#
# $RCSfile: SYBYLAtomTypes.csv,v $
# $Date: 2015/02/28 20:48:32 $
# $Revision: 1.14 $
#
# Author: Manish Sud <msud@san.rr.com>
#
# Copyright (C) 2015 Manish Sud. All rights reserved.
#
# This file is part of MayaChemTools.
#
# MayaChemTools is free software; you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
# Software Foundation; either version 3 of the License, or (at your option) any
# later version.
#
# MayaChemTools is distributed in the hope that it will be useful, but without
# any warranty; without even the implied warranty of merchantability of fitness
# for a particular purpose.  See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
# Boston, MA, 02111-1307, USA.
#
#
# Original data sources:
#     o Clark et al. [ Ref 79-80 ]
#
# Notes:
#     o 53 - 8 = 45 SYBYL atom types are listed 
#     o AtomTypes::SYBYLAtomTypes.pm module is used to assign SYBYL atom types
#     o 8 SYBYL atom types are not listed and not assigned to any atom:
#
#         O.spc - oxygen in SPC water model
#         O.t3p - oxygen in TIP3P water model
#         H.spc - hydrogen in SPC water model
#         H.t3p - hydrogen in TIP3P water model
#         Du - dummy
#         Du.C - dummy with the weight of carbon
#         HEV - heavy (non H) atom
#         LP - lone pair
#
#     o N.pl3 atom type is assigned to Nitrogens in a guadinium group attached
#       to Carbon C.cat
#
"AtomType","Description"
"C.3","sp3 carbon"
"C.2","sp2 carbon"
"C.1","sp carbon"
"C.ar","aromatic carbon"
"C.cat","carbocation, used only in a guadinium group"
"N.3","sp3 nitrogen"
"N.2","sp2 nitrogen"
"N.1","sp nitrogen"
"N.ar","aromatic nitrogen"
"N.am","amide nitrogen"
"N.pl3","trigonal planar nitrogen"
"N.4","sp3 positively charged nitrogen"
"O.3","sp3 oxygen"
"O.2","sp2 oxygen"
"O.co2","oxygen in carboxylate or phosphate group"
"S.3","sp3 sulfur"
"S.2","sp2 sulfur"
"S.o","sulfoxide sulfur"
"S.o2","sulfone sulfur"
"P.3","sp3 phosphorous"
"F","fluorine"
"Cl","chlorine"
"Br","bromine"
"I","iodine"
"H","hydrogen"
"ANY","any atom"
"HAL","halogen"
"HET","heteroatom (N, O, S, P)"
"Li","lithium"
"Na","sodium"
"Mg","magnesium"
"Al","aluminum"
"Si","silicon"
"K","potassium"
"Ca","calcium"
"Cr.th","chromium (tetrahedral)"
"Cr.oh","chromium (octahedral)"
"Mn","manganese"
"Fe","iron"
"Co.oh","cobalt (octahedral)"
"Cu","copper"
"Zn","zinc"
"Se","selenium"
"Mo","molybdenum"
"Sn","tin"
