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Committer: Bazaar Package Importer
Author(s): Michael Banck
Date: 2002-02-01 01:19:44 UTC
Revision ID: james.westby@ubuntu.com-20020201011944-4a9guzcsnpezzawx

Tags: upstream-1.99

Import upstream version 1.99

files added:

AUTHORS

COPYING

ChangeLog

INSTALL

Makefile.in

README

THANKS

config.guess

config.sub

configure

configure.in

doc/FAQ

doc/Migration

doc/Primer.html

doc/babel.1

install-sh

ltconfig

ltmain.sh

missing

mkinstalldirs

src/Makefile

src/Makefile.in

src/StdAfx.cpp

src/StdAfx.h

src/Vector.cpp

src/Vector.h

src/alchemy.cpp

src/amber.cpp

src/aromatic.h

src/aromatic.txt

src/atom.cpp

src/atomtyp.h

src/atomtyp.txt

src/balst.cpp

src/base.cpp

src/base.h

src/bgf.cpp

src/bin2hex.pl

src/binary.cpp

src/binary.h

src/binary_io.cpp

src/binary_io.h

src/bitgrid.cpp

src/bitgrid.h

src/bitvec.cpp

src/bitvec.h

src/bond.cpp

src/box.cpp

src/c3d.cpp

src/cacao.cpp

src/cache.cpp

src/car.cpp

src/ccc.cpp

src/chains.cpp

src/chains.h

src/chdrw.cpp

src/chiral.cpp

src/chiral.h

src/commandline.cpp

src/commandline.h

src/csr.cpp

src/cssr.cpp

src/ctransform.cpp

src/ctransform.h

src/cwrap.cpp

src/cwrap.h

src/data.cpp

src/data.h

src/dmol.cpp

src/element.h

src/element.txt

src/extable.h

src/extable.txt

src/feat.cpp

src/fh.cpp

src/fileformat.cpp

src/fileformat.h

src/gamess.cpp

src/gaussian.cpp

src/generic.cpp

src/generic.h

src/ghemical.cpp

src/grid.cpp

src/grid.h

src/gromos96.cpp

src/hin.cpp

src/jaguar.cpp

src/main.cpp

src/matrix.cpp

src/matrix.h

src/mdl.cpp

src/mmod.cpp

src/mol.cpp

src/mol.h

src/mol2.cpp

src/molchrg.cpp

src/molchrg.h

src/molvector.cpp

src/molvector.h

src/mopac.cpp

src/mpqc.cpp

src/nwchem.cpp

src/obifstream.h

src/oblib.dsp

src/oblib.dsw

src/obutil.cpp

src/obutil.h

src/parsmart.cpp

src/parsmart.h

src/parsmi.cpp

src/patty.cpp

src/patty.h

src/pdb.cpp

src/phmodel.cpp

src/phmodel.h

src/phmodel.txt

src/phmodeldata.h

src/qchem.cpp

src/quat.c

src/rand.cpp

src/report.cpp

src/resdata.h

src/resdata.txt

src/ring.cpp

src/ring.h

src/rotor.cpp

src/rotor.h

src/smarts.cpp

src/smarts.h

src/smi.cpp

src/smi.h

src/tinker.cpp

src/tokenst.cpp

src/typer.cpp

src/typer.h

src/types.h

src/types.txt

src/unichem.cpp

src/version.h.in

src/xed.cpp

src/xyz.cpp

stamp-h.in

stamp.h

test

test/Makefile

test/Makefile.in

test/attype.00.smi

test/main.cpp

test/ringresults.txt

test/ringtest.cpp

test/smartsresults.txt

test/smartstest.cpp

test/smartstest.txt

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src/atomtyp.txt

################################################################################

# OELib file: atomtyp.txt #

# #

# INTHYB: used to assign the internal hybridization values for atoms #

# IMPVAL: used to assign the implicit valence of an atom #

# EXTTYP: used to assign the external type of an atom for translation to #

# package specific types (I.E. Sybyl Mol2) #

# #

# The LAST PATTERN MATCHED is used to assign values with the corresponding #

# INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed #

# in the EXTRA DEFINITIONS section #

# #

################################################################################

INTHYB [C] 3 #sp3 carbon

INTHYB [c,$(C=*)] 2 #sp2 carbon

INTHYB [$([#6]([#8D1])[#8D1])] 2 #sp2 carbon

INTHYB [$(C#*),$(C(=*)=*)] 1 #sp carbon

INTHYB [N] 3 #sp3 nitrogen

INTHYB [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen

INTHYB [$(N#*),$([ND2](=*)=*)] 1 #sp nitrogen

INTHYB [O] 3 #sp3 oxygen

INTHYB [o,$(O=*),$(O[#6,#7,#8]=,:*)] 2 #sp2 oxygen

INTHYB [$([#8D1][#6][#8D1])] 2 #sp2 oxygen

INTHYB [$(O#*)] 1 #sp oxygen

INTHYB [D4] 3 #any 4 valent atom

INTHYB [P] 3 #sp3 phosphorus

INTHYB [#15;$([PD1]=*)] 2 #sp2 phosphorus

INTHYB [S] 3 #sp3 sulfur

INTHYB [#16;s,$([SD1]=*)] 2 #sp2 sulfur

INTHYB [B] 2 #sp2 boron

INTHYB [BD4] 3 #sp3 boron

#IMPLICIT VALENCE RULES

IMPVAL [#6^3] 4

IMPVAL [#6^2] 3

IMPVAL [#6^1] 2

IMPVAL [#6^3-] 3

IMPVAL [#6^2-] 2

IMPVAL [c+] 2

IMPVAL [#8^3] 2

IMPVAL [#8^2] 2

IMPVAL [$([#8]=*)] 1

IMPVAL [#8-] 1

IMPVAL [$([#8D1]~[#7D3]~[#8D1])] 1

IMPVAL [$([#8D1]~[#6]~[#8D1])] 1

IMPVAL [N^3] 3

IMPVAL [N^3+] 4

IMPVAL [N^2] 3

IMPVAL [N^2-,N^3-] 2

IMPVAL [ND1^1] 1

IMPVAL [ND2^1] 2

IMPVAL [$(N([OD1])*)] 3

IMPVAL [$(NC=O)] 3

IMPVAL [$(N(~[OD1])~[OD1])] 3

IMPVAL [$([Nr0]C=[Nr0])] 3

IMPVAL [$(N=*)] 2

IMPVAL [$([Nr0]=C[Nr0])] 3

#IMPVAL [$([Nr0]=C[Nr0])] 2 #uncomment this line for cansmi testing

IMPVAL [$([#7D1-]=*)] 1

IMPVAL [n] 2

IMPVAL [n-] 2

IMPVAL [n+] 3

IMPVAL [#15D4] 4

IMPVAL [#15D3] 3

IMPVAL [#15D2] 3

IMPVAL [#15D1^3] 3

IMPVAL [#15D1^2] 3

IMPVAL [$([#15]=[#6])] 2

IMPVAL [pD2] 2

IMPVAL [#16D4] 4

IMPVAL [#16D3] 3

IMPVAL [#16D2] 2

IMPVAL [$([#16D1]-*)] 2

IMPVAL [#16D1^2] 1

IMPVAL [s] 2

IMPVAL [#16D1-] 1

IMPVAL [#5] 3

IMPVAL [as] 3

#EXTERNAL TYPE RULES

EXTTYP [#7^3] N3

EXTTYP [#7X4+] N3+

EXTTYP [#7^2] Npl

EXTTYP [#7^1] N1

EXTTYP [$(N=*)] N2

EXTTYP [$([Nr0]C(=[Nr0])[Nr0])] Ng+

EXTTYP [$([Nr0]=C([Nr0])[Nr0])] Ng+

EXTTYP [$([ND1]=C[ND1])] Ng+

EXTTYP [$([ND1]C=[ND1])] Ng+

EXTTYP [$(N(O)*)] Nox

100

EXTTYP [$(NC=[O,S])] Nam

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EXTTYP [$(N(~[OD1])~[OD1])] Ntr

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EXTTYP [n] Nar

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EXTTYP [#6^3] C3

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EXTTYP [#6^2] C2

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EXTTYP [$(C(=O)[OD1])] Cac

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EXTTYP [c] Car

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EXTTYP [#6^1] C1

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EXTTYP [#6+] C+

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EXTTYP [#6-] C-

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EXTTYP [#8^3] O3

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EXTTYP [#8^2] O2

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EXTTYP [$(Oa)] O2

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#Uncomment the following 2 lines for correct sybyl atom typing

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#EXTTYP [$([OD2]C=[O,S])] O3 #ester oxygen

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#EXTTYP [$(Oa)] O3 #aromatic ether

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EXTTYP [#8-] O-

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EXTTYP [$([#8D1]~[#6]~[#8D1])] O.co2

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EXTTYP [#15] P

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EXTTYP [#15X4+] P3+

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EXTTYP [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])] Pac

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EXTTYP [#15;$([#15D3](~[OD1])~[OD1])] Pac

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EXTTYP [#16] S3

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EXTTYP [#16D3+,#16X3+] S3+

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EXTTYP [#16;s,$([SD1]=*)] S2

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EXTTYP [#16D4;$(S(=O)(=O))] So2

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EXTTYP [#16D3;$(S(=O))] Sox

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EXTTYP [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])] Sac

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EXTTYP [#16;$([#16D3](~[OD1])~[OD1])] Sac

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EXTTYP [#5] B2

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EXTTYP [#5D4] B3

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######################## Add Extra Definitions Here ##############################

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############################# End Extra Definitions ##############################

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