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- Committer: Bazaar Package Importer
- Author(s): Michael Banck
- Date: 2004-05-19 21:47:27 UTC
- mfrom: (1.1.1 upstream)
- Revision ID: james.westby@ubuntu.com-20040519214727-31y54lrvns5df8gn
Tags: 1.6.3-2
* debian/menu (needs, section): Quote entries.
* debian/rules.old: Removed file.
* chemtool.1: Added section and removed to superfluous spaces.
* debian/control (Standards-Version): Bumped to 3.6.1.0.
* debian/chemtool.install: Renamed to...
* debian/install: This.
* debian/chemtool.xpm: New file, a 32x32 version of chemtool.xpm.
* debian/install: Install debian/chemtool.xpm into /usr/share/pixmaps.
* debian/rules.old: Removed file.
* chemtool.1: Added section and removed to superfluous spaces.
* debian/control (Standards-Version): Bumped to 3.6.1.0.
* debian/chemtool.install: Renamed to...
* debian/install: This.
* debian/chemtool.xpm: New file, a 32x32 version of chemtool.xpm.
* debian/install: Install debian/chemtool.xpm into /usr/share/pixmaps.
- files added:
- NEWS
- debian/patches
- debian/patches-held
- pld
- files removed:
- examples/camphor
- files modified:
- ChangeLog
added
removed
README
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-------------------------------------------------------------------------------
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Chemtool Version 1.5
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Chemtool Version 1.6.1
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-------------------------------------------------------------------------------
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Chemtool is a program for drawing organic molecules easily and store them as
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a X bitmap file. It runs under the X Window System using the GTK widget set.
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An older version (1.1.8) that requires only the standard Athena Widget Set
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(Xlib) is still available for situations where GTK cannot be installed for
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some reason. In principle, all features added since 1.1.8 could be
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back-ported to the Xlib-based version if necessary.
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----------------------> Usage:
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This program is intended to be very simple to use. You should be able to
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find out most things by yourself. :-)
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Most operations in chemtool can be accomplished using the mouse - the
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first (usually the left) button is used to select or place things, the
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middle button modifies properties (e.g. reverses the direction of a bond),
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and the right button is used to delete objects.
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The program offers essentially unlimited undo/redo, two text fonts plus
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symbols, seven colors, drawing at several zoom scales, and square and
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hexagonal backdrop grids for easier alignment.
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Drawing of bonds:
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appropriate angular positions. Dragging the mouse while holding down the
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button draws a line in the desired direction.
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All bonds are initially drawn as single lines (or the linetype that is
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preselected from the menubar) that can be converted to other types later.
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Pressing the middle mousebutton on a bond increments its type code (see below),
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while pressing the third (usually the right) button deletes the bond next
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The bond style chooser in the center of the button bar determines the type
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of bond that is drawn - initially, this is a single bond. If you want to
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change the type of a bond later, either click on it with the middle button
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of your mouse to advance to the next type(s), or select the appropriate type
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in the chooser and then switch to bondtype mode and pick all bonds that you
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want to change over to the new type. Pressing the middle mousebutton on a
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bond when in 'Bondtype' mode reverses the direction of that bond.
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The bond types available in chemtool are
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- a single bond
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- a double bond (with one line shorter than the other)
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- a double bond (having the shorter line on the opposite side)
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- a centered double bond
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- a triple bond (with the flanking lines shorter than the center)
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- a wedge-shaped bond
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- a dashed wedge-shaped bond
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- a wavy line
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- a dashed wide line
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- a half arrow
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- an arrow
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- a wide bond
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- a circle
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- a dotted line
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- a single bond that 'cuts out' a segment from any bond it crosses
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- a triple bond (with equal line lengths)
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- a quadruple bond
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The additional bond type available in the pulldown menu,
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- curved arrow
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is special insofar as no other bond type can be converted to or from
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this type. (it is actually a shortcut for one of the curve-drawing functions
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described below).
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Pressing the third (usually the right) mouse button deletes the bond next
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to the cursor position.
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Semiautomatic drawing of rings:
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Rings of 3 to 12 members can be drawn easily by holding down the Ctrl key
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'Move' mode, where they can be dragged around to change the form of a curve
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after it is drawn.
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Setting bond style:
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In bond style mode, clicking on any bond in the diagram cycles its representation
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through the sequence
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- double bond
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- double bond (shorter line on the other side)
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- centered double bond
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- triple bond
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- wedge-shaped bond
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- dashed wedge-shaped bond
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- wavy line
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- half arrow
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- arrow
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- wide bond
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- circle
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- dotted line
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- single bond that 'cuts out' a segment from any bond it crosses
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The additional bond type available in the pulldown menu,
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- curved arrow
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is only available for drawing. It is actually a shortcut for one of
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the curve drawing functions described above, with the second and third
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control points automatically generated. As such, it can not be converted
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to or from any of the conventional bond types.
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For drawing curved arrows, there is also a predefined function in the bond
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style chooser. This is actually a shortcut for one of the curve drawing
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functions described above, with the second and third control points
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automatically generated. As such, it can not be converted to or from any
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of the conventional bond types.
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(One can, however, convert it to any of the other curve types, e.g. to change
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the type of arrowhead). The shape of the arrow will usually need to be
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adjusted by shifting the control point that appears alongside it in 'Move'
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mode.
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Pressing the middle mousebutton on a bond when in 'Bondtype' mode reverses
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the direction of that bond.
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Inserting text:
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Text written into the text box can be positioned with the cursor and may
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appear left, middle or right-aligned in the drawing.
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appear left, middle or right-aligned in the drawing. The font size can
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be selected from the chooser to the right of the text entry field, while
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the 't/T' button next to the text-alignment buttons lets you switch between
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two fonts - Helvetica for regular labels, and Times Roman for descriptions.
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Like the line drawings, text can be in any of the colors available on the
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color selector. If you want to change the color, font or alignment of a
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label afterwards, just choose the appropriate combination of settings and
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then select the desired label with the left mouse button. When the text
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entry area is empty, this will just update the properties without changing
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the text itself. When the text entry area is not empty, its contents will
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also replace the text of the label. Copying the text of a label to the
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entry area is done with the middle mouse button, while the right mouse
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button deletes the selected label.
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There are two special characters to be used for sub- and superscripting
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the following character:
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'_' to shift down (e.g. CH_3)
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The control character '|' is used to itializise the following character,
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as in |t-Bu.
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as in |t-Bu, while the '#' character boldfaces it.
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The special character '@' switches to symbol mode, which uses the standard
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X11 symbol font. All alphabetic keys produce the corresponding greek
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Labeling shortcuts :
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In all bond drawing modes, several keyboard shortcuts are available to
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simplify adding atom symbols at the current drawing position (the endpoint
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of the last line drawn, or the spot last clicked on).
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The keys 'c','h','n','o','s','p' and 'r' insert the corresponding letter,
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'l' (lowercase L) inserts 'Cl', while '1', '2', '3' insert CH,CH_2 and CH_3,
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respectively. The asterisk key (*) inserts a filled circle. The keys of the
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numeric keypad can be used to draw short 'electron pair' lines next to an
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add atom symbols without having to leave drawing mode. The label is placed
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at the current drawing position (the endpoint of the last line drawn, or
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the spot last clicked on).
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The keys 'c','h','n','o','s','p' and 'r' insert the corresponding capital
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letter, 'l' (lowercase L) inserts 'Cl', while '1', '2', '3' insert CH,CH_2
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and CH_3, respectively. The asterisk key (*) inserts a filled circle.
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Pressing the space bar once allows you to enter arbitrary labels, which will
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be placed at the current position when you press the Return key.
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The keys of the numeric keypad can be used to draw short 'electron pair' lines next to an
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element symbol - if one imagines the element symbol to be sitting on the
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central '5' key, each key draws the appropriate electron pair for its
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position.
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Centering:
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If there is not enough space for your molecule you can
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put it in the middle of the sheet with the center button.
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Exporting to foreign formats:
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You can export your molecules as an X bitmap, an encapsulated postscript file,
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an input file for Brian Smith' XFig program, as an MDL molfile, or in the
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PicTeX format.
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The PicTeX and Postscript output functions rely on the fig2dev program from the
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transfig package.
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You can create the outputs in different sizes according to the current zoom
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scale. The PicTeX and Postscript modes additionally allow scaling to an
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arbitrary percentage selectable on the export menu .
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To include the PicTeX-file in your LaTeX document, you will need the pictex
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macro package. Depending on the versions you use, you might also have to load
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the 'color' package in the preamble of your LaTeX file.
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If you experience 'TeX capacity exceeded' error messages, increase the
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extra_mem_bot parameter in your texmf.cnf file (usually located in
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/usr/share/texmf/web2c, /usr/local/texmf or /etc/texmf).
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Pictex is known for its unusual (by tex standards) memory requirements, and
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the standard settings often do not account for this (although you may find a
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comment a la 'change this if you use pictex' in the texmf.cnf file).
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Something like extra_mem_bot=400000 should not hurt on any moderately modern
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system.
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Selecting all or parts of a drawing for transformations:
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For quick numbering of the atoms in a molecule, switch to one of the text
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modes, hold down the Control key and pick each atom in succession with
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the left mouse button. Numbering starts at 1, and the sequence can be reset
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at any time by clicking the right mouse button. If you need to use your own
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numbering scheme, clicking the middle button (while still holding down the
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Control key) makes it pick up whatever number is in the text entry field.
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Moving, rotating, flipping or scaling objects
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Using the 'Mark' button, you can easily select parts of the current drawing
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by enclosing them with a 'rubberband' rectangle. The selected parts will appearhighlighted in blue and are immediately available for
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by enclosing them with a 'rubberband' rectangle. If you need to add atoms
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outside of the rectangular area to your selection, simply draw another
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rubberband around them while holding down the Ctrl key.
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The selected parts will appear highlighted in blue and are immediately
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available for
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- moving: simply drag the fragment to the desired position with the mouse
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while holding down the left mouse button. Pressing the Ctrl key
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(usually the right) mouse button after it is highlighted.
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- optimizing: clicking on the 'bucket and broom' symbol invokes a function
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that removes overlapping (duplicate) bonds and labels from
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the drawing.
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the drawing and tries to straighten bonds that are almost
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horizontal or vertical.
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- bracketing and framing: clicking on the bracket button invokes a pop-up
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menu offering a choice of brackets and various boxes. The chosen item
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is drawn in the size and position determined by the marker box that was
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drawn by the user.
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Centering the drawing:
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If there is not enough space for your molecule you can
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put it in the middle of the sheet with the center button.
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Exporting to foreign formats:
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You can export your molecules as an X bitmap, an encapsulated postscript file,
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an input file for Brian Smith' XFig program, as an MDL molfile, or in the
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PicTeX format.
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The PicTeX and Postscript output functions rely on the fig2dev program from the
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transfig package.
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You can create the outputs in different sizes according to the current zoom
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scale. The PicTeX and Postscript modes additionally allow scaling to an
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arbitrary percentage selectable on the export menu .
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To include the PicTeX-file in your LaTeX document, you will need the pictex
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macro package. Depending on the versions you use, you might also have to load
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the 'color' package in the preamble of your LaTeX file.
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If you experience 'TeX capacity exceeded' error messages, increase the
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extra_mem_bot parameter in your texmf.cnf file (usually located in
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/usr/share/texmf/web2c, /usr/local/texmf or /etc/texmf).
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Pictex is known for its unusual (by tex standards) memory requirements, and
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the standard settings often do not account for this (although you may find a
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comment a la 'change this if you use pictex' in the texmf.cnf file).
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Something like extra_mem_bot=400000 should not hurt on any moderately modern
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system.
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Adding previously saved figures:
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button. Marking a file in the dialog automatically displays its contents
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in a small preview window.
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The newly added molecule is automatically made active so that it can be
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repositioned as desired.
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repositioned as desired. If you want to add it to a predefined position
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on another molecule, you can mark that attachment site by left-clicking
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on it instead of dragging the marker rectangle. A small green dot will
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appear at what is now the reference position for the new part. If you save
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molecules with such a marker set, it will in turn define their attachment
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site when they are added to another drawing.
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Adding one of the predefined templates:
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Pressing the 'Templates' button opens a second window with a small collection
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of predefined structures. Simply click on the preview of the desired molecule
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to add it to your drawing. The Template window can be kept open throughout a
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chemtool session - if it is hidden by another window, you can move it to the
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front by clicking the 'Template' button in chemtool again.
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Choosing 'Templates' from the 'Tools' menu opens a second window with a small
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collection of predefined structures.
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Simply click on the image of the desired molecule to add it to your drawing.
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The Template window can be kept open throughout a chemtool session - if it
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is hidden by another window, you can move it to the front by clicking the
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'Template' button in chemtool again.
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The data in the template system differ from normal chemtool drawings only by
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the fact that they are stored within the program, and in a slightly awkward
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format (x and y coordinates listed separately in the source file templates.h).
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Chemtool is able to import files written either in the PDB format originally
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used by the Protein Databank (which is now also written by most modeling
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packages), or in the molfile (V2000) format developed by MDL Inc. for their
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ISIS products. As both formats can contain 3D information, while chemtool
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ISIS products.
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As both formats can contain 3D information, while chemtool
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at least currently does 2D drawing only, the molecule is imported as a temporary3D image first, which can be rotated using the mouse (with Z-axis rotation
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initiated by pressing the Ctrl key simultaneously with the (left) mouse
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button 1). After pressing the Return key, the current orientation is stored
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from CONECT records, if present, or guessed from the interatomic distances.
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In MDL import mode, C atom labels are automatically suppressed, and bond
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types are preserved where possible.
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If you have a version of the BABEL program installed - either the original
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Babel written by Pat Walters or the current OpenBabel effort - chemtool will
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automatically offer a menu option for importing from any of the file formats
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this supports.
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Determining sum formula and molecular weight:
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reaction arrows and by the 'aromatic ring' symbol, so you should avoid these
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and check the plausibility of the generated sum formula where possible.
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The following common abbreviations are known to cht:
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Ac # C2 H3 O # Acetyl
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Ade # C5 H4 N5 # Adeninyl
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Bn # C7 H7 # Benzyl
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Bu # C4 H9 # Butyl
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Bz # C7 H5 O # Benzoyl
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BOC # C5 H9 O2 # Butyloxycarbonyl
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CE # C3 H4 N # Cyanoethyl
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Cyt # C4 H4 N3 O # Cytosinyl
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DBAM # C9 H19 N # Dibutylaminomethylene, biradical
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DMAM # C3 H7 N # Dimethylaminomethylen, biradical
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DMTr # C21 H19 O2 # Dimethoxytrityl
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Et # C2 H5 # Ethyl
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Gua # C5 H4 N5 O # Guaninyl
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iBu # C4 H9 # iso-Butyl
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iPr # C3 H7 # iso-Propyl
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Me # C H3 # Methyl
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Ms # C H3 S O2 # Mesyl
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MOC # C2 H3 O2 # Methoxycarbonyl
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MOM # C2 H5 O # Methoxymethyl
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MMTr # C20 H16 O # Monomethoxytrityl
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Ph # C6 H5 # Phenyl
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@F (phi)# C6 H5 # Phenyl
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Pr # C3 H7 # Propyl
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TBDMS # C6 H15 Si # tert-Butyldimethylsilyl
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TBDPS # C16 H19 Si # tert-Butyldiphenylsilyl
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tBu # C4 H9 # tert-Butyl
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Tf # C F3 S O2 # Triflyl
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Thy # C5 H5 N2 O2 # Thyminyl
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TMS # C3 H9 Si # Trimethylsilyl
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TMTr # C22 H22 O3 # Dimethoxytrityl
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Tol # C8 H7 O # Tolyl
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Tr # C19 H15 # Trityl
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Ts # C7 H7 S O2 # Tosyl
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Ura # C4 H3 N2 O2 # Uracilyl
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Z # C8 H7 O2 # Benzyloxycarbonyl
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Drawing functions not available within Chemtool:
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For features not currently supported by chemtool, like color or
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For features not currently supported by chemtool, like patterns or
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general line-drawing functions, getting Brian Smith's XFig
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drawing package from www-epb.lbl.gov/xfig is highly recommended.
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About the only thing it does not offer is support for 'chemical' linetypes
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general-purpose features of xfig seems rather pointless.)
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----------------------> Early history (T.Volk):
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15.Feb.1998 I fixed a bug that sometimes crashed the program,
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when one use the center or zoom function.
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27.Feb.1998 Another (crash) bug was fixed.
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28.Feb.1998 Adding new features :
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export to xfig and PicTeX;
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moving of objects;
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12.Mar.1998 The LaTeX and xfig-output works with 3 different
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zoom factors.
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for later changes see the file ChangeLog
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----------------------> Licensing :
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Licensing :
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For license information see the file 'COPYING' in this package, i.e. the
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GNU General Public License. This software comes with ABSOLUTELY NO WARRANTY.
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----------------------> Primary Authors:
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Thomas Volk (program creator, maintainer up to 1.1.1)
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Hauffstrasse 12
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89077 Ulm
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Germany
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E-Mail: Thomas.Volk@student.uni-ulm.de
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(then a student of chemistry and biology at Ulm University)
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Dr. Martin Kroeker (primary developer since 1.1.2)
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Zum Markwald 6
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63165 Muehlheim
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Germany
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martin@ruby.chemie.uni-freiburg.de or mk@daveg.com
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martin@ruby.chemie.uni-freiburg.de
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Webpage: http://www.uni-ulm.de/~s_tvolk
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Alternative site and Development versions:
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Webpage:
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http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html
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Loggerhead is a web-based interface for Breezy
Version: 2.0.1