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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, 0 insertions, 127 deletions
diff --git a/java/joelib2/data/plain/phmodel.txt b/java/joelib2/data/plain/phmodel.txt deleted file mode 100644 index 5ae19fa..0000000 --- a/java/joelib2/data/plain/phmodel.txt +++ /dev/null @@ -1,127 +0,0 @@ -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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