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VENDOR: http://joelib.sf.net
RELEASE_VERSION: $Revision: 1.3 $
RELEASE_DATE: $Date: 2005/01/07 07:18:15 $
################################################################################
# #
# Used to assign the internal atom type to an atom. #
# It is allowed to use assigned hybridisation patterns here, e.g. [#6^3] #
# The LAST PATTERN MATCHED is used to assign values. Additions to this file #
# should be placed in the EXTRA DEFINITIONS section #
# #
################################################################################
# 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.
########################################################################
[#7^3] N3
[#7X4+] N3+
[#7^2] Npl
[#7^1] N1
[$(N=*)] N2
[$([Nr0]C(=[Nr0])[Nr0])] Ng+
[$([Nr0]=C([Nr0])[Nr0])] Ng+
[$([NQ1]=C[NQ1])] Ng+
[$([NQ1]C=[NQ1])] Ng+
[$(N(O)*)] Nox
[$(NC=[O,S])] Nam
[$(N(~[OQ1])~[OQ1])] Ntr
[n] Nar
[#6^3] C3
[#6^2] C2
[$(C(=O)[OQ1])] Cac
[c] Car
[#6^1] C1
[#6+] C+
[#6-] C-
[#8^3] O3
[#8^2] O2
[$(Oa)] O2
#Uncomment the following 2 lines for correct sybyl atom typing
[$([OQ2]C=[O,S])] O3 #ester oxygen
[$(Oa)] O3 #aromatic ether
[#8-] O-
[$([#8Q1]~[#6]~[#8Q1])] Oco2
[#15] P
[#15X4+] P3+
[#15;$([#15Q4](~[OQ1])(~[OQ1])~[OQ1])] Pac
[#15;$([#15Q3](~[OQ1])~[OQ1])] Pac
[#16] S3
[#16Q3+,#16X3+] S3+
[#16;s,$([SQ1]=*)] S2
[#16Q4;$(S(=O)(=O))] So2
[#16Q3;$(S(=O))] Sox
[#16;$([#16Q4](~[OQ1])(~[OQ1])~[OQ1])] Sac
[#16;$([#16Q3](~[OQ1])~[OQ1])] Sac
[#5] B2
[#5Q4] B3
######################## Add Extra Definitions Here ##############################
############################# End Extra Definitions ##############################
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