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1 #
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2 # $RCSfile: AromaticityModelsData.csv,v $
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3 # $Date: 2015/02/28 20:48:22 $
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4 # $Revision: 1.7 $
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5 #
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6 # Author: Manish Sud <msud@san.rr.com>
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7 #
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8 # Copyright (C) 2015 Manish Sud. All rights reserved.
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9 #
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10 # This file is part of MayaChemTools.
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11 #
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12 # MayaChemTools is free software; you can redistribute it and/or modify it under
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13 # the terms of the GNU Lesser General Public License as published by the Free
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14 # Software Foundation; either version 3 of the License, or (at your option) any
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15 # later version.
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16 #
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17 # MayaChemTools is distributed in the hope that it will be useful, but without
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18 # any warranty; without even the implied warranty of merchantability of fitness
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19 # for a particular purpose. See the GNU Lesser General Public License for more
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20 # details.
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21 #
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22 # You should have received a copy of the GNU Lesser General Public License
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23 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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24 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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25 # Boston, MA, 02111-1307, USA.
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26 #
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27 #
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28 # Notes:
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29 # . What is aromaticity? [ Ref 124 ] It's in the code of the implementer, did you
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30 # say? Agree. The implementation of aromaticity varies widely across different
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31 # packages [ Ref 125 ]; additionally, the implementation details are not always
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32 # completely available, and it's not possible to figure out the exact implementation
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33 # of aromaticity across various packages. Using the publicly available information,
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34 # however, one can try to reproduce the available results to the extent possible,
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35 # along with parameterizing all the control parameters used to implement different
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36 # aromaticity models, and that's exactly what the current release of MayaChemTools
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37 # does.
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38 # . Molecule.pm module retrieves data from this file during class instantiation
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39 # and makes it available to class method DetectAromaticity for detecting
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40 # aromaticity corresponding to a specific model.
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41 # . Any new added aromaticity model using existing parameters would work
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42 # as expected, without modifying the code; addition of new parameters,
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43 # however, requires its implementation in the code.
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44 # . Parameter values of Yes, No and None are internally mapped to 1, 0 and
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45 # an empty string, respectively.
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46 # . For parameter names containing List in their name and comma delimited set
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47 # of values, a new parameter is generated for each model by appending MapRef
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48 # to specified parameter name, which is then assigned a hash reference containing
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49 # key and value pairs corresponding to comma delimited values.
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50 #
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51 #
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52 "ParameterName","MDLAromaticityModel","TriposAromaticityModel","MMFFAromaticityModel","ChemAxonBasicAromaticityModel","ChemAxonGeneralAromaticityModel","DaylightAromaticityModel","MayaChemToolsAromaticityModel"
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53 "AllowHeteroRingAtoms","No","No","Yes","Yes","Yes","Yes","Yes"
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54 "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"
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55 "AllowExocyclicDoubleBonds","No","No","No","No","Yes","Yes","Yes"
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56 "AllowHomoNuclearExocyclicDoubleBonds","NA","NA","NA","NA","No","No","No"
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57 "AllowElectronegativeRingAtomExocyclicDoubleBonds","NA","NA","NA","NA","No","No","No"
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58 "AllowRingAtomFormalCharge","No","No","No","No","Yes","No","Yes"
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59 "AllowHeteroRingAtomFormalCharge","NA","NA","NA","NA","Yes","NA","Yes"
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60 "MinimumRingSize","None","None","None","5","None","None","None"
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