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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./HydrogenBondsDescriptors.html" title="HydrogenBondsDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MolecularDescriptors.html" title="MolecularDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::MolecularComplexityDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/MolecularComplexityDescriptors.html" title="View source code">Code</a> | <a href="./../pdf/MolecularComplexityDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MolecularComplexityDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MolecularComplexityDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MolecularComplexityDescriptors.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>MolecularComplexityDescriptors</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>use MolecularDescriptors::MolecularComplexityDescriptors;</p>
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26 <p>use MolecularDescriptors::MolecularComplexityDescriptors qw(:all);</p>
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27 <p>
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28 </p>
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29 <h2>DESCRIPTION</h2>
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30 <p><strong>MolecularComplexityDescriptors</strong> class provides the following methods:</p>
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31 <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>
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32 , <a href="#getmolecularcomplexitytypeabbreviation">GetMolecularComplexityTypeAbbreviation</a>, <a href="#maccskeyssize">MACCSKeysSize</a>, <a href="#setatomidentifiertype">SetAtomIdentifierType</a>
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33 , <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setdistancebinsize">SetDistanceBinSize</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a>
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34 , <a href="#setmaxdistance">SetMaxDistance</a>, <a href="#setmaxpathlength">SetMaxPathLength</a>, <a href="#setmindistance">SetMinDistance</a>, <a href="#setminpathlength">SetMinPathLength</a>
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35 , <a href="#setmolecularcomplexitytype">SetMolecularComplexityType</a>, <a href="#setneighborhoodradius">SetNeighborhoodRadius</a>, <a href="#setnormalizationmethodology">SetNormalizationMethodology</a>
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36 , <a href="#stringifymolecularcomplexitydescriptors">StringifyMolecularComplexityDescriptors</a>
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37 </p><p><strong>MolecularComplexityDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn
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38 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
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39 in <strong>MolecularComplexityDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's
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40 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
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41 <div class="OptionsBox">
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42 Set<PropertyName>(<PropertyValue>);
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43 <br/> $PropertyValue = Get<PropertyName>();
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44 <br/> Delete<PropertyName>();</div>
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45 <p>The current release of MayaChemTools supports calculation of molecular complexity using
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46 <em>MolecularComplexityType</em> parameter corresponding to number of bits-set or unique
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47 keys [ Ref 117-119 ] in molecular fingerprints. The valid values for <em>MolecularComplexityType</em>
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48 are:</p>
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49 <div class="OptionsBox">
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50 AtomTypesFingerprints
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51 <br/> ExtendedConnectivityFingerprints
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52 <br/> MACCSKeys
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53 <br/> PathLengthFingerprints
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54 <br/> TopologicalAtomPairsFingerprints
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55 <br/> TopologicalAtomTripletsFingerprints
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56 <br/> TopologicalAtomTorsionsFingerprints
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57 <br/> TopologicalPharmacophoreAtomPairsFingerprints
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58 <br/> TopologicalPharmacophoreAtomTripletsFingerprints</div>
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59 <p>Default value for <em>MolecularComplexityType</em>: <em>MACCSKeys</em>.</p>
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60 <p><em>AtomIdentifierType</em> parameter name corresponds to atom types used during generation of
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61 fingerprints. The valid values for <em>AtomIdentifierType</em> are: <em>AtomicInvariantsAtomTypes,
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62 DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
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63 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</em>. <em>AtomicInvariantsAtomTypes</em>
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64 is not supported for following values of <em>MolecularComplexityType</em>: <em>MACCSKeys,
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65 TopologicalPharmacophoreAtomPairsFingerprints, TopologicalPharmacophoreAtomTripletsFingerprints</em>.
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66 <em>FunctionalClassAtomTypes</em> is the only valid value of <em>AtomIdentifierType</em> for topological
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67 pharmacophore fingerprints.</p>
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68 <p>Default value for <em>AtomIdentifierType</em>: <em>AtomicInvariantsAtomTypes</em> for all fingerprints;
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69 <em>FunctionalClassAtomTypes</em> for topological pharmacophore fingerprints.</p>
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70 <p><em>AtomicInvariantsToUse</em> parameter name and values are used during <em>AtomicInvariantsAtomTypes</em>
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71 value of parameter <em>AtomIdentifierType</em>. It's a list of space separated valid atomic invariant atom types.</p>
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72 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB, H, Ar, RA, FC, MN, SM</em>.
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73 Default value for <em>AtomicInvariantsToUse</em> parameter are set differently for different fingerprints
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74 using <em>MolecularComplexityType</em> parameter as shown below:</p>
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75 <div class="OptionsBox">
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76 MolecularComplexityType AtomicInvariantsToUse</div>
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77 <div class="OptionsBox">
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78 AtomTypesFingerprints AS X BO H FC
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79 <br/> TopologicalAtomPairsFingerprints AS X BO H FC
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80 <br/> TopologicalAtomTripletsFingerprints AS X BO H FC
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81 <br/> TopologicalAtomTorsionsFingerprints AS X BO H FC</div>
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82 <div class="OptionsBox">
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83 ExtendedConnectivityFingerprints AS X BO H FC MN
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84 <br/> PathLengthFingerprints AS</div>
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85 <p><em>FunctionalClassesToUse</em> parameter name and values are used during <em>FunctionalClassAtomTypes</em>
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86 value of parameter <em>AtomIdentifierType</em>. It's a list of space separated valid atomic invariant atom types.</p>
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87 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.</p>
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88 <p>Default value for <em>FunctionalClassesToUse</em> parameter is set to:</p>
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89 <div class="OptionsBox">
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90 HBD HBA PI NI Ar Hal</div>
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91 <p>for all fingerprints except for the following two <em>MolecularComplexityType</em> fingerints:</p>
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92 <div class="OptionsBox">
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93 MolecularComplexityType FunctionalClassesToUse</div>
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94 <div class="OptionsBox">
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95 TopologicalPharmacophoreAtomPairsFingerprints HBD HBA P, NI H
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96 <br/> TopologicalPharmacophoreAtomTripletsFingerprints HBD HBA PI NI H Ar</div>
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97 <p><em>MACCSKeysSize</em> parameter name is only used during <em>MACCSKeys</em> value of
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98 <em>MolecularComplexityType</em> and corresponds to size of MACCS key set. Possible
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99 values: <em>166 or 322</em>. Default value: <em>166</em>.</p>
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100 <p><em>NeighborhoodRadius</em> parameter name is only used during <em>ExtendedConnectivityFingerprints</em>
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101 value of <em>MolecularComplexityType</em> and corresponds to atomic neighborhoods radius for
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102 generating extended connectivity fingerprints. Possible values: positive integer. Default value:
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103 <em>2</em>.</p>
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104 <p><em>MinPathLength</em> and <em>MaxPathLength</em> parameters are only used during <em>PathLengthFingerprints</em>
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105 value of <em>MolecularComplexityType</em> and correspond to minimum and maximum path lengths to use
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106 for generating path length fingerprints. Possible values: positive integers. Default value: <em>MinPathLength - 1</em>;
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107 <em>MaxPathLength - 8</em>.</p>
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108 <p><em>UseBondSymbols</em> parameter is only used during <em>PathLengthFingerprints</em> value of
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109 <em>MolecularComplexityType</em> and indicates whether bond symbols are included in atom path
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110 strings used to generate path length fingerprints. Possible value: <em>Yes or No</em>. Default value:
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111 <em>Yes</em>.</p>
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112 <p><em>MinDistance</em> and <em>MaxDistance</em> parameters are only used during <em>TopologicalAtomPairsFingerprints</em>
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113 and <em>TopologicalAtomTripletsFingerprints</em> values of <em>MolecularComplexityType</em> and correspond to
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114 minimum and maximum bond distance between atom pairs during topological pharmacophore fingerprints.
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115 Possible values: positive integers. Default value: <em>MinDistance - 1</em>; <em>MaxDistance - 10</em>.</p>
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116 <p><em>UseTriangleInequality</em> parameter is used during these values for <em>MolecularComplexityType</em>:
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117 <em>TopologicalAtomTripletsFingerprints</em> and <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.
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118 Possible values: <em>Yes or No</em>. It determines wheter to apply triangle inequality to distance triplets.
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119 Default value: <em>TopologicalAtomTripletsFingerprints - No</em>;
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120 <em>TopologicalPharmacophoreAtomTripletsFingerprints - Yes</em>.</p>
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121 <p><em>DistanceBinSize</em> parameter is used during <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>
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122 value of <em>MolecularComplexityType</em> and corresponds to distance bin size used for binning
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123 distances during generation of topological pharmacophore atom triplets fingerprints. Possible
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124 value: positive integer. Default value: <em>2</em>.</p>
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125 <p><em>NormalizationMethodology</em> is only used for these values for <em>MolecularComplexityType</em>:
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126 <em>ExtendedConnectivityFingerprints</em>, <em>TopologicalPharmacophoreAtomPairsFingerprints</em>
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127 and <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>. It corresponds to normalization
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128 methodology to use for scaling the number of bits-set or unique keys during generation of
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129 fingerprints. Possible values during <em>ExtendedConnectivityFingerprints</em>: <em>None or
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130 ByHeavyAtomsCount</em>; Default value: <em>None</em>. Possible values during topological
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131 pharmacophore atom pairs and triplets fingerprints: <em>None or ByPossibleKeysCount</em>;
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132 Default value: <em>None</em>. <em>ByPossibleKeysCount</em> corresponds to total number of
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133 possible topological pharmacophore atom pairs or triplets in a molecule.</p>
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134 <p>
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135 </p>
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136 <h2>METHODS</h2>
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137 <dl>
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138 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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139 <dd>
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140 <div class="OptionsBox">
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141 $NewMolecularComplexityDescriptors = new MolecularDescriptors::
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142 MolecularComplexityDescriptors(
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143 <br/> %NamesAndValues);</div>
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144 <p>Using specified <em>MolecularComplexityDescriptors</em> property names and values hash, <strong>new</strong>
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145 method creates a new object and returns a reference to newly created <strong>MolecularComplexityDescriptors</strong>
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146 object. By default, the following properties are initialized:</p>
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147 <div class="OptionsBox">
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148 Molecule = ''
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149 <br/> Type = 'MolecularComplexity'
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150 <br/> MolecularComplexityType = 'MACCSKeys'
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151 <br/> AtomIdentifierType = ''
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152 <br/> MACCSKeysSize = 166
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153 <br/> NeighborhoodRadius = 2
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154 <br/> MinPathLength = 1
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155 <br/> MaxPathLength = 8
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156 <br/> UseBondSymbols = 1
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157 <br/> MinDistance = 1
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158 <br/> MaxDistance = 10
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159 <br/> UseTriangleInequality = ''
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160 <br/> DistanceBinSize = 2
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161 <br/> NormalizationMethodology = 'None'
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162 <br/> @DescriptorNames = ('MolecularComplexity')
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163 <br/> @DescriptorValues = ('None')</div>
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164 <p>Examples:</p>
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165 <div class="OptionsBox">
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166 $MolecularComplexityDescriptors = new MolecularDescriptors::
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167 MolecularComplexityDescriptors(
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168 'Molecule' => $Molecule);</div>
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169 <div class="OptionsBox">
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170 $MolecularComplexityDescriptors = new MolecularDescriptors::
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171 MolecularComplexityDescriptors();</div>
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172 <div class="OptionsBox">
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173 $MolecularComplexityDescriptors->SetMolecule($Molecule);
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174 <br/> $MolecularComplexityDescriptors->GenerateDescriptors();
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175 <br/> print "MolecularComplexityDescriptors: $MolecularComplexityDescriptors\n";</div>
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176 </dd>
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177 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
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178 <dd>
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179 <div class="OptionsBox">
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180 $MolecularComplexityDescriptors->GenerateDescriptors();</div>
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181 <p>Calculates MolecularComplexity value for a molecule and returns <em>MolecularComplexityDescriptors</em>.</p>
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182 </dd>
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183 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
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184 <dd>
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185 <div class="OptionsBox">
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186 @DescriptorNames = $MolecularComplexityDescriptors->GetDescriptorNames();
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187 <br/> @DescriptorNames = MolecularDescriptors::MolecularComplexityDescriptors::
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188 GetDescriptorNames();</div>
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189 <p>Returns all available descriptor names as an array.</p>
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190 </dd>
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191 <dt><strong><a name="getmolecularcomplexitytypeabbreviation" class="item"><strong>GetMolecularComplexityTypeAbbreviation</strong></a></strong></dt>
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192 <dd>
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193 <div class="OptionsBox">
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194 $Abbrev = $MolecularComplexityDescriptors->
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195 GetMolecularComplexityTypeAbbreviation();
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196 <br/> $Abbrev = MolecularDescriptors::MolecularComplexityDescriptors::
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197 GetMolecularComplexityTypeAbbreviation($ComplexityType);</div>
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198 <p>Returns abbreviation for a specified molecular complexity type or corresponding to
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199 <em>MolecularComplexityDescriptors</em> object.</p>
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200 </dd>
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201 <dt><strong><a name="setmaccskeyssize" class="item"><strong>SetMACCSKeysSize</strong></a></strong></dt>
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202 <dd>
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203 <div class="OptionsBox">
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204 $MolecularComplexityDescriptors->MACCSKeysSize($Size);</div>
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205 <p>Sets MACCS keys size and returns <em>MolecularComplexityDescriptors</em>.</p>
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206 </dd>
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207 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
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208 <dd>
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209 <div class="OptionsBox">
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210 $MolecularComplexityDescriptors->SetAtomIdentifierType($IdentifierType);</div>
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211 <p>Sets atom <em>IdentifierType</em> to use during fingerprints generation corresponding to
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212 <em>MolecularComplexityType</em> and returns <em>MolecularComplexityDescriptors</em>.</p>
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213 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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214 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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215 TPSAAtomTypes, UFFAtomTypes</em>.</p>
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216 </dd>
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217 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
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218 <dd>
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219 <div class="OptionsBox">
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220 $MolecularComplexityDescriptors->SetAtomicInvariantsToUse($ValuesRef);
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221 <br/> $MolecularComplexityDescriptors->SetAtomicInvariantsToUse(@Values);</div>
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222 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
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223 for fingerprints generation and returns <em>MolecularComplexityDescriptors</em>.</p>
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224 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
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225 H, Ar, RA, FC, MN, SM</em>. Default value [ Ref 24 ]: <em>AS,X,BO,H,FC,MN</em>.</p>
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226 <p>The atomic invariants abbreviations correspond to:</p>
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227 <div class="OptionsBox">
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228 AS = Atom symbol corresponding to element symbol</div>
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229 <div class="OptionsBox">
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230 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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231 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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232 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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233 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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234 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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235 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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236 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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237 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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238 <br/> RA = Ring atom annotation indicating whether atom is a ring
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239 <br/> FC<+n/-n> = Formal charge assigned to atom
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240 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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241 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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242 3 (triplet)</div>
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243 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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244 <div class="OptionsBox">
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245 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></div>
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246 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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247 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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248 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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249 are also allowed:</p>
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250 <div class="OptionsBox">
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251 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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252 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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253 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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254 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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255 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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256 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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257 <br/> H : NumOfImplicitAndExplicitHydrogens
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258 <br/> Ar : Aromatic
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259 <br/> RA : RingAtom
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260 <br/> FC : FormalCharge
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261 <br/> MN : MassNumber
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262 <br/> SM : SpinMultiplicity</div>
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263 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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264 atom types.</p>
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265 </dd>
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266 <dt><strong><a name="setdistancebinsize" class="item"><strong>SetDistanceBinSize</strong></a></strong></dt>
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267 <dd>
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268 <div class="OptionsBox">
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269 $MolecularComplexityDescriptors->SetDistanceBinSize($BinSize);</div>
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270 <p>Sets distance bin size used to bin distances between atom pairs in atom triplets for
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271 topological pharmacophore atom triplets fingerprints generation and returns
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272 <em>MolecularComplexityDescriptors</em>.</p>
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273 </dd>
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274 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
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275 <dd>
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276 <div class="OptionsBox">
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277 $MolecularComplexityDescriptors->SetFunctionalClassesToUse($ValuesRef);
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278 <br/> $MolecularComplexityDescriptors->SetFunctionalClassesToUse(@Values);</div>
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279 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
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280 for fingerprints generation and returns <em>MolecularComplexityDescriptors</em>.</p>
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281 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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282 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
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283 <p>The functional class abbreviations correspond to:</p>
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284 <div class="OptionsBox">
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285 HBD: HydrogenBondDonor
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286 <br/> HBA: HydrogenBondAcceptor
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287 <br/> PI : PositivelyIonizable
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288 <br/> NI : NegativelyIonizable
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289 <br/> Ar : Aromatic
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290 <br/> Hal : Halogen
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291 <br/> H : Hydrophobic
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292 <br/> RA : RingAtom
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293 <br/> CA : ChainAtom</div>
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294 <div class="OptionsBox">
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295 Functional class atom type specification for an atom corresponds to:</div>
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296 <div class="OptionsBox">
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297 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
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298 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
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299 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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300 <div class="OptionsBox">
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301 HydrogenBondDonor: NH, NH2, OH
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302 <br/> HydrogenBondAcceptor: N[!H], O
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303 <br/> PositivelyIonizable: +, NH2
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304 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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305 </dd>
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306 <dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt>
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307 <dd>
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308 <div class="OptionsBox">
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309 $MolecularComplexityDescriptors->SetMaxDistance($MaxDistance);</div>
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310 <p>Sets maximum distance to use during topological atom pairs and triplets fingerprints
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311 generation and returns <em>MolecularComplexityDescriptors</em>.</p>
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312 </dd>
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313 <dt><strong><a name="setmaxpathlength" class="item"><strong>SetMaxPathLength</strong></a></strong></dt>
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314 <dd>
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315 <div class="OptionsBox">
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316 $MolecularComplexityDescriptors->SetMaxPathLength($Length);</div>
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317 <p>Sets maximum path length to use during path length fingerprints generation and returns
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318 <em>MolecularComplexityDescriptors</em>.</p>
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319 </dd>
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320 <dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt>
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321 <dd>
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322 <div class="OptionsBox">
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323 $MolecularComplexityDescriptors->SetMinDistance($MinDistance);</div>
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324 <p>Sets minimum distance to use during topological atom pairs and triplets fingerprints
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325 generation and returns <em>MolecularComplexityDescriptors</em>.</p>
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326 </dd>
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327 <dt><strong><a name="setminpathlength" class="item"><strong>SetMinPathLength</strong></a></strong></dt>
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328 <dd>
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329 <div class="OptionsBox">
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330 $MolecularComplexityDescriptors->SetMinPathLength($MinPathLength);</div>
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331 <p>Sets minimum path length to use during path length fingerprints generation and returns
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332 <em>MolecularComplexityDescriptors</em>.</p>
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333 </dd>
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334 <dt><strong><a name="setmolecularcomplexitytype" class="item"><strong>SetMolecularComplexityType</strong></a></strong></dt>
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335 <dd>
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336 <div class="OptionsBox">
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337 $MolecularComplexityDescriptors->SetMolecularComplexityType($ComplexityType);</div>
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338 <p>Sets molecular complexity type to use for calculating its value and returns
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339 <em>MolecularComplexityDescriptors</em>.</p>
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340 </dd>
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341 <dt><strong><a name="setneighborhoodradius" class="item"><strong>SetNeighborhoodRadius</strong></a></strong></dt>
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342 <dd>
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343 <div class="OptionsBox">
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344 $MolecularComplexityDescriptors->SetNeighborhoodRadius($Radius);</div>
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345 <p>Sets neighborhood radius to use during extended connectivity fingerprints generation and
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346 returns <em>MolecularComplexityDescriptors</em>.</p>
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347 </dd>
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348 <dt><strong><a name="setnormalizationmethodology" class="item"><strong>SetNormalizationMethodology</strong></a></strong></dt>
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349 <dd>
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350 <div class="OptionsBox">
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351 $MolecularComplexityDescriptors->SetNormalizationMethodology($Methodology);</div>
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352 <p>Sets normalization methodology to use during calculation of molecular complexity
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353 corresponding to extended connectivity, topological pharmacophore atom pairs and
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354 tripletes fingerprints returns <em>MolecularComplexityDescriptors</em>.</p>
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355 </dd>
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356 <dt><strong><a name="stringifymolecularcomplexitydescriptors" class="item"><strong>StringifyMolecularComplexityDescriptors</strong></a></strong></dt>
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357 <dd>
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358 <div class="OptionsBox">
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359 $String = $MolecularComplexityDescriptors->
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360 StringifyMolecularComplexityDescriptors();</div>
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361 <p>Returns a string containing information about <em>MolecularComplexityDescriptors</em> object.</p>
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362 </dd>
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363 </dl>
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364 <p>
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365 </p>
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366 <h2>AUTHOR</h2>
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367 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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368 <p>
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369 </p>
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370 <h2>SEE ALSO</h2>
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371 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
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372 </p>
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373 <p>
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374 </p>
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375 <h2>COPYRIGHT</h2>
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376 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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377 <p>This file is part of MayaChemTools.</p>
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378 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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379 the terms of the GNU Lesser General Public License as published by the Free
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380 Software Foundation; either version 3 of the License, or (at your option)
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381 any later version.</p>
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382 <p> </p><p> </p><div class="DocNav">
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383 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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384 <tr align="left" valign="top"><td width="33%" align="left"><a href="./HydrogenBondsDescriptors.html" title="HydrogenBondsDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MolecularDescriptors.html" title="MolecularDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::MolecularComplexityDescriptors.pm</strong></td></tr>
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385 </table>
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386 </div>
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387 <br />
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388 <center>
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389 <img src="../../images/h2o2.png">
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390 </center>
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391 </body>
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392 </html>
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