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* data/*.txt: Update comments and fix minor formatting changes.

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This commit is contained in:
Geoffrey Hutchison
2008-03-13 21:52:14 +00:00
parent 08ca81ccb4
commit 43e3757cab
13 changed files with 12455 additions and 72 deletions
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2
data/Makefile.am
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@@ -5,7 +5,7 @@ table_DATA = \
atomtyp.txt element.txt isotope-small.txt phmodel.txt \
patterns.txt torlib.txt types.txt space-groups.txt \
SMARTS_InteLigand.txt fragments.txt \
mm2.prm ghemical.prm UFF.prm ringtyp.txt \
ghemical.prm UFF.prm ringtyp.txt \
mmffoop.par mmffchg.par mmfftor.par mmffang.par \
mmffpbci.par mmffdef.par \
mmffvdw.par mmffstbn.par mmffbndk.par mmffprop.par mmffbond.par \

2
data/Makefile.in
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@@ -190,7 +190,7 @@ table_DATA = \
atomtyp.txt element.txt isotope-small.txt phmodel.txt \
patterns.txt torlib.txt types.txt space-groups.txt \
SMARTS_InteLigand.txt fragments.txt \
mm2.prm ghemical.prm UFF.prm ringtyp.txt \
ghemical.prm UFF.prm ringtyp.txt \
mmffoop.par mmffchg.par mmfftor.par mmffang.par \
mmffpbci.par mmffdef.par \
mmffvdw.par mmffstbn.par mmffbndk.par mmffprop.par mmffbond.par \

30
data/UFF.prm
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@@ -1,14 +1,20 @@
//
// OBForceField Parameters for UFF, the Universal Force Field
// J. Am. Chem. Soc. (1992) 114(25) p. 10024-10035.
// The parameters in this file are taken from the UFF implementation in RDKit
// http://rdkit.org/
//
// Atom typing rules are based on UFF published atom descriptions
// [SMARTS] [atomtype] [description]
// These must be sorted according to the element and complexity of the type rule
// (i.e., generic rules first, more specific rules later)
#
# Open Babel file: UFF.prm
#
# Force field parameters for UFF, the Universal Force Field
# Used by OBForceField and OBUFFForceField
#
# J. Am. Chem. Soc. (1992) 114(25) p. 10024-10035.
# The parameters in this file are taken from the UFF implementation in RDKit
# http://rdkit.org/
#
# Atom typing rules are based on UFF published atom descriptions
# atom [SMARTS] [atomtype] [description]
# These must be sorted according to the element and complexity
# of the type rule (i.e., generic rules first, more specific rules later)
#
# Parameters follow later
# param Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
atom [#1] H_ Generic hydrogen
atom [#1D2] H_b Bridging hydrogen
@@ -138,7 +144,7 @@ atom [#101] Md6+3
atom [#102] No6+3
atom [#103] Lw6+3
//Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
# Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
param H_ 0.354 180 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371
param H_b 0.46 83.5 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371
param He4+4 0.849 90 2.362 0.056 15.24 0.098 0 0 9.66 14.92 1.3

2
data/aromatic.txt
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@@ -1,6 +1,6 @@
##############################################################################
# #
# Open Babel file: aromatic.txt #
# Open Babel file: aromatic.txt # # #
# #
# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
# Some portions Copyright (c) 2001-2005 Geoffrey R. Hutchison #

2
data/atomtyp.txt
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@@ -1,6 +1,6 @@
##############################################################################
# #
# Open Babel file: atomtyp.txt #
# Open Babel file: atomtyp.txt # # #
# #
# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
# Some portions Copyright (c) 2001-2003 Geoffrey R. Hutchison #

6
data/bondtyp.txt
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@@ -8,12 +8,12 @@
# Used by bondtyper.cpp::OBBondTyper (and thus OBMol::PerceiveBondOrders() #
# #
# List of functional groups with double, triple (etc.) bond orders #
# Pattern Atom1 Atom2 Bond Order (repeat as needed) #
# Pattern Atom1 Atom2 Bond Order (repeat as needed) #
# * = Any atom (for setting non-multiple bonds) #
# #
# NOTE: These are applied in order, first to last. #
# NOTE: These are applied in order, first to last. #
# So it's generally better to have a long (specifc) SMARTS first. #
# (all bonds must be single bonds to match)
# (all bonds must be single bonds to match) #
# #
##############################################################################

12448
data/fragments.txt
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File diff suppressed because it is too large Load Diff

2
data/isotope-small.txt
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@@ -1,6 +1,6 @@
##############################################################################
# #
# Open Babel file: isotope-small.txt #
# Open Babel file: isotope-small.txt #
# #
# Copyright (c) 2002-2003 by Geoffrey R. Hutchison #
# Part of the Open Babel package, under the GNU General Public License (GPL)#

14
data/isotope.txt
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@@ -1,6 +1,6 @@
##############################################################################
# #
# Open Babel file: isotope.txt #
# Open Babel file: isotope.txt #
# #
# Copyright (c) 2002-2004 by Geoffrey R. Hutchison #
# Part of the Open Babel package, under the GNU General Public License (GPL)#
@@ -14,12 +14,12 @@
# (we don't currently have a math package that can deal with sig. fig.) #
# so trailing zeros may not be significant and/or useful #
# #
# Values are compiled from: #
# "The Ame2003 atomic mass evaluation (II)" #
# by G.Audi, A.H.Wapstra and C.Thibault #
# Nuclear Physics A729 p. 337-676, December 22, 2003. #
# as made available in the mass.mas03round file #
# (these are values for publication) #
# Values are compiled from: #
# "The Ame2003 atomic mass evaluation (II)" #
# by G.Audi, A.H.Wapstra and C.Thibault #
# Nuclear Physics A729 p. 337-676, December 22, 2003. #
# as made available in the mass.mas03round file #
# (these are values for publication) #
# #
# Currently: 110 lines (neutron, H to Mt) #
# (note that since element 0 often represents a dummy atom, the default #

4
data/phmodel.txt
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@@ -1,6 +1,6 @@
##############################################################################
# #
# Open Babel file: phmodel.txt #
# Open Babel file: phmodel.txt #
# #
# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
# Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison #
@@ -10,7 +10,7 @@
# #
# TRANSFORM: chemical transforms can be used to modify formal charges, bond #
# orders, and to delete atoms (i.e hydrogens). Changes are applied#
# to vector bound atoms (use the [:#] SMARTS notation) and bonds #
# to vector bound atoms (use the [:#] SMARTS notation) and bonds #
# between vector bound atoms. #
# SEEDCHARGE: used to seed partial charges. Seed partial charges #
# are used as initial values in Gasteiger charge calculation #

10
data/resdata.txt
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@@ -1,16 +1,16 @@
##############################################################################
# #
# Open Babel file: resdata.txt #
# Open Babel file: resdata.txt #
# #
# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
# Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison #
# Part of the Open Babel package, under the GNU General Public License (GPL)#
# #
# Residue records are specified as follows: (used by data.cpp:OBResidueData)#
# RES <name> #
# ATOM Name Type Hybridization (hydrogens are implicit) #
# BOND Name1 Name2 BondOrder (where Name1, Name2 are ATOM records)#
# END #
# RES <name> #
# ATOM Name Type Hybridization (hydrogens are implicit) #
# BOND Name1 Name2 BondOrder (where Name1, Name2 are ATOM records) #
# END #
# #
##############################################################################

3
data/ringtyp.txt
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@@ -1,11 +1,12 @@
##############################################################################
# #
# Open Babel file: atomtyp.txt #
# Open Babel file: ringtyp.txt #
# #
# Copyright (c) 2007 Tim Vandermeersch #
# Part of the Open Babel package, under the GNU General Public License (GPL)#
# #
# SMARTS patterns for ring typing (used by typer.cpp:OBRingTyper) #
# (involved in MMFF94 atom typing, among other things) #
# #
# RINGTYP: used to assign the ring types #
# #

2
data/types.txt
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@@ -1,6 +1,6 @@
##############################################################################
# #
# Open Babel file: types.txt #
# Open Babel file: types.txt #
# #
# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
# Some portions Copyright (c) 2001-2005 Geoffrey R. Hutchison #