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