#
# $RCSfile: TPSAAtomTypes.csv,v $
# $Date: 2015/02/28 20:48:33 $
# $Revision: 1.10 $
#
# 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 source:
#     o Table 1, Ertl et al. [ Ref 90 ]
#
# Notes:
#     o 47 TPSA atom types are listed
#     o AtomTypes::TPSAAtomTypes.pm module is used to assign TPSA atom types using
#       an internal atom environment detection methodology. SMARTS strings are listed for
#       reference purposed and are not used by TPSAAtomTypes.pm module.
#     o AtomType symbols were not used in publication by Ertl et al; these are assigned and
#       used only by MayaChemTools.
#         o Number in AtomType symbol for an element simply correspond to its order of
#            appearance in Table 1 [ Ref 90-91 ]
#
#     o N, O, P and S are used to indicate atom environments not explicitly defined in Table1.
#        And their TPSA contributions are dynamically calculated using formulas from TPSA.c
#        code developed by Peter Ertl :
#
#         o N = 30.5 - X*8.2 + H*1.5 or 0.0 for negative value
#         o O = 28.5 - X*8.6 + H*1.5 or 0.0 for negative value
#       
#         where X = Number of heavy atom neighbors; H = Number of implicit and explicit
#         hydrogen atom neighbors
#  
#         o P = 0.0
#         o O = 0.0
#
#     o Number of atom type symbols for:
#         o N: 27
#         o O: 7
#         o P: 5
#         o S: 8
#
"AtomType","SMARTS","TPSAContribution","Comments"
"N1","[N](-*)(-*)-*","3.24",""
"N2","[N](-*)=*","12.36",""
"N3","[N]#*","23.79",""
"N4","[N](-*)(=*)=*","11.68","As in nitro group"
"N5","[N](=*)#*","13.60","Middle nitrogen in azide group"
"N6","[N]1(-*)-*-*-1","3.01","Atom in a 3 membered ring"
"N7","[NH](-*)-*","12.03",""
"N8","[NH]1-*-*-1","21.94","Atom in a 3 membered ring"
"N9","[NH]=*","23.85",""
"N10","[NH2]-*","26.02",""
"N11","[N+](-*)(-*)(-*)-*","0.00",""
"N12","[N+](-*)(-*)=*","3.01",""
"N13","[N+](-*)#*","4.36","Nitrogen in isocyano group"
"N14","[NH+](-*)(-*)-*","4.44",""
"N15","[NH+](-*)=*","13.97",""
"N16","[NH2+](-*)-*","16.61",""
"N17","[NH2+]=*","25.59",""
"N18","[NH3+]-*","27.64",""
"N19","[n](:*):*","12.89",""
"N20","[n](:*)(:*):*","4.41",""
"N21","[n](-*)(:*):*","4.93",""
"N22","[n](=*)(:*):*","8.39","As in pyridine N-oxide"
"N23","[nH](:*):*","15.79",""
"N24","[n+](:*)(:*):*","4.10",""
"N25","[n+](-*)(:*):*","3.88",""
"N26","[nH+](:*):*","14.14",""
"N","[#7]","0.00","Any other Nitrogen; Contribution: 30.5 - X*8.2 + H*1.5 or 0.0 for negative value"
"O1","[O](-*)-*","9.23",""
"O2","[O]1-*-*-1","12.53","Atom in a 3 membered ring"
"O3","[O]=*","17.07",""
"O4","[OH]-*","20.23",""
"O5","[O-]-*","23.06",""
"O6","[o](:*):*","13.14",""
"O","[#8]","0.00","Any other Oxygen; Contribution: 28.5 - X*8.6 + H*1.5 or 0.0 for negative value"
"S1","[S](-*)-*","25.30",""
"S2","[S]=*","32.09",""
"S3","[S](-*)(-*)=*","19.21",""
"S4","[S](-*)(-*)(=*)=*","8.38",""
"S5","[SH]-*","38.80",""
"S6","[s](:*):*","28.24",""
"S7","[s](=*)(:*):*","21.70",""
"S","[#16]","0.00","Any other Sulfur"
"P1","[P](-*)(-*)-*","13.59",""
"P2","[P](-*)=*","34.14",""
"P3","[P](-*)(-*)(-*)=*","9.81",""
"P4","[PH](-*)(-*)=*","23.47",""
"P","[#15]","0.00","Any other Phosphorus"
