions, mixtures, etc. and there is a small enumerated controlled vocabulary, but this can be extended through dictionaries.

9058

<h:p>substanceList can have an amount child. This can indicate the amount of a solution or mixture; this example describes 100 ml of 0.1M NaOH(aq). Although apparently longwinded it is precise and fully machine-interpretable</h:p></h:div>

9059

<h:div class="curation">Added role attribute, 2003-03-12.</h:div>

9060

<h:div class="example" href="substanceList1.xml"/>

9061

</xsd:documentation>

9062

</xsd:annotation>

9063

<xsd:complexType>

9064

<xsd:sequence>

9065

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

9066

<xsd:element ref="amount" minOccurs="0"/>

9067

9068

<xsd:element ref="substance" minOccurs="0" maxOccurs="unbounded"/>

9069

<!-- PMR 2003-01-26

9070

<xsd:sequence>

9071

<xsd:element ref="scalar" minOccurs="0" maxOccurs="unbounded"/>

9072

<xsd:element ref="array" minOccurs="0" maxOccurs="unbounded"/>

9073

<xsd:element ref="matrix" minOccurs="0" maxOccurs="unbounded"/>

9074

<xsd:element ref="list" minOccurs="0" maxOccurs="unbounded"/>

9075

</xsd:sequence>

9076

-->

9077

<xsd:element ref="propertyList" minOccurs="0"/>

9078

9079

</xsd:sequence>

9080

<xsd:attributeGroup ref="dictRef"/>

9081

<xsd:attributeGroup ref="convention"/>

9082

<xsd:attributeGroup ref="title"/>

9083

<xsd:attributeGroup ref="id"/>

9084

<xsd:attributeGroup ref="substanceListType"/>

9085

<xsd:attributeGroup ref="role"/>

9086

<xsd:attributeGroup ref="ref"/>

9087

</xsd:complexType>

9088

</xsd:element><xsd:element name="symmetry" id="el.symmetry">

9089

<xsd:annotation>

9090

<xsd:documentation>

9091

<h:div class="summary">Molecular, crystallographic or other symmetry.</h:div>

9092

<h:div class="description">

9093

<h:p>

9094

<h:tt>symmetry</h:tt> provides a label and/or symmetry operations for molecules

9095

or crystals. Point and spacegroups can be specified by strings, though these are not

9096

enumerated, because of variability in syntax (spaces, case-sensitivity, etc.),

9097

potential high symmetries (e.g. TMV disk is D17) and

9098

non-standard spacegroup settings. Provision is made for explicit symmetry operations

9099

through <matrix> child elements.</h:p>

9100

<h:p>By default the axes of symmetry are defined by the symbol - thus C2v requires

9101

z to be the unique axis, while P21/c requires b/y. Spacegroups imply the semantics

9102

defined in International Tables for Crystallography, (Int Union for Cryst., Munksgaard).

9103

Point groups are also defined therein. </h:p>

9104

<h:p>The element may also be used to give a label for the symmetry species (irreducible

9105

representation) such as "A1u" for a vibration or orbital.

9106

</h:p>

9107

<h:p>The matrices should be 3x3 for point group operators and 3x4 for spacegroup operators.

9108

The use of crystallographic notation ("x,1/2+y,-z") is not supported - this would

9109

be <matrix>1 0 0 0.0 0 1 0 0.5 0 0 1 0.0<matrix>.</h:p>

9110

<h:p>The default convention for point group symmetry is <h:tt>Schoenflies</h:tt> and for

9111

spacegroups is "H-M". Other conventions (e.g. "Hall") must be specfied through

9112

the <h:tt>convention</h:tt> attribute.</h:p>

9113

<h:p>This element implies that the Cartesians or fractional coordinates in a molecule

9114

are oriented appropriately. In some cases it may be useful to specify the symmetry of

9115

an arbitarily oriented molecule and the <molecule> element has the attribute

9116

<h:tt>symmetryOriented</h:tt> for this purpose.</h:p>

9117

<h:p>It may be better to use transform3 to hold the symmetry as they have fixed shape and

9118

have better defined mathematical operators.</h:p>

9119

</h:div>

9120

<h:div class="example" href="symmetry1.xml"/>

9121

<h:div class="curation">2005-11-03 PMR. Added transform3 as children. </h:div>

9122

</xsd:documentation>

9123

</xsd:annotation>

9124

<xsd:complexType>

9125

<xsd:sequence>

9126

<xsd:element ref="matrix" minOccurs="0" maxOccurs="unbounded"/>

9127

<xsd:element ref="transform3" minOccurs="0" maxOccurs="unbounded"/>

9128

</xsd:sequence>

9129

<xsd:attributeGroup ref="dictRef"/>

9130

<xsd:attributeGroup ref="convention"/>

9131

<xsd:attributeGroup ref="title"/>

9132

<xsd:attributeGroup ref="id"/>

9133

<xsd:attributeGroup ref="pointGroup"/>

9134

<xsd:attributeGroup ref="spaceGroup"/>

9135

<xsd:attributeGroup ref="irreducibleRepresentation"/>

9136

<xsd:attributeGroup ref="number">

9137

<xsd:annotation>

9138

<xsd:documentation>

9139

<h:div class="specific">The rotational symmetry number. Used for calculation of entropy, etc.</h:div>

9140

</xsd:documentation>

9141

</xsd:annotation>

9142

</xsd:attributeGroup>

9143

</xsd:complexType>

9144

</xsd:element><xsd:element name="system" id="el.system">

9145

<xsd:annotation>

9146

<xsd:documentation>

9147

<h:div class="summary">The complete system of components in a calculation.</h:div>

9148

<h:div class="description">There is no controlled vocabulary.</h:div>

9149

</xsd:documentation>

9150

</xsd:annotation>

9151

9152

<xsd:complexType>

9153

<xsd:sequence>

9154

<xsd:any minOccurs="0" maxOccurs="unbounded" processContents="lax"/>

9155

</xsd:sequence>

9156

<xsd:attributeGroup ref="dimensionality"/>

9157

<xsd:attributeGroup ref="periodicity"/>

9158

<xsd:attributeGroup ref="title"/>

9159

<xsd:attributeGroup ref="id"/>

9160

<xsd:attributeGroup ref="convention"/>

9161

<xsd:attributeGroup ref="dictRef"/>

9162

</xsd:complexType>

9163

</xsd:element><xsd:element name="table" id="el.table">

9164

<xsd:annotation>

9165

<xsd:documentation>

9166

<h:div class="summary">A rectangular table of any quantities.</h:div>

9167

<h:div class="description">

9168

<h:p>By default <h:tt>table</h:tt> represents a rectangular table of any simple quantities

9169

representable as XSD or CML dataTypes. There are three layouts, columnwise, rowwise and

9170

without markup. In all cases it is essential that the columns, whether explicit or

9171

otherwise, are homogeneous within the column. Also the metadata for each column must

9172

be given explicitly

9173

9174

<li>columns: For the first <h:tt>columns</h:tt> columns,

9175

where each column is a (homogeneous) <h:a href="el.array">array</h:a> of

9176

size <h:tt>rows</h:tt> data. This is the "normal" orientation of data tables

9177

but the table display could be transposed by XSLT transformation if required.

9178

Access is to columns, and thence to the data within them. DataTyping, delimiters,

9179

etc are delegated to the arrays, which must all be of the same size.

9180

</li>

9181

<li>rows: with explicit <tt>row</tt>s. The metadata is carried in a <tt>header</tt>

9182

element. Within each row the data are whitespace (or delimiter) separated.</li>

9183

<li>content: with a single <tt>content</tt> with columns moving fastest. The metadata is

9184

carried in a <tt>header</tt>

9185

element. Within the content the data are whitespace (or delimiter) separated.</li>

9186

</ul>

9187

For

9188

verification it is recommended that tables carry <h:tt>rows</h:tt> and <h:tt>columns</h:tt> attributes.

9189

</h:p>

9190

</h:div>

9191

<h:div class="example" href="table1.xml"/>

9192

<h:div class="example" href="table2.xml"/>

9193

<h:div class="example" href="table3.xml"/>

9194

</xsd:documentation>

9195

</xsd:annotation>

9196

<xsd:complexType>

9197

<xsd:sequence>

9198

<xsd:choice>

9199

9200

<xsd:element ref="array" minOccurs="0" maxOccurs="unbounded"/>

9201

9202

<xsd:sequence>

9203

<xsd:element ref="tableHeader" minOccurs="1" maxOccurs="1"/>

9204

<xsd:choice>

9205

9206

<xsd:element ref="trow" minOccurs="0" maxOccurs="unbounded"/>

9207

9208

<xsd:element ref="tableContent" minOccurs="0" maxOccurs="1"/>

9209

</xsd:choice>

9210

</xsd:sequence>

9211

</xsd:choice>

9212

</xsd:sequence>

9213

<xsd:attributeGroup ref="rows"/>

9214

<xsd:attributeGroup ref="columns"/>

9215

<xsd:attributeGroup ref="units"/>

9216

<xsd:attributeGroup ref="dataType"/>

9217

<xsd:attributeGroup ref="title"/>

9218

<xsd:attributeGroup ref="id"/>

9219

<xsd:attributeGroup ref="convention"/>

9220

<xsd:attributeGroup ref="dictRef"/>

9221

</xsd:complexType>

9222

</xsd:element><xsd:element name="tableContent" id="el.tableContent">

9223

<xsd:annotation>

9224

<xsd:documentation>

9225

<h:div class="summary">Unmarked content of a table.</h:div>

9226

<h:div class="description">

9227

<h:p>Metadata for rows must be defined in tableHeader. The elements of the

9228

table are ASCII strings in this content. They can be separated by whitespace

9229

or by a defined single character delimiter (see array for more information).

9230

</h:p>

9231

</h:div>

9232

<h:div class="example" href="table7.xml"/>

9233

</xsd:documentation>

9234

</xsd:annotation>

9235

<xsd:complexType>

9236

<xsd:simpleContent>

9237

<xsd:extension base="xsd:string">

9238

<xsd:attributeGroup ref="title"/>

9239

<xsd:attributeGroup ref="id"/>

9240

<xsd:attributeGroup ref="delimiter"/>

9241

<xsd:attributeGroup ref="convention"/>

9242

<xsd:attributeGroup ref="dictRef"/>

9243

</xsd:extension>

9244

</xsd:simpleContent>

9245

</xsd:complexType>

9246

</xsd:element><xsd:element name="tableHeader" id="el.tableHeader">

9247

<xsd:annotation>

9248

<xsd:documentation>

9249

<h:div class="summary">Header for a table.</h:div>

9250

<h:div class="description">

9251

<h:p>Used when the table has trow children or tableContent child.

9252

Contains the metadata as trows.</h:p>

9253

</h:div>

9254

<h:div class="example" href="table6.xml"/>

9255

<h:div class="example" href="table7.xml"/>

9256

</xsd:documentation>

9257

</xsd:annotation>

9258

<xsd:complexType>

9259

<xsd:sequence>

9260

<xsd:element ref="trow" minOccurs="0" maxOccurs="unbounded"/>

9261

</xsd:sequence>

9262

<xsd:attributeGroup ref="title"/>

9263

<xsd:attributeGroup ref="id"/>

9264

<xsd:attributeGroup ref="convention"/>

9265

<xsd:attributeGroup ref="dictRef"/>

9266

</xsd:complexType>

9267

</xsd:element><xsd:element name="tableRow" id="el.tableRow">

9268

<xsd:annotation>

9269

<xsd:documentation>

9270

<h:div class="summary">Explicit row of a table.</h:div>

9271

<h:div class="description">

9272

<h:p>Metadata for rows must be defined in tableHeader.</h:p>

9273

</h:div>

9274

<h:div class="example" href="table2.xml"/>

9275

</xsd:documentation>

9276

</xsd:annotation>

9277

<xsd:complexType>

9278

<xsd:simpleContent>

9279

<xsd:extension base="xsd:string">

9280

<xsd:attributeGroup ref="title"/>

9281

<xsd:attributeGroup ref="id"/>

9282

<xsd:attributeGroup ref="delimiter"/>

9283

<xsd:attributeGroup ref="convention"/>

9284

<xsd:attributeGroup ref="dictRef"/>

9285

</xsd:extension>

9286

</xsd:simpleContent>

9287

</xsd:complexType>

9288

</xsd:element><xsd:element name="tcell" id="el.tcell">

9289

<xsd:annotation>

9290

<xsd:documentation>

9291

<h:div class="summary">A cell in a row of a table.</h:div>

9292

<h:div class="description">tcell may either carry the header information

9293

for a column OR be a dat container of the table. Normally it contains

9294

simpleContent, but may also contain a single child element. It should

9295

NOT contain multiple children of any sort.</h:div>

9296

<h:div class="example" href="table5.xml"/>

9297

<h:div class="example" href="table6.xml"/>

9298

<h:div class="example" href="tabler.xml"/>

9299

</xsd:documentation>

9300

</xsd:annotation>

9301

<xsd:complexType mixed="true">

9302

<xsd:sequence minOccurs="1">

9303

<xsd:any processContents="lax" minOccurs="0"/>

9304

</xsd:sequence>

9305

<xsd:attributeGroup ref="units"/>

9306

<xsd:attributeGroup ref="dataType"/>

9307

<xsd:attributeGroup ref="title"/>

9308

<xsd:attributeGroup ref="id"/>

9309

<xsd:attributeGroup ref="convention"/>

9310

<xsd:attributeGroup ref="dictRef"/>

9311

</xsd:complexType>

9312

</xsd:element><xsd:element name="torsion" id="el.torsion">

9313

<xsd:annotation>

9314

<xsd:documentation>

9315

<h:div class="summary">A torsion angle ("dihedral") between 4 distinct atoms.</h:div>

9316

<h:div class="description">

9317

<h:p>The atoms need not be formally bonded. It can be used for:</h:p>

9318

<h:ul>

9319

<h:li>Recording experimentally determined torsion angles (e.g. in

9320

a crystallographic paper).</h:li>

9321

<h:li>Providing the torsion component for internal coordinates (e.g.

9322

z-matrix).</h:li>

9323

</h:ul>

9324

<h:p>Note that the order of atoms is important.</h:p></h:div>

9325

<h:div class="example" href="torsion1.xml"/>

9326

<h:div class="curation">2006-02-07: PMR. Fixed torsionAngleUnits</h:div>

9327

</xsd:documentation>

9328

</xsd:annotation>

9329

<xsd:complexType>

9330

<xsd:simpleContent>

9331

<xsd:extension base="torsionAngleType">

9332

<xsd:attributeGroup ref="title"/>

9333

<xsd:attributeGroup ref="id"/>

9334

<xsd:attributeGroup ref="convention"/>

9335

<xsd:attributeGroup ref="dictRef"/>

9336

<xsd:attributeGroup ref="atomRefs4"/>

9337

<xsd:attributeGroup ref="angleUnits"/>

9338

<xsd:attributeGroup ref="errorValue"/>

9339

<xsd:attributeGroup ref="errorBasis"/>

9340

<xsd:attributeGroup ref="min"/>

9341

<xsd:attributeGroup ref="max"/>

9342

<xsd:attributeGroup ref="ref"/>

9343

</xsd:extension>

9344

</xsd:simpleContent>

9345

</xsd:complexType>

9346

</xsd:element><xsd:element name="transform3" id="el.transform3">

9347

<xsd:annotation>

9348

<xsd:documentation>

9349

<h:div class="summary">A transform in 3-space.</h:div>

9350

<h:div class="description">A 3-D transform. Conventionally a 4x4 matrix.</h:div>

9351

</xsd:documentation>

9352

</xsd:annotation>

9353

<xsd:complexType>

9354

<xsd:simpleContent>

9355

<xsd:extension base="matrix44Type">

9356

<xsd:attributeGroup ref="convention"/>

9357

<xsd:attributeGroup ref="dictRef"/>

9358

<xsd:attributeGroup ref="id"/>

9359

<xsd:attributeGroup ref="title"/>

9360

</xsd:extension>

9361

</xsd:simpleContent>

9362

</xsd:complexType>

9363

</xsd:element><xsd:element name="transitionState" id="el.transitionState">

9364

<xsd:annotation>

9365

<xsd:documentation>

9366

<h:div class="summary">The transition state in a reaction.</h:div>

9367

<h:div class="description">

9368

<h:p>This will normally contain a <h:tt>molecule</h:tt> which in its 2D representation will have partial bonds. These are yet to be formalized for the <h:tt>molecule</h:tt> element.</h:p>

9369

<h:p>Although spectators may stabilise or otherwise interact with the transitionState they are not contained within it.</h:p>

9370

<h:p>A <h:tt>propertyList</h:tt> is provided to capture transitionState properties.</h:p>

9371

<h:p>Still experimental.</h:p></h:div>

9372

<h:div class="example" href="transitionState1.xml"/>

9373

</xsd:documentation>

9374

</xsd:annotation>

9375

9376

<xsd:complexType>

9377

<xsd:sequence>

9378

<xsd:element ref="molecule"/>

9379

<xsd:element ref="propertyList" minOccurs="0"/>

9380

</xsd:sequence>

9381

<xsd:attributeGroup ref="title"/>

9382

<xsd:attributeGroup ref="id"/>

9383

<xsd:attributeGroup ref="convention"/>

9384

<xsd:attributeGroup ref="dictRef"/>

9385

</xsd:complexType>

9386

</xsd:element><xsd:element name="trow" id="el.trow">

9387

<xsd:annotation>

9388

<xsd:documentation>

9389

<h:div class="summary">A row in a table.</h:div>

9390

<h:div class="description">trow may either carry all the header information,

9391

OR be a row of the table. In both cases it must contain tcells.

9392

</h:div>

9393

<h:div class="example" href="table5.xml"/>

9394

<h:div class="example" href="table6.xml"/>

9395

<h:div class="example" href="tabler.xml"/>

9396

</xsd:documentation>

9397

</xsd:annotation>

9398

<xsd:complexType>

9399

<xsd:sequence>

9400

<xsd:element ref="tcell" minOccurs="0" maxOccurs="unbounded"/>

9401

</xsd:sequence>

9402

<xsd:attributeGroup ref="dataType">

9403

<xsd:annotation>

9404

<xsd:documentation>

9405

<h:div class="specific">Only required when in tableHeader.

9406

This indicates that the objects in the cells of this row are

9407

of the type given by this value (normally "title",

9408

"units", "dictRef", "id").</h:div>

9409

</xsd:documentation>

9410

</xsd:annotation>

9411

</xsd:attributeGroup>

9412

<xsd:attributeGroup ref="title"/>

9413

<xsd:attributeGroup ref="id"/>

9414

<xsd:attributeGroup ref="convention"/>

9415

<xsd:attributeGroup ref="dictRef"/>

9416

</xsd:complexType>

9417

</xsd:element><xsd:element name="unit" id="el.unit">

9418

<xsd:annotation>

9419

<xsd:documentation>

9420

<h:div class="summary">A scientific unit.</h:div>

9421

<h:div class="description">

9422

<h:p>A scientific unit. Units are of the following types:</h:p>

9423

<h:ul>

9424

<h:li>SI Units. These may be one of the seven fundamental types

9425

(e.g. meter) or may be derived (e.g. joule). An SI unit is

9426

identifiable because it has no parentSI attribute and will have

9427

a unitType attribute. 2005-122-17 - this may be obsolete; PMR</h:li>

9428

<h:li>nonSI Units. These will normally have a parent SI unit

9429

(e.g. calorie has joule as an SI parent). </h:li>

9430

<h:li>

9431

Constructed units. These use a syntax of the form:

9432

<h:pre>

9433

<unit id="g.s-1" name="gram per second"

9434

unitType="myUnitType:massPerTime">

9435

9436

9437

</unit>

9438

</h:pre>

9439

This defines a new unit (g.s-1) which is composed from two

9440

existing units (units:g and siUnits:s) to create a new unit. The

9441

conversion to SI is computed from the two child units and may be

9442

added as a 'multiplierToSI' attribute. Only siUnits or units with

9443

'multiplierToSI' can be used as child units; 'constantToSI cannot

9444

be used yet. If the new unit points to a unitType then the dimension

9445

can be checked. Thus if the published dimension of massPerTime does not

9446

agree with mass.length-1 an error is throwable.

9447

Alternatively a new unitType can be added as a child.

9448

</h:li>

9449

</h:ul>

9450

<h:p>

9451

The relationship of a unit to its SI parent is potentially complex and

9452

inconsistencies may arise. The following are available:

9453

<h:ul>

9454

<h:li>parentSI. This points to the ID of a parent SI unit. If this ID is the

9455

same as the current unit the implication is that this is an SI unit.

9456

</h:li>

9457

<h:li>isSI. a boolean indicating whether the current unit is SI.

9458

</h:li>

9459

<h:li>multiplierToSI and constantToSI. If these are 1.0 and 0.0 (or missing)

9460

the implication is that this unit is SI. However this is fragile as units can

9461

be defined without these attributes and a unit could coincidentally have

9462

no numeric differences but not be an SI unit.

9463

</h:li>

9464

</h:ul>

9465

</h:p>

9466

</h:div>

9467

9468

<h:div class="example" href="unit1.xml"/>

9469

<h:div class="curation">2003:04-09 Description or parentSI attribute enhance.</h:div>

9470

</xsd:documentation>

9471

<xsd:appinfo>

9472

</xsd:appinfo>

9473

</xsd:annotation>

9474

9475

<xsd:complexType>

9476

<xsd:choice minOccurs="0" maxOccurs="unbounded">

9477

<xsd:element ref="description"/>

9478

<xsd:element ref="annotation"/>

9479

<xsd:element ref="definition" minOccurs="0" maxOccurs="1"/>

9480

<xsd:element ref="unit" minOccurs="0" maxOccurs="unbounded">

9481

<xsd:annotation>

9482

<xsd:documentation>

9483

<h:div class="summary">Child unit used to build new unit.</h:div>

9484

<h:div class="description">

9485

<h:p>These children must have 'units' and 'power' attributes.</h:p></h:div>

9486

</xsd:documentation>

9487

</xsd:annotation>

9488

</xsd:element>

9489

<xsd:element ref="unitType" minOccurs="0" maxOccurs="1">

9490

<xsd:annotation>

9491

<xsd:documentation>

9492

<h:div class="summary">Child unitType describing type of new unit.</h:div>

9493

<h:div class="description">

9494

<h:p>This can be added by the author (in which case they are

9495

responsible for checking consistency) or calculated by the software

9496

from the child units.</h:p></h:div>

9497

</xsd:documentation>

9498

</xsd:annotation>

9499

</xsd:element>

9500

</xsd:choice>

9501

9502

<xsd:attributeGroup ref="id"/>

9503

<xsd:attributeGroup ref="units">

9504

<xsd:annotation>

9505

<xsd:documentation>

9506

<h:div class="summary">Reference to a unit.</h:div>

9507

<h:div class="description">

9508

<h:p>This is used for the identification of child units when

9509

new units are composed from existing ones. Athough the syntax looks

9510

unusual it takes advantage of the tools for resolving units. See above for

9511

syntax.

9512

</h:p></h:div>

9513

</xsd:documentation>

9514

</xsd:annotation>

9515

</xsd:attributeGroup>

9516

<xsd:attributeGroup ref="title"/>

9517

<xsd:attributeGroup ref="abbreviation">

9518

<xsd:annotation>

9519

<xsd:documentation>

9520

<h:div class="summary">Abbreviation for the unit.</h:div>

9521

<h:div class="description">

9522

<h:p>This may be obsolete and symbol should be preferred.</h:p></h:div>

9523

</xsd:documentation>

9524

</xsd:annotation>

9525

</xsd:attributeGroup>

9526

<xsd:attributeGroup ref="symbol">

9527

<xsd:annotation>

9528

<xsd:documentation>

9529

<h:div class="summary">Symbol for the unit.</h:div>

9530

<h:div class="description">

9531

<h:p>This may be used for typographical display but NOT for identification

9532

as there is considerable variation in use.</h:p></h:div>

9533

<h:div class="curation">2006-01-29: PMR. Added attribute.</h:div>

9534

</xsd:documentation>

9535

</xsd:annotation>

9536

</xsd:attributeGroup>

9537

<xsd:attributeGroup ref="name"/>

9538

<xsd:attributeGroup ref="parentSI"/>

9539

<xsd:attributeGroup ref="isSI"/>

9540

<xsd:attributeGroup ref="unitType"/>

9541

9542

<xsd:attributeGroup ref="multiplierToData"/>

9543

<xsd:attributeGroup ref="multiplierToSI"/>

9544

<xsd:attributeGroup ref="constantToSI"/>

9545

9546

<xsd:attributeGroup ref="power">

9547

<xsd:annotation>

9548

<xsd:documentation>

9549

<h:div class="summary">Power of unit used to creat new one.</h:div>

9550

<h:div class="description">

9551

<h:p>Only allowed on child units</h:p></h:div>

9552

</xsd:documentation>

9553

</xsd:annotation>

9554

</xsd:attributeGroup>

9555

</xsd:complexType>

9556

</xsd:element><xsd:element name="unitList" id="el.unitList">

9557

<xsd:annotation>

9558

<xsd:documentation>

9559

<h:div class="summary">A container for several unit entries.</h:div>

9560

<h:div class="description">Usually forms the complete units dictionary

9561

(along with metadata). Note: this used to hold both units and unitTypes

9562

(though in separate files). This was unwieldy and unitTypeList has been

9563

created to hold unitTypes. Implementers are recommended to change

9564

any unitList/unitType to unitTypeList/unitType</h:div>

9565

<h:div class="example" href="unitList1.xml"/>

9566

<h:div class="curation">2005-12-15. PMR. added namespace

9567

and dictionaryPrefix.</h:div>

9568

<h:div class="curation">2005-12-17. PMR. added siNamespace .</h:div>

9569

<h:div class="curation">2006-01-28. PMR. deprecated use for holding unitType.</h:div>

9570

</xsd:documentation>

9571

</xsd:annotation>

9572

9573

<xsd:complexType>

9574

<xsd:sequence>

9575

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

9576

<xsd:element ref="unitType" minOccurs="0" maxOccurs="unbounded">

9577

<xsd:annotation>

9578

<xsd:documentation>

9579

<h:div class="deprecated">2006-01-28: PMR. use unitTypeList.</h:div>

9580

</xsd:documentation>

9581

</xsd:annotation>

9582

</xsd:element>

9583

<xsd:element ref="unit" minOccurs="0" maxOccurs="unbounded"/>

9584

</xsd:sequence>

9585

<xsd:attributeGroup ref="title"/>

9586

<xsd:attributeGroup ref="id"/>

9587

<xsd:attributeGroup ref="convention"/>

9588

<xsd:attributeGroup ref="dictRef"/>

9589

<xsd:attributeGroup ref="unitListType">

9590

<xsd:annotation>

9591

<xsd:documentation>

9592

<h:div class="deprecated">2006-01-28: PMR. use unitTypeList.</h:div>

9593

</xsd:documentation>

9594

</xsd:annotation>

9595

</xsd:attributeGroup>

9596

<xsd:attributeGroup ref="namespace"/>

9597

<xsd:attributeGroup ref="siNamespace"/>

9598

<xsd:attributeGroup ref="dictionaryPrefix"/>

9599

<xsd:attributeGroup ref="href">

9600

<xsd:annotation>

9601

<xsd:documentation>

9602

<h:div class="specific">Maps dictRef prefix to the location of a dictionary. This requires the prefix and the physical URI address to be contained within the same file. We can anticipate that better mechanisms will arise - perhaps through XMLCatalogs. At least it works at present.</h:div>

9603

</xsd:documentation>

9604

</xsd:annotation>

9605

</xsd:attributeGroup>

9606

</xsd:complexType>

9607

</xsd:element><xsd:element name="unitType" id="el.unitType">

9608

<xsd:annotation>

9609

<xsd:documentation>

9610

<h:div class="summary">The type of a scientific unit.</h:div>

9611

<h:div class="description">

9612

<h:p>Mandatory for SI Units, optional for nonSI units since they should be able to obtain this from their parent. For complex derived units without parents it may be useful.</h:p>

9613

<h:p>Used within a unitList</h:p>

9614

<h:p>Distinguish carefully from <h:a href="st.unitsType">unitsType</h:a>

9615

which is primarily used for attributes describing the units that elements

9616

carry</h:p></h:div>

9617

<!--

9618

<h:div class="example" href="unit2.xml"></h:div>

9619

-->

9620

<h:div class="example" href="unitType1.xml"/>

9621

<!--

9622

<h:div class="example" href="unitType2.xml"></h:div>

9623

-->

9624

<h:div class="curation">2006-02-06: PMR. Added preserve and symbol attributes.</h:div>

9625

</xsd:documentation>

9626

</xsd:annotation>

9627

9628

<xsd:complexType>

9629

<xsd:choice minOccurs="0" maxOccurs="unbounded">

9630

<xsd:element ref="annotation"/>

9631

<xsd:element ref="dimension" minOccurs="0" maxOccurs="unbounded"/>

9632

<xsd:element ref="description" minOccurs="0" maxOccurs="unbounded"/>

9633

<xsd:element ref="definition" minOccurs="0" maxOccurs="1"/>

9634

</xsd:choice>

9635

<xsd:attributeGroup ref="id"/>

9636

<xsd:attributeGroup ref="name"/>

9637

<xsd:attributeGroup ref="title"/>

9638

<xsd:attributeGroup ref="parentSI"/>

9639

<xsd:attributeGroup ref="abbreviation"/>

9640

<xsd:attributeGroup ref="preserve"/>

9641

<xsd:attributeGroup ref="symbol"/>

9642

</xsd:complexType>

9643

</xsd:element><xsd:element name="unitTypeList" id="el.unitTypeList">

9644

<xsd:annotation>

9645

<xsd:documentation>

9646

<h:div class="summary">A container for several unitType entries.</h:div>

9647

<h:div class="description">Usually forms the complete unitTypes dictionary

9648

(along with metadata). Note: unitTypes used to be held under unitList, but

9649

this was complicated to implement and unitTypeList makes a clean separation.

9650

</h:div>

9651

<h:div class="example" href="unitTypeList1.xml"/>

9652

<h:div class="curation">2006-01-28. PMR. created.</h:div>

9653

</xsd:documentation>

9654

</xsd:annotation>

9655

9656

<xsd:complexType>

9657

<xsd:sequence>

9658

<xsd:element ref="metadataList" minOccurs="0" maxOccurs="unbounded"/>

9659

<xsd:element ref="unitType" minOccurs="0" maxOccurs="unbounded"/>

9660

</xsd:sequence>

9661

<xsd:attributeGroup ref="title"/>

9662

<xsd:attributeGroup ref="id"/>

9663

<xsd:attributeGroup ref="convention"/>

9664

<xsd:attributeGroup ref="dictRef"/>

9665

<xsd:attributeGroup ref="namespace"/>

9666

<xsd:attributeGroup ref="siNamespace"/>

9667

<xsd:attributeGroup ref="dictionaryPrefix"/>

9668

<xsd:attributeGroup ref="href">

9669

<xsd:annotation>

9670

<xsd:documentation>

9671

<h:div class="specific">Maps dictRef prefix to the location of a

9672

dictionary. This requires the prefix and the physical URI address

9673

to be contained within the same file. We can anticipate that

9674

better mechanisms will arise - perhaps through XMLCatalogs. At

9675

least it works at present.</h:div>

9676

</xsd:documentation>

9677

</xsd:annotation>

9678

</xsd:attributeGroup>

9679

</xsd:complexType>

9680

</xsd:element><xsd:element name="vector3" id="el.vector3">

9681

<xsd:annotation>

9682

<xsd:documentation>

9683

<h:div class="summary">A vector in 3-space.</h:div>

9684

<h:div class="description">The vector may have magnitude but is not rooted on

9685

any points (use line3).</h:div>

9686

</xsd:documentation>

9687

</xsd:annotation>

9688

<xsd:complexType>

9689

<xsd:simpleContent>

9690

<xsd:extension base="vector3Type">

9691

<xsd:attributeGroup ref="convention"/>

9692

<xsd:attributeGroup ref="dictRef"/>

9693

<xsd:attributeGroup ref="id"/>

9694

<xsd:attributeGroup ref="title"/>

9695

<xsd:attributeGroup ref="units"/>

9696

</xsd:extension>

9697

</xsd:simpleContent>

9698

</xsd:complexType>

9699

</xsd:element><xsd:element name="xaxis" id="el.xaxis">

9700

<xsd:annotation>

9701

<xsd:documentation>

9702

<h:div class="summary">The x-axis.</h:div>

9703

<h:div class="description">A container for all information relating to the x-axis (including scales, offsets, etc.) and the data themselves (in an <h:tt>array</h:tt>). Note: AniML uses "xValues" so avoid confusion with this.</h:div>

9704

9705

<h:div class="example" href="xaxis1.xml"/>

9706

</xsd:documentation>

9707

</xsd:annotation>

9708

9709

<xsd:complexType>

9710

<xsd:sequence>

9711

<xsd:element ref="array">

9712

<xsd:annotation>

9713

<xsd:documentation>

9714

<h:div>The x-data. These must match the y-data in number and order. There are tools to allow scaling and transformation (though unscaled data must be very carefully defined).</h:div>

9715

</xsd:documentation>

9716

</xsd:annotation>

9717

</xsd:element>

9718

</xsd:sequence>

9719

<xsd:attributeGroup ref="dictRef"/>

9720

<xsd:attributeGroup ref="convention"/>

9721

<xsd:attributeGroup ref="title"/>

9722

<xsd:attributeGroup ref="id"/>

9723

<xsd:attributeGroup ref="ref"/>

9724

<xsd:attributeGroup ref="multiplierToData"/>

9725

<xsd:attributeGroup ref="constantToData"/>

9726

</xsd:complexType>

9727

</xsd:element><xsd:element name="yaxis" id="el.yaxis">

9728

<xsd:annotation>

9729

<xsd:documentation>

9730

<h:div class="summary">The y-axis.</h:div>

9731

<h:div class="description">A container for all information relating to the y-axis (including scales, offsets, etc.) and the data themselves (in an <h:tt>array</h:tt>).</h:div>

9732

<h:div class="example" href="yaxis1.xml"/>

9733

</xsd:documentation>

9734

</xsd:annotation>

9735

9736

9737

<xsd:complexType>

9738

<xsd:sequence>

9739

<xsd:element ref="array">

9740

<xsd:annotation>

9741

<xsd:documentation>

9742

<h:div>The y-data. These must match the x-data in number and order. There are tools to allow scaling and transformation (though unscaled data must be very carefully defined).</h:div>

9743

</xsd:documentation>

9744

</xsd:annotation>

9745

</xsd:element>

9746

</xsd:sequence>

9747

<xsd:attributeGroup ref="dictRef"/>

9748

<xsd:attributeGroup ref="convention"/>

9749

<xsd:attributeGroup ref="title"/>

9750

<xsd:attributeGroup ref="id"/>

9751

<xsd:attributeGroup ref="ref"/>

9752

<xsd:attributeGroup ref="multiplierToData"/>

9753

<xsd:attributeGroup ref="constantToData"/>

9754

</xsd:complexType>

9755

</xsd:element><xsd:element name="zMatrix" id="el.zMatrix">

9756

<xsd:annotation>

9757

<xsd:documentation>

9758

<h:div class="summary">A zMatrix.</h:div>

9759

<h:div class="description">A container for <h:tt>length</h:tt>, <h:tt>angle</h:tt> and <h:tt>torsion</h:tt>, which must be arranged in the conventional zMatrix format.</h:div>

9760

<h:div class="example" href="zMatrix1.xml"/>

9761

</xsd:documentation>

9762

</xsd:annotation>

9763

9764

<xsd:complexType>

9765

<xsd:sequence>

9766

<xsd:choice minOccurs="0" maxOccurs="unbounded">

9767

<xsd:element ref="length"/>

9768

<xsd:element ref="angle"/>

9769

<xsd:element ref="torsion"/>

9770

</xsd:choice>

9771

</xsd:sequence>

9772

<xsd:attributeGroup ref="title"/>

9773

<xsd:attributeGroup ref="id"/>

9774

<xsd:attributeGroup ref="convention"/>

9775

<xsd:attributeGroup ref="dictRef"/>

9776

</xsd:complexType>

9777

</xsd:element></xsd:schema>

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