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1 NAME
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2 RingsCountDescriptors
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3
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4 SYNOPSIS
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5 use MolecularDescriptors::RingsCountDescriptors;
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6
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7 use MolecularDescriptors::RingsCountDescriptors qw(:all);
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8
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9 DESCRIPTION
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10 RingsCountDescriptors class provides the following methods:
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11
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12 new, GenerateDescriptors, GetDescriptorNames,
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13 StringifyRingsCountDescriptors
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14
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15 RingsCountDescriptors is derived from MolecularDescriptors class which
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16 in turn is derived from ObjectProperty base class that provides methods
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17 not explicitly defined in RingsCountDescriptors, MolecularDescriptors or
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18 ObjectProperty classes using Perl's AUTOLOAD functionality. These
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19 methods are generated on-the-fly for a specified object property:
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20
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21 Set<PropertyName>(<PropertyValue>);
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22 $PropertyValue = Get<PropertyName>();
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23 Delete<PropertyName>();
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24
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25 RingsCountDescriptors class doesn't perform any ring or aromaticity
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26 detection before counting their number in a molecule. Instead, it
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27 assumes ring and aromaticity detection have been performed by caller
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28 using DetectRings [Ref 31] and DetectAromaticity methods available in
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29 Molecule.
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30
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31 DetectAromaticity method available in Molecule class assigns aromaticity
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32 to rings using Huckel rule as explained below:
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33
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34 o Ring aromaticity is determined using Huckel's rule: a ring containing
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35 4n + 2 pi electrons is considered aromatic.
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36
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37 o Hetrocyclic rings containing N, O and S atoms fall into two classes:
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38 Basic aromatic and Non-basic aromatic. In Basic aromatic hetrocyclic
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39 rings, heteroatom itself is involved in a double bond. (e.g. Pyridine)
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40 However, in non-basic hetrocyclic rings, heteroatom might have an
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41 attached hydrogen atom and the remaining lone pair contribute to
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42 electron delocalization and contributes to 4n + 2 electrons. (e.g.
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43 Pyrrole, Furan)
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44
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45 o For molecules containing fused rings, each fused ring set is
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46 considered as one aromatic system for counting pi electrons to satisfy
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47 Huckel's rule; In case of a failure, rings in fused set are treated
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48 individually for aromaticity detection. Additionally, non-fused rings
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49 are handled on their own during aromaticity detection.
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50
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51 METHODS
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52 new
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53 $NewRingsCountDescriptors = new MolecularDescriptors::
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54 RingsCountDescriptors(
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55 %NamesAndValues);
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56
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57 Using specified *RingsCountDescriptors* property names and values
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58 hash, new method creates a new object and returns a reference to
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59 newly created RingsCountDescriptors object. By default, the
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60 following properties are initialized:
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61
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62 Molecule = ''
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63 Type = 'RingsCount'
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64
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65 @DescriptorNames = ('Rings', 'AromaticRings')
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66 @DescriptorValues = ('None', 'None')
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67
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68 Examples:
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69
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70 $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors(
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71 'Molecule' => $Molecule);
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72
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73 $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors();
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74
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75 $RingsCountDescriptors->SetMolecule($Molecule);
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76 $RingsCountDescriptors->GenerateDescriptors();
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77 print "RingsCountDescriptors: $RingsCountDescriptors\n";
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78
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79 GenerateDescriptors
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80 $RingsCountDescriptors->GenerateDescriptors();
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81
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82 Calculate number of rings and aromatic rings in a molecule and
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83 returns *RingsCountDescriptors*.
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84
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85 GetDescriptorNames
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86 @DescriptorNames = $RingsCountDescriptors->GetDescriptorNames();
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87 @DescriptorNames = MolecularDescriptors::RingsCountDescriptors::
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88 GetDescriptorNames();
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89
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90 Returns all available descriptor names as an array.
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91
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92 StringifyRingsCountDescriptors
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93 $String = $RingsCountDescriptors->
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94 StringifyRingsCountDescriptors();
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95
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96 Returns a string containing information about
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97 *RingsCountDescriptors* object.
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98
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99 AUTHOR
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100 Manish Sud <msud@san.rr.com>
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101
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102 SEE ALSO
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103 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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104
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105 COPYRIGHT
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106 Copyright (C) 2015 Manish Sud. All rights reserved.
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107
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108 This file is part of MayaChemTools.
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109
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110 MayaChemTools is free software; you can redistribute it and/or modify it
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111 under the terms of the GNU Lesser General Public License as published by
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112 the Free Software Foundation; either version 3 of the License, or (at
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113 your option) any later version.
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114
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