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1 NAME
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2 MolecularVolumeDescriptors
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3
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4 SYNOPSIS
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5 use MolecularDescriptors::MolecularVolumeDescriptors;
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6
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7 use MolecularDescriptors::MolecularVolumeDescriptors qw(:all);
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8
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9 DESCRIPTION
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10 MolecularVolumeDescriptors class provides the following methods:
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11
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12 new, GenerateDescriptors, GetDescriptorNames,
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13 GetVDWAtomRadiiAndVolumesData, StringifyMolecularVolumeDescriptors
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14
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15 MolecularVolumeDescriptors is derived from MolecularDescriptors class
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16 which in turn is derived from ObjectProperty base class that provides
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17 methods not explicitly defined in MolecularVolumeDescriptors,
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18 MolecularDescriptors or ObjectProperty classes using Perl's AUTOLOAD
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19 functionality. These methods are generated on-the-fly for a specified
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20 object property:
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21
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22 Set<PropertyName>(<PropertyValue>);
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23 $PropertyValue = Get<PropertyName>();
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24 Delete<PropertyName>();
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25
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26 van der Waals molecular volume [ Ref 93 ] (A**3/molecule) of a molecule
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27 is calculated using atomic and bonds contributions along with
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28 adjustments for aromatic and non-aromatic rings using the following
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29 equation:
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30
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31 vdwMolecularVolume = SumOfAtomicVDWVolumeContributions
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32 - 5.92 * NumOfBonds
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33 - 14.7 * NumOfAromaticRings
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34 - 3.8 * NumOfNonAromaticRings
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35
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36 van der Waals atomic volume for atoms is taken from data file
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37 VDWAtomRadiiAndVolumes.csv distributed with MayaChemTools. It contains
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38 van der Waals atom radii and atom and volumes data for 38 elements;
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39 Table 2 [ Ref 93 ] contains data for only 15 elements. After converting
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40 valid van der Waals atom radius data from pm (picometer) to A (Angstrom)
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41 available under column name VanderWaalsRadius in
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42 PeriodicTableElementsData.csv data file, van der Waals atom volume is
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43 calculated using: 4/3 * PI * (Radius ** 3). For elements specified in
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44 Table 2 [ Ref 93 ] - H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, Te, I -
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45 the van der Waals atom radii and calculated atom volumes match the
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46 values in the table.
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47
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48 METHODS
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49 new
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50 $NewMolecularVolumeDescriptors = new MolecularDescriptors::
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51 MolecularVolumeDescriptors(
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52 %NamesAndValues);
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53
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54 Using specified *MolecularVolumeDescriptors* property names and
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55 values hash, new method creates a new object and returns a reference
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56 to newly created MolecularVolumeDescriptors object. By default, the
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57 following properties are initialized:
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58
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59 Molecule = ''
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60 Type = 'MolecularVolume'
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61 @DescriptorNames = ('MolecularVolume')
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62 @DescriptorValues = ('None')
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63
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64 Examples:
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65
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66 $MolecularVolumeDescriptors = new MolecularDescriptors::
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67 MolecularVolumeDescriptors();
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68
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69 $MolecularVolumeDescriptors->SetMolecule($Molecule);
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70 $MolecularVolumeDescriptors->GenerateDescriptors();
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71 print "MolecularVolumeDescriptors: $MolecularVolumeDescriptors\n";
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72
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73 GenerateDescriptors
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74 $MolecularVolumeDescriptors->GenerateDescriptors();
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75
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76 Calculate van der Waals molecular volume descriptor for a molecule
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77 and returns *MolecularVolumeDescriptors*.
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78
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79 GetDescriptorNames
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80 @DescriptorNames = $MolecularVolumeDescriptors->GetDescriptorNames();
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81 @DescriptorNames = MolecularDescriptors::MolecularVolumeDescriptors::
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82 GetDescriptorNames();
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83
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84 Returns all available descriptor names as an array.
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85
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86 GetVDWAtomRadiiAndVolumesData
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87 $VDWVolumeDataMapRef = $MolecularVolumeDescriptors->
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88 GetVDWAtomRadiiAndVolumesData();
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89 $VDWVolumeDataMapRef = MolecularDescriptors::MolecularVolumeDescriptors::
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90 GetVDWAtomRadiiAndVolumesData();
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91
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92 Returns a hash reference to van der Waals atom symbols corresponding
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93 to atom types and associated data loaded from
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94 VDWAtomRadiiAndVolumes.csv data file as a reference to hash with the
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95 following hash data format:
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96
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97 @{$VDWVolumeDataMap{AtomTypes}} - Array of all possible atom
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98 types for all atom symbols
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99 @{$VDWVolumeDataMap->{ColLabels}} - Array of column labels
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100 %{$VDWVolumeDataMap->{DataCol<Num>}} - Hash keys pair:
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101 DataCol<Num>, AtomType
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102
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103 StringifyMolecularVolumeDescriptors
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104 $String = $MolecularVolumeDescriptors->
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105 StringifyMolecularVolumeDescriptors();
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106
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107 Returns a string containing information about
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108 *MolecularVolumeDescriptors* object.
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109
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110 AUTHOR
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111 Manish Sud <msud@san.rr.com>
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112
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113 SEE ALSO
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114 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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115
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116 COPYRIGHT
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117 Copyright (C) 2015 Manish Sud. All rights reserved.
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118
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119 This file is part of MayaChemTools.
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120
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121 MayaChemTools is free software; you can redistribute it and/or modify it
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122 under the terms of the GNU Lesser General Public License as published by
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123 the Free Software Foundation; either version 3 of the License, or (at
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124 your option) any later version.
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125
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