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Diffstat (limited to 'java/joelib2/data/plain/phmodel.txt')
| -rw-r--r-- | java/joelib2/data/plain/phmodel.txt | 127 |
1 files changed, 127 insertions, 0 deletions
diff --git a/java/joelib2/data/plain/phmodel.txt b/java/joelib2/data/plain/phmodel.txt new file mode 100644 index 0000000..5ae19fa --- /dev/null +++ b/java/joelib2/data/plain/phmodel.txt @@ -0,0 +1,127 @@ +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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