From 3cd136861c68b8c24cc653c903c620d55be4b294 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 2 Apr 2012 09:18:14 +0200 Subject: Remove PC descriptor --- java/joelib2/data/plain/phmodel.txt | 127 ------------------------------------ 1 file changed, 127 deletions(-) delete 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 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 -- cgit v1.2.3