From e77cc376aaff8ca481fdace6d5795c5b5feb0e87 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 20 Feb 2012 14:45:20 +0100 Subject: Added pc descriptor calc service --- java/joelib2/data/plain/phmodel.txt | 127 ++++++++++++++++++++++++++++++++++++ 1 file changed, 127 insertions(+) create mode 100644 java/joelib2/data/plain/phmodel.txt (limited to 'java/joelib2/data/plain/phmodel.txt') 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 -- cgit v1.2.3