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author | deepakjadmin |
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date | Wed, 20 Jan 2016 09:23:18 -0500 |
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# # $RCSfile: AromaticityModelsData.csv,v $ # $Date: 2015/02/28 20:48:22 $ # $Revision: 1.7 $ # # 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. # # # Notes: # . What is aromaticity? [ Ref 124 ] It's in the code of the implementer, did you # say? Agree. The implementation of aromaticity varies widely across different # packages [ Ref 125 ]; additionally, the implementation details are not always # completely available, and it's not possible to figure out the exact implementation # of aromaticity across various packages. Using the publicly available information, # however, one can try to reproduce the available results to the extent possible, # along with parameterizing all the control parameters used to implement different # aromaticity models, and that's exactly what the current release of MayaChemTools # does. # . Molecule.pm module retrieves data from this file during class instantiation # and makes it available to class method DetectAromaticity for detecting # aromaticity corresponding to a specific model. # . Any new added aromaticity model using existing parameters would work # as expected, without modifying the code; addition of new parameters, # however, requires its implementation in the code. # . Parameter values of Yes, No and None are internally mapped to 1, 0 and # an empty string, respectively. # . For parameter names containing List in their name and comma delimited set # of values, a new parameter is generated for each model by appending MapRef # to specified parameter name, which is then assigned a hash reference containing # key and value pairs corresponding to comma delimited values. # # "ParameterName","MDLAromaticityModel","TriposAromaticityModel","MMFFAromaticityModel","ChemAxonBasicAromaticityModel","ChemAxonGeneralAromaticityModel","DaylightAromaticityModel","MayaChemToolsAromaticityModel" "AllowHeteroRingAtoms","No","No","Yes","Yes","Yes","Yes","Yes" "HeteroRingAtomsList","None","None","N,O,P,S","N,O,P,S,As,Se","N,O,P,S,As,Se","N,O,P,S,As,Se","N,O,P,S,As,Se,Te" "AllowExocyclicDoubleBonds","No","No","No","No","Yes","Yes","Yes" "AllowHomoNuclearExocyclicDoubleBonds","NA","NA","NA","NA","No","No","No" "AllowElectronegativeRingAtomExocyclicDoubleBonds","NA","NA","NA","NA","No","No","No" "AllowRingAtomFormalCharge","No","No","No","No","Yes","No","Yes" "AllowHeteroRingAtomFormalCharge","NA","NA","NA","NA","Yes","NA","Yes" "MinimumRingSize","None","None","None","5","None","None","None"