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1 NAME
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2 HydrogenBondsDescriptors
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3
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4 SYNOPSIS
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5 use MolecularDescriptors::HydrogenBondsDescriptors;
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6
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7 use MolecularDescriptors::HydrogenBondsDescriptors qw(:all);
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8
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9 DESCRIPTION
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10 HydrogenBondsDescriptors class provides the following methods:
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11
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12 new, GenerateDescriptors, GetDescriptorNames, SetHydrogenBondsType,
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13 StringifyHydrogenBondsDescriptors
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14
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15 HydrogenBondsDescriptors 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 HydrogenBondsDescriptors,
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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 The current release of MayaChemTools supports identification of two
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27 types of hydrogen bond donor and acceptor atoms with these names:
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28
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29 HBondsType1 or HydrogenBondsType1
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30 HBondsType2 or HydrogenBondsType2
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31
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32 The names of these hydrogen bond types are rather arbitrary. However,
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33 their definitions have specific meaning and are as follows:
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34
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35 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:
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36
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37 Donor: NH, NH2, OH - Any N and O with available H
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38 Acceptor: N[!H], O - Any N without available H and any O
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39
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40 HydrogenBondsType2 [ Ref 91 ]:
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41
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42 Donor: NH, NH2, OH - N and O with available H
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43 Acceptor: N, O - And N and O
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44
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45 By default, *HydrogenBondsType2* is used to calculate number hydrogen
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46 bond donor and acceptor atoms. This corresponds to RuleOf5 definition of
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47 hydrogen bond donors and acceptors.
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48
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49 METHODS
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50 new
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51 $HydrogenBondsDescriptors = new MolecularDescriptors::
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52 HydrogenBondsDescriptors(%NamesAndValues);
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53
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54 Using specified *HydrogenBondsDescriptors* property names and values
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55 hash, new method creates a new object and returns a reference to
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56 newly created HydrogenBondsDescriptors 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 = 'HydrogenBonds'
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61 HydrogenBondsType = 'HBondsType2'
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62 @DescriptorNames = ('HydrogenBondDonors', 'HydrogenBondAcceptors')
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63 @DescriptorValues = ('None', 'None')
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64
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65 Examples:
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66
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67 $HydrogenBondsDescriptors = new MolecularDescriptors::
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68 HydrogenBondsDescriptors();
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69
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70 $HydrogenBondsDescriptors = new MolecularDescriptors::
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71 HydrogenBondsDescriptors(
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72 'HydrogenBondsType' => 'HBondsType2');
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73
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74 $HydrogenBondsDescriptors->SetMolecule($Molecule);
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75 $HydrogenBondsDescriptors->GenerateDescriptors();
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76 print "HydrogenBondsDescriptors: $HydrogenBondsDescriptors\n";
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77
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78 GenerateDescriptors
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79 $HydrogenBondsDescriptors->GenerateDescriptors();
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80
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81 Calculates number of hydrogen bond donors and acceptors a molecule
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82 and returns *HydrogenBondsDescriptors*.
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83
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84 GetDescriptorNames
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85 @DescriptorNames = $HydrogenBondsDescriptors->GetDescriptorNames();
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86 @DescriptorNames = MolecularDescriptors::HydrogenBondsDescriptors::
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87 GetDescriptorNames();
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88
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89 Returns all available descriptor names as an array.
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90
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91 SetHydrogenBondsType
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92 $HydrogenBondsDescriptors->SetHydrogenBondsType($HBondsType);
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93
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94 Sets value of hydrogen bonds type to use during calculation of
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95 descriptors and returns *HydrogenBondsDescriptors*. Possible values:
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96 *HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2*.
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97
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98 StringifyHydrogenBondsDescriptors
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99 $String = $HydrogenBondsDescriptors->
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100 StringifyHydrogenBondsDescriptors();
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101
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102 Returns a string containing information about
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103 *HydrogenBondsDescriptors* object.
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104
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105 AUTHOR
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106 Manish Sud <msud@san.rr.com>
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107
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108 SEE ALSO
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109 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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110
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111 COPYRIGHT
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112 Copyright (C) 2015 Manish Sud. All rights reserved.
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113
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114 This file is part of MayaChemTools.
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115
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116 MayaChemTools is free software; you can redistribute it and/or modify it
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117 under the terms of the GNU Lesser General Public License as published by
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118 the Free Software Foundation; either version 3 of the License, or (at
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119 your option) any later version.
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120
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