#
# $RCSfile: SLogPAtomTypes.csv,v $
# $Date: 2015/02/28 20:48:32 $
# $Revision: 1.13 $
#
# 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, Wildman et al. [ Ref 89 ]
#
# Notes:
#     o 72 SLogP atom types are listed 
#     o AtomTypes::SLogPAtomTypes.pm module is used to assign ALogP atom types using
#       an internal atom environment detection methodology. SMARTS strings are listed for
#       reference purposed and are not used by SLogPAtomTypes.pm module.
#     o For AtomTypeSymbols - N10, N12, O12, Hal, Me2 -not parametrized for MR contribution,
#        the AtomTypeSymbols are mapped to supplemental atom types or other atom types and
#        the MR values of mapped AtomTypeSymbols are used:
#         o N10 - NS
#         o N12 - NS 
#         o O12 - OS
#         o Hal - Me1
#         o Me2 - Me1
#
#     o SMARTS description [ Copied from Ref 89 ]
#
#         o 'A' and 'a' are used to represent any non-hydrogen aliphatic and aromatic element,
#           respectively. This includes Carbon.
# 
#         o '[#X]' is used to specify any non-hydrogen, non-carbon element, and
#           aromaticity may be specified by including the appropriate 'A' or 'a', as in '[A#X]'
#           or '[a#X]'.
# 
#         o '[#N]' specifies any element in the subset of elements O, N, F, Cl, and Br,
#           subject to the same aromaticity control.
# 
#         o Common organic elements (B, C, N, O, P, S, F, Cl, Br, and I) may be specified
#           by their symbol, where the lower case (b, c, n, o, p, s) would indicate aromaticity.
#           Other elements may be specified using '[# atomic number]', with 'A' and 'a' again as
#           aromaticity controls, such that '[a#7]' indicates an aromatic Nitrogen, as does 'n'.
# 
#         o Symbols -, =, #, and : indicate single, double, triple, and aromatic bonds, respectively.
#           Absence of a specific bond symbol implies a single or aromatic bond.
# 
#         o The number of attached hydrogens is specified using H, so '[CH4]' would match the
#           Carbon in methane. Charge is indicated with + and - such that '[#7+*]' indicates a
#           positively charged Nitrogen.
# 
#         o 'X' without '#' is used to specify the total number of bonds, including those to implicit
#           hydrogens, so '[CX4]' would match the Carbon in methane as well as the quaternary
#           Carbon of a tert-butyl group. All other notation follows that of the original SMARTS.
#
#     o Number of atom type symbols for:
#         o C: 28
#         o N: 15
#         o O: 13
#         o P: 1
#         o S: 3
#         o H: 5
#         o F, Cl, Br, I: 1 each
#         o Ionic halogen: 1
#         o p-block elements: 1
#         o d-block elements: 1
#
"AtomType","Description","SMARTS","LogPContribution","MRContribution"
"C1","primary, secondary aliphatic","'[CH4]','[CH3]C','[CH2](C)C'","0.1441","2.503"
"C2","tertiary, quaternary aliphatic","'[CH](C)(C)C','[C](C)(C)(C)C'","0.0000","2.433"
"C3","primary, secondary heteroatom","'[CH3][(N,O,P,S,F,Cl,Br,I)]','[CH2X4](N,O,P,S,F,Cl,Br,I)]'","-0.2035","2.753"
"C4","tertiary, quaternary heteroatom","'[CH1X4][(N,O,P,S,F,Cl,Br,I)]','[CH0X4][(N,O,P,S,F,Cl,Br,I)]'","-0.2051","2.731"
"C5","C = heteroatom","'[C]=[A#X]'","-0.2783","5.007"
"C6","C = C aliphatic","'[CH2]=C','[CH1](=C)A','[CH0](=C)(A)A','[C](=C)=C'","0.1551","3.513"
"C7","acetylene, nitrile","'[CX2]#A'","0.00170","3.888"
"C8","primary aromatic carbon","'[CH3]c'","0.08452","2.464"
"C9","primary aromatic heteroatom","'[CH3][a#X]'","-0.1444","2.412"
"C10","secondary aromatic","'[CH2X4]a'","-0.0516","2.488"
"C11","tertiary aromatic","'[CHX4]a'","0.1193","2.582"
"C12","quaternary aromatic","'[CH0X4]a'","-0.0967","2.576"
"C13","aromatic heteroatom","'[cH0]-[!(C,N,O,S,F,Cl,Br,I)]'","-0.5443","4.041"
"C14","aromatic halide","'[c][#9]'","0.0000","3.257"
"C15","aromatic halide","'[c][#17]'","0.2450","3.564"
"C16","aromatic halide","'[c][#35]'","0.1980","3.180"
"C17","aromatic halide","'[c][#53]'","0.0000","3.104"
"C18","aromatic","'[cH]'","0.1581","3.350"
"C19","aromatic bridgehead","'[c](:a)(:a):a'","0.2955","4.346"
"C20","quaternary aromatic","'[c](:a)(:a)-a'","0.2713","3.904"
"C21","quaternary aromatic","'[c](:a)(:a)-C'","0.1360","3.509"
"C22","quaternary aromatic","'[c](:a)(:a)-N'","0.4619","4.067"
"C23","quaternary aromatic","'[c](:a)(:a)-O'","0.5437","3.853"
"C24","quaternary aromatic","'[c](:a)(:a)-S'","0.1893","2.673"
"C25","quaternary aromatic","'[c](:a)(:a)=C','[c](:a)(:a)=N','[c](:a)(:a)=O'","-0.8186","3.135"
"C26","C = C aromatic","'[C](=C)(a)A','[C](=C)(c)a','[CH](=C)a','[C]=c'","0.2640","4.305"
"C27","aliphatic heteroatom","'[CX4][!(C,N,O,P,S,F,Cl,Br,I)]'","0.2148","2.693"
"CS","carbon supplemental not matching any basic C type","'[#6]'","0.08129","3.243"
"H1","hydrocarbon","'[#1][#6]','[#1][#1]'","0.1230","1.057"
"H2","alcohol","'[#1]O[CX4]','[#1]Oc','[#1]O[!(C,N,O,S)]','[#1][!C,N,O)]'","-0.2677","1.395"
"H3","amine","'[#1][#7]','[#1]O[#7]'","0.2142","0.9627"
"H4","acid","'[#1]OC=[#6]','[#1]OC=[#7]','[#1]OC=O','[#1]OC=S','[#1]OO','[#1]OS'","0.2980","1.805"
"HS","hydrogen supplemental not matching any basic H type","'[#1]'","0.1125","1.112"
"N1","primary amine","'[NH2+0]A'","-1.0190","2.262"
"N2","secondary amine","'[NH+0](A)A'","-0.7096","2.173"
"N3","primary aromatic amine","'[NH2+0]a'","-1.0270","2.827"
"N4","secondary aromatic amine","'[NH+0](A)a','[NH+0](a)a'","-0.5188","3.000"
"N5","imine","'[NH+0]=A','[NH+0]=a'","0.08387","1.757"
"N6","substituted imine","'[N+0](=A)A','[N+0](=A)a','[N+0](=a)A','[N+0](=a)a'","0.1836","2.428"
"N7","tertiary amine","'[N+0](A)(A)A'","-0.3187","1.839"
"N8","tertiary aromatic amine","'[N+0](a)(A)A','[N+0](a)(a)A','[N+0](a)(a)a'","-0.4458","2.819"
"N9","nitrile","'[N+0]#A'","0.01508","1.725"
"N10","protonated amine","'[NH3+*]','[NH2+*]','[NH+*]'","-1.950","2.134"
"N11","unprotonated aromatic","'[n+0]'","-0.3239","2.202"
"N12","protonated aromatic","'[n+*]'","-1.119","2.134"
"N13","quaternary amine","'[NH0+*](A)(A)(A)A','[NH0+*](=A)(A)A','[NH0+*](=A)(A)a','[NH0+*](=[#6])=[#7]'","-0.3396","0.2604"
"N14","other ionized nitrogen","'[N+*]#A','[N-*]','[N+*](=[N-*])=N'","0.2887","3.359"
"NS","nitrogen supplemental not matching any basic N type","'[#7]'","-0.4806","2.134"
"O1","aromatic","'[o]'","0.1552","1.080"
"O2","alcohol","'[OH]','[OH2]'","-0.2893","0.8238"
"O3","aliphatic ether","'[O](C)C','[O](C)[A#X]','[O]([A#X])[A#X]'","-0.0684","1.085"
"O4","aromatic ether","'[O](A)a','[O](a)a'","-0.4195","1.182"
"O5","oxide","'[O]=[#8]','[O]=[#7]','[OX1-*][#7]'","0.0335","3.367"
"O6","oxide","'[OX1-*][#16]'","-0.3339","0.7774"
"O7","oxide","'[OX1-*][!(N,S)]'","-1.189","0.000"
"O8","aromatic carbonyl","'[O]=c'","0.1788","3.135"
"O9","carbonyl aliphatic","'[O]=[CH]C','[O]=C(C)C','[O]=C(C)[A#X]','[O]=[CH]N','[O]=[CH]O','[O]=[CH2]','[O]=[CX2]=O'","-0.1526","0.000"
"O10","carbonyl aromatic","'[O]=[CH]c','[O]=C(C)c','[O]=C(c)c','[O]=C(c)[a#X]','[O]=C(c)[A#X]','[O]=C(C)[a#X]'","0.1129","0.2215"
"O11","carbonyl heteroatom","'[O]=C([A#X])[A#X]','[O]=C([A#X])[a#X]','[O]=C([a#X])[a#X]'","0.4833","0.3890"
"O12","acid","'[O-1]C(=O)'","-1.326","0.6865"
"OS","oxygen supplemental not matching any basic O type","'[#8]'","-0.1188","0.6865"
"F","fluorine","'[#9-0]'","0.4202","1.108"
"Cl","chlorine","'[#17-0]'","0.6895","5.853"
"Br","bromine","'[#35-0]'","0.8456","8.927"
"I","iodine","'[#53-0]'","0.8857","14.02"
"Hal","ionic halogens","'[#9-*]','[#17-*]','[#35-*]',[#53-*]','[#53+*]'","-2.996","5.754"
"P","phosphorous","'[#15]'","0.8612","6.920"
"S1","aliphatic","'[S-0]'","0.6482","7.591"
"S2","ionic sulfur","'[S-*]','[S+*]'","-0.0024","7.365"
"S3","aromatic","'[s]'","0.6237","6.691"
"Me1","all remaining p-block elements","","-0.3808","5.754"
"Me2","all remaining d-block elements","","-0.0025","5.754"
