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VENDOR: http://joelib.sf.net
RELEASE_VERSION: $Revision: 1.3 $
RELEASE_DATE: $Date: 2005/01/28 13:49:11 $
##########################################################################
#
# 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
# between vector bound atoms.
# SEEDCHARGE: used to seed partial charges. Seed partial charges
# are used as initial values in Gasteiger-Marsili charge calculation
#
#########################################################################
# Copyright OELIB: OpenEye Scientific Software, Santa Fe,
# U.S.A., 1999,2000,2001
# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of
# Tuebingen, Germany, 2001,2002,2003,2004,2005
# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany,
# 2003,2004,2005
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation version 2 of the License.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
########################################################################
#carboxylic acid
TRANSFORM O=CO[#1:1] >> O=CO
TRANSFORM O=C[OQ1-0:1] >> O=C[O-:1]
#charged amine
TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1]
#imidazole: note pKa=7.0, histidine pKa=6.0
#if you uncomment this, also uncomment the seedcharge statement below
#TRANSFORM [nQ2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1
#imine
TRANSFORM [NQ3+0:1]=[#6] >> [NQ3+:1]=[#6]
#tetrazole
TRANSFORM [nQ2:1]([#1:2])1[nQ2-0][nQ2-0][nQ2-0]c1 >> [n-:1]1nnnc1
TRANSFORM [nQ2-0]1[nQ2:1]([#1:2])[nQ2-0][nQ2-0]c1 >> n1[n-:1]nnc1
TRANSFORM [nQ2-0:1]1[nQ2-0][nQ2-0][nQ2-0]c1 >> [n-:1]1nnnc1
#azide
TRANSFORM [NQ2:1]=[NQ2:2]=A >> [N:1]=[N+:2]=A
TRANSFORM [NQ1:1]=[NQ2:2]=A >> [N-:1]=[N+:2]=A
#hydroxamic acid
TRANSFORM O=CN[OQ1-0:1][#1:2] >> O=CN[O-:1]
TRANSFORM O=CN[OQ1-0:1] >> O=CN[O-:1]
#sulfinic acid
TRANSFORM [SQ3](=O)[OQ1:1] >> [SQ3](=O)[O-:1]
TRANSFORM [SQ3](=O)[O:1][#1:2] >> [SQ3](=O)[O-:1]
#sulfonic acid
TRANSFORM [SQ4]([!Q1])(=O)(=O)[OQ1:1] >> [SQ4]([!Q1])(=O)(=O)[O-:1]
TRANSFORM [SQ4]([!Q1])(=O)(=O)[O:1][#1:2] >> [SQ4]([!Q1])(=O)(=O)[O-:1]
#sulfuric acid
TRANSFORM [SQ4]([!Q1])(=O)(=O)[OQ1:1] >> [SQ4]([!Q1])(=O)(=O)[O-:1]
TRANSFORM [SQ4]([!Q1])(=O)(=O)[O:1][#1:2] >> [SQ4]([!Q1])(=O)(=O)[O-:1]
#guanidine or amidine
# causes problem in SMARTS parser
#TRANSFORM [#6^2+0:1](=[N^2+0:2])(-[N^2]) >> [#6+:1](=N-:2)(-N)
#phosphoate ester
TRANSFORM [PQ4](=O)([OQ2])([OQ2])[OQ1:1] >> [PQ4](=O)([OQ2])([OQ2])[O-:1]
TRANSFORM [PQ4](=O)([OQ2])([OQ2])[OQ1:1][#1:2] >> [PQ4](=O)([OQ2])([OQ2])[O-:1]
#phosphoric acid
TRANSFORM O=P([!Q1])([O:1][#1:2])[O:3][#1:4] >> O=P([*Q2,*Q3])([O:1])[O:3]
TRANSFORM O=P([!Q1])([O:1][#1:2])[OQ1] >> O=P([!Q1])([O:1])O
TRANSFORM O=P([*Q2,*Q3])([OQ1:1])[OQ1:2] >> O=P([*Q2,*Q3])([O-:1])[O-:2]
#phosphate
#
# Seeding partial charges for gasteiger-marsili calculation
#
#carboxylic acid
SEEDCHARGE C(=O)[O-] 0.0 -0.5 -0.5
#amines
SEEDCHARGE [N+] 1.0
#tetrazole
SEEDCHARGE [nQ2]1[nQ2][nQ2][nQ2]c1 -0.2 -0.2 -0.2 -0.2 -0.2
#sulfinic
SEEDCHARGE [SQ3](=O)[O-] 0.0 -0.5 -0.5
#sulfuric acid
SEEDCHARGE [SQ4](=O)(=O)([O-])[OH1] 0.0 -0.33 -0.33 -0.33 0.0
#sulfonic acid
SEEDCHARGE [SQ4]([Q2])(~[OQ1])(~[OQ1])~[OQ1] 0.0 0.0 -0.33 -0.33 -0.33
#guanidine
SEEDCHARGE [#7^2]~[C^2](~[N^2])~[N^2] 0.33 0.0 0.33 0.33
#amidine
SEEDCHARGE [#6]~[C^2](~[N^2])~[N^2] 0.0 0.0 0.5 0.5
#phosphoate ester
SEEDCHARGE [PQ4](=O)([OQ2])([OQ2])[OQ1] 0.0 -0.5 0.0 0.0 -0.5
#phosphoric acid
SEEDCHARGE O=P([!Q1])([O-])[O-] -0.66 0.0 0.0 -0.66 -0.66
#phosphuric acid
SEEDCHARGE P(=O)(=O)([O-])[O-] 0.0 0.0 0.0 -0.5 -0.5
#phosphonic acid
SEEDCHARGE [#6]P(~[OQ1])(~[OQ1])~[OQ1] 0.0 0.0 -0.33 -0.33 -0.33
#hydroxamic acid
SEEDCHARGE O=C[N;!$(N(C=O)C=O)][OQ1] -0.5 0.0 0.0 -0.5
SEEDCHARGE O=CN([OQ1])NC=O -0.33 0.0 0.0 -0.33 0.0 -0.33
#imidazole: note pKa=7.0, histidine pKa=6.0
#if you uncomment this, also uncomment the seedcharge statement below
#SEEDCHARGE [n+H]1c[nH]cc1 0.5 0.0 0.5 0.0 0.0
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