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