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0 4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1 <html>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	2 <head>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	3 <title>MayaChemTools:Code:MolecularDescriptors::MolecularComplexityDescriptors.pm</title>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	6 </head>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	8 <br/>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	9 <center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	11 </center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	12 <br/>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	13 <pre>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	14 <a name="package-MolecularDescriptors::MolecularComplexityDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularComplexityDescriptors</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	15 2 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	16 3 <span class="c"># $RCSfile: MolecularComplexityDescriptors.pm,v $</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	18 5 <span class="c"># $Revision: 1.15 $</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	19 6 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	21 8 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	23 10 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	24 11 <span class="c"># This file is part of MayaChemTools.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	25 12 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	29 16 <span class="c"># later version.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	30 17 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	34 21 <span class="c"># details.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	35 22 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	40 27 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	41 28
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	47 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	48 35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	49 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	50 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	51 38 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	52 39 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	53 40 <span class="k">use</span> <span class="w">Fingerprints::AtomTypesFingerprints</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	54 41 <span class="k">use</span> <span class="w">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	55 42 <span class="k">use</span> <span class="w">Fingerprints::MACCSKeys</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	56 43 <span class="k">use</span> <span class="w">Fingerprints::PathLengthFingerprints</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	57 44 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	58 45 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	59 46 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	60 47 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	61 48 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	62 49
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	63 50 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	64 51
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	65 52 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	66 53 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	67 54 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames GetMolecularComplexityTypeAbbreviation)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	68 55
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	69 56 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	70 57
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	71 58 <span class="c"># Setup class variables...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	72 59 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	73 60 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	74 61
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	75 62 <span class="c"># Overload Perl functions...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	76 63 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecularComplexityDescriptors'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	77 64
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	78 65 <span class="c"># Class constructor...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	79 <a name="new-"></a> 66 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	80 67 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	81 68
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	82 69 <span class="c"># Initialize object...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	83 70 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	84 71 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> \|\| <span class="i">$Class</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	85 72 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	86 73
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	87 74 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	88 75
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	89 76 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	90 77 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	91 78
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	92 79 <span class="c"># Initialize class ...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	93 <a name="_InitializeClass-"></a> 80 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	94 81 <span class="c">#Class name...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	95 82 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	96 83
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	97 84 <span class="c"># Descriptor names...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	98 85 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'MolecularComplexity'</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	99 86
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	100 87 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	101 88
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	102 89 <span class="c"># Get descriptor names as an array.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	103 90 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	104 91 <span class="c"># This functionality can be either invoked as a class function or an</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	105 92 <span class="c"># object method.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	106 93 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	107 <a name="GetDescriptorNames-"></a> 94 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	108 95 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	109 96 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	110 97
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	111 98 <span class="c"># Initialize object data...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	112 99 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	113 <a name="_InitializeMolecularComplexityDescriptors-"></a> 100 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptors</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	114 101 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	115 102
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	116 103 <span class="c"># Type of MolecularDescriptor...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	117 104 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'MolecularComplexity'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	118 105
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	119 106 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	120 107 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	121 108 <span class="c"># corresponding to number of bits-set or unique keys [ Ref 117-119 ] in molecular</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	122 109 <span class="c"># fingerprints. The following types of fingerprints based molecular complexity measures</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	123 110 <span class="c"># are supported:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	124 111 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	125 112 <span class="c"># AtomTypesFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	126 113 <span class="c"># ExtendedConnectivityFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	127 114 <span class="c"># MACCSKeys</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	128 115 <span class="c"># PathLengthFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	129 116 <span class="c"># TopologicalAtomPairsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	130 117 <span class="c"># TopologicalAtomTripletsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	131 118 <span class="c"># TopologicalAtomTorsionsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	132 119 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	133 120 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	134 121 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	135 122 <span class="c"># Default: MACCSKeys</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	136 123 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	137 124 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	138 125
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	139 126 <span class="c"># Atom types to use for generating fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	140 127 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	141 128 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	142 129 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	143 130 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	144 131 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	145 132 <span class="c"># Notes:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	146 133 <span class="c"># . AtomicInvariantsAtomTypes for all supported MolecularComplexityType except for</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	147 134 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints and TopologicalPharmacophoreAtomTripletsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	148 135 <span class="c"># . This value is not used for MACCSKeys</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	149 136 <span class="c"># . FunctionalClassAtomTypes is the only valid value during topological pharmacophore fingerprints.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	150 137 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	151 138 <span class="c"># . Default values for AtomicInvariantsToUse and FunctionalClassesToUse are set appropriately</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	152 139 <span class="c"># for different types of fingerprints as shown below.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	153 140 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	154 141 <span class="c"># MolecularComplexityType AtomicInvariantsToUse</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	155 142 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	156 143 <span class="c"># AtomTypesFingerprints AS, X, BO, H, FC</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	157 144 <span class="c"># TopologicalAtomPairsFingerprints AS, X, BO, H, FC</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	158 145 <span class="c"># TopologicalAtomTripletsFingerprints AS, X, BO, H, FC</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	159 146 <span class="c"># TopologicalAtomTorsionsFingerprints AS, X, BO, H, FC</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	160 147 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	161 148 <span class="c"># ExtendedConnectivityFingerprints AS, X, BO, H, FC, MN</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	162 149 <span class="c"># PathLengthFingerprints AS</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	163 150 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	164 151 <span class="c"># Default for FunctionalClassesToUse for all fingerprints is set to:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	165 152 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	166 153 <span class="c"># HBD, HBA, PI, NI, Ar, Hal</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	167 154 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	168 155 <span class="c"># except for the following two MolecularComplexityType fingerprints:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	169 156 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	170 157 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints HBD, HBA, PI, NI, H</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	171 158 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints HBD, HBA, PI, NI, H, Ar</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	172 159 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	173 160 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	174 161
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	175 162 <span class="c"># Size of MACCS key set: 166 or 322...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	176 163 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	177 164 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="n">166</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	178 165
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	179 166 <span class="c"># Atomic neighborhoods radius for extended connectivity fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	180 167 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	181 168
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	182 169 <span class="c"># Minimum and maximum path lengths to use for path length fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	183 170 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	184 171 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="n">8</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	185 172
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	186 173 <span class="c"># By default bond symbols are included in atom path strings used to generate path length</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	187 174 <span class="c"># fingerprints... ...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	188 175 <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	189 176
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	190 177 <span class="c"># Minimum and maximum bond distance between atom pairs during topological</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	191 178 <span class="c"># atom pairs/triplets fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	192 179 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	193 180 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	194 181
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	195 182 <span class="c"># Determines whether to apply triangle inequality to distance triplets...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	196 183 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	197 184 <span class="c"># Default for TopologicalAtomTripletsFingerprints: 0</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	198 185 <span class="c"># Default for TopologicalPharmacophoreAtomTripletsFingerprints: 1</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	199 186 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	200 187 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	201 188
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	202 189 <span class="c"># Distance bin size used for binning distances during generation of</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	203 190 <span class="c"># topological pharmacophore atom triplets fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	204 191 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	205 192 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="n">2</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	206 193
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	207 194 <span class="c"># Normalization methodology to use for scaling the number of bits-set or unique keys</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	208 195 <span class="c"># for:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	209 196 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	210 197 <span class="c"># ExtendedConnectivityFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	211 198 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	212 199 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	213 200 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	214 201 <span class="c"># This option is gnored for all other types of fingerprints.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	215 202 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	216 203 <span class="c"># Possible values during extended connectivity fingerprints: None or ByHeavyAtomsCount. Default:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	217 204 <span class="c"># None.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	218 205 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	219 206 <span class="c"># Possible values during topological pharmacophore atom pairs and tripletes fingerprints: None,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	220 207 <span class="c"># or ByPossibleKeysCount. Default: None. ByPossibleKeysCount corresponds to total number of</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	221 208 <span class="c"># possible topological pharmacophore atom pairs or triplets in a molecule.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	222 209 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	223 210 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	224 211 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="q">'None'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	225 212
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	226 213 <span class="c"># Intialize descriptor names and values...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	227 214 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	228 215
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	229 216 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	230 217 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	231 218
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	232 219 <span class="c"># Initialize object properties...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	233 220 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	234 <a name="_InitializeMolecularComplexityDescriptorsProperties-"></a> 221 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptorsProperties</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	235 222 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	236 223
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	237 224 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	238 225 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	239 226 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	240 227 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	241 228 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	242 229
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	243 230 <span class="c"># Make sure MolecularComplexityType is set...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	244 231 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	245 232 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">'MACCSKeys'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	246 233 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	247 234
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	248 235 <span class="c"># Make sure AtomIdentifierType is set...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	249 236 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	250 237 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	251 238 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	252 239 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	253 240 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	254 241
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	255 242 <span class="c"># Make sure UseTriangleInequality is set...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	256 243 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalAtomTripletsFingerprints\|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	257 244 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">UseTriangleInequality</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	258 245 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	259 246 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	260 247 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	261 248
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	262 249 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	263 250 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	264 251
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	265 252 <span class="c"># Initialize atom identifer type...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	266 253 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	267 <a name="_InitializeAtomIdentifierType-"></a> 254 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierType</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	268 255 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	269 256 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	270 257
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	271 258 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	272 259 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	273 260 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	274 261
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	275 262 <span class="i">$AtomIdentifierType</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints\|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> ? <span class="q">'FunctionalClassAtomTypes'</span> <span class="co">:</span> <span class="q">'AtomicInvariantsAtomTypes'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	276 263
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	277 264 <span class="i">$This</span><span class="i">->SetAtomIdentifierType</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	278 265
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	279 266 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	280 267 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	281 268
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	282 269 <span class="c"># Get abbreviation for specified molecular complexity type or using descriptors object...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	283 270 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	284 271 <span class="c"># This functionality can be either invoked as a class function or an</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	285 272 <span class="c"># object method.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	286 273 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	287 <a name="GetMolecularComplexityTypeAbbreviation-"></a> 274 <span class="k">sub </span><span class="m">GetMolecularComplexityTypeAbbreviation</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	288 275 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	289 276 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ComplexityType</span><span class="cm">,</span> <span class="i">%ComplexityTypeToAbbrev</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	290 277
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	291 278 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecularComplexityDescriptors</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	292 279 <span class="i">$This</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	293 280 <span class="i">$ComplexityType</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	294 281 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	295 282 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	296 283 <span class="i">$ComplexityType</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	297 284 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	298 285
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	299 286 <span class="i">%ComplexityTypeToAbbrev</span> = <span class="s">(</span><span class="k">lc</span> <span class="q">'AtomTypesFingerprints'</span> <span class="cm">=></span> <span class="q">'ATFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'ExtendedConnectivityFingerprints'</span> <span class="cm">=></span> <span class="q">'ECFP'</span><span class="cm">,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	300 287 <span class="k">lc</span> <span class="q">'MACCSKeys'</span> <span class="cm">=></span> <span class="q">'MACCSKeys'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'PathLengthFingerprints'</span> <span class="cm">=></span> <span class="q">'PLFP'</span><span class="cm">,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	301 288 <span class="k">lc</span> <span class="q">'TopologicalAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TAPFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'TopologicalAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	302 289 <span class="k">lc</span> <span class="q">'TopologicalAtomTorsionsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	303 290 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPAPFP'</span><span class="cm">,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	304 291 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPATFP'</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	305 292
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	306 293 <span class="k">return</span> <span class="k">exists</span> <span class="i">$ComplexityTypeToAbbrev</span>{<span class="k">lc</span> <span class="i">$ComplexityType</span>} ? <span class="i">$ComplexityTypeToAbbrev</span>{<span class="k">lc</span> <span class="i">$ComplexityType</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	307 294 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	308 295
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	309 296 <span class="c"># Set MACCS key set size...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	310 297 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	311 <a name="SetMACCSKeysSize-"></a> 298 <span class="k">sub </span><span class="m">SetMACCSKeysSize</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	312 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	313 300
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	314 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	315 302 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: Size value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	316 303 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	317 304 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(166\|322)/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	318 305 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: The current release of MayaChemTools doesn't support MDL MACCS $Value keys..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	319 306 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	320 307 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="i">$Value</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	321 308
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	322 309 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	323 310 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	324 311
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	325 312 <span class="c"># Set minimum path length...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	326 313 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	327 <a name="SetMinPathLength-"></a> 314 <span class="k">sub </span><span class="m">SetMinPathLength</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	328 315 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	329 316
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	330 317 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	331 318 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinPathLength: MinPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	332 319 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	333 320 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	334 321
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	335 322 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	336 323 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	337 324
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	338 325 <span class="c"># Set maximum path length...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	339 326 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	340 <a name="SetMaxPathLength-"></a> 327 <span class="k">sub </span><span class="m">SetMaxPathLength</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	341 328 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	342 329
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	343 330 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	344 331 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxPathLength: MaxPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	345 332 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	346 333 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	347 334
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	348 335 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	349 336 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	350 337
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	351 338 <span class="c"># Set minimum bond distance between atom pairs during topological and topological</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	352 339 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	353 340 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	354 <a name="SetMinDistance-"></a> 341 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	355 342 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	356 343
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	357 344 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	358 345 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	359 346 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	360 347 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	361 348
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	362 349 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	363 350 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	364 351
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	365 352 <span class="c"># Set maximum bond distance between atom pairs during topological and topological</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	366 353 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	367 354 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	368 <a name="SetMaxDistance-"></a> 355 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	369 356 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	370 357
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	371 358 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	372 359 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	373 360 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	374 361 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	375 362
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	376 363 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	377 364 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	378 365
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	379 366 <span class="c"># Set atom neighborhood radius...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	380 367 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	381 <a name="SetNeighborhoodRadius-"></a> 368 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	382 369 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	383 370
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	384 371 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	385 372 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	386 373 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	387 374
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	388 375 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	389 376 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	390 377 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	391 378 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	392 379
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	393 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	394 381 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	395 382
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	396 383 <span class="c"># Set molecular complexity type...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	397 384 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	398 <a name="SetMolecularComplexityType-"></a> 385 <span class="k">sub </span><span class="m">SetMolecularComplexityType</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	399 386 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	400 387
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	401 388 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(AtomTypesFingerprints\|ExtendedConnectivityFingerprints\|MACCSKeys\|PathLengthFingerprints\|TopologicalAtomPairsFingerprints\|TopologicalAtomTripletsFingerprints\|TopologicalAtomTorsionsFingerprints\|TopologicalPharmacophoreAtomPairsFingerprints\|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	402 389 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecularComplexityType: MolecularComplexityType value, $Value, is not valid. Supported values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	403 390 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	404 391
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	405 392 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="i">$Value</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	406 393
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	407 394 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	408 395 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	409 396
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	410 397 <span class="c"># Set distance bin size for binning pharmacophore atom pair distances in atom triplets...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	411 398 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	412 <a name="SetDistanceBinSize-"></a> 399 <span class="k">sub </span><span class="m">SetDistanceBinSize</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	413 400 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	414 401
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	415 402 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	416 403 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDistanceBinSize: DistanceBinSize value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	417 404 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	418 405 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="i">$Value</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	419 406
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	420 407 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	421 408 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	422 409
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	423 410 <span class="c"># Set normalization methodology to use for scaling the number of bits-set or unique keys</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	424 411 <span class="c"># in fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	425 412 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	426 <a name="SetNormalizationMethodology-"></a> 413 <span class="k">sub </span><span class="m">SetNormalizationMethodology</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	427 414 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	428 415
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	429 416 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount\|ByPossibleKeysCount\|None)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	430 417 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	431 418 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	432 419
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	433 420 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	434 421 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^(ExtendedConnectivityFingerprints\|TopologicalPharmacophoreAtomPairsFingerprints\|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	435 422 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: Normalization is not supported for MolecularComplexityType: $This->{MolecularComplexityType}. Valid MolecularComplexityType values: ExtendedConnectivityFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	436 423 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	437 424
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	438 425 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span> && <span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount\|None)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	439 426 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByHeavyAtomsCount..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	440 427 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	441 428
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	442 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints\|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span> && <span class="i">$Value</span> !~ <span class="q">/^(ByPossibleKeysCount\|None)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	443 430 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByPossibleKeysCount..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	444 431 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	445 432 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	446 433
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	447 434 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	448 435
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	449 436 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	450 437 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	451 438
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	452 439 <span class="c"># Set intial atom identifier type..</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	453 440 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	454 <a name="SetAtomIdentifierType-"></a> 441 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	455 442 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IdentifierType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	456 443
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	457 444 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes\|FunctionalClassAtomTypes\|DREIDINGAtomTypes\|EStateAtomTypes\|MMFF94AtomTypes\|SLogPAtomTypes\|SYBYLAtomTypes\|TPSAAtomTypes\|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	458 445 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	459 446 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	460 447
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	461 448 <span class="c"># FunctionalClassAtomTypes is the only valid atom identifier type for pharmacophore fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	462 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints\|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	463 450 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	464 451 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported type for $This->{MolecularComplexityType} complexity type: FunctionalClassAtomTypes."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	465 452 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	466 453 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	467 454
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	468 455 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	469 456 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	470 457 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	471 458
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	472 459 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	473 460
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	474 461 <span class="c"># Initialize identifier type information...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	475 462 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	476 463
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	477 464 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	478 465 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	479 466
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	480 467 <span class="c"># Calculate molecular complexity [ Ref 117-119 ] of a molecule using its fingerprints.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	481 468 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	482 469 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	483 470 <span class="c"># corresponding to the number of bits-set or unique keys in molecular fingerprints. The</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	484 471 <span class="c"># following types of fingerprints based molecular complexity measures are supported:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	485 472 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	486 473 <span class="c"># AtomTypesFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	487 474 <span class="c"># ExtendedConnectivityFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	488 475 <span class="c"># MACCSKeys</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	489 476 <span class="c"># PathLengthFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	490 477 <span class="c"># TopologicalAtomPairsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	491 478 <span class="c"># TopologicalAtomTripletsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	492 479 <span class="c"># TopologicalAtomTorsionsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	493 480 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	494 481 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	495 482 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	496 483 <span class="c"># After the molecular complexity value has been calculated, it can also be normalized by</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	497 484 <span class="c"># by scaling the number of bits-set or unique keys for following types of fingerprints:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	498 485 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	499 486 <span class="c"># ExtendedConnectivityFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	500 487 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	501 488 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	502 489 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	503 490 <span class="c"># Two types of normalization methodologies are supported: by heavy atoms count for</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	504 491 <span class="c"># extended connectivity fingerprints; by possible keys count for topological pharmacophore</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	505 492 <span class="c"># atom pairs and triplets fingerprints.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	506 493 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	507 <a name="GenerateDescriptors-"></a> 494 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	508 495 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	509 496
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	510 497 <span class="c"># Initialize descriptor values...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	511 498 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	512 499
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	513 500 <span class="c"># Check availability of molecule...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	514 501 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	515 502 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	516 503 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	517 504 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	518 505
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	519 506 <span class="c"># Calculate descriptor values...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	521 508 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate MolecularComplexity values corresponding to assigned MolecularComplexity atom types..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	522 509 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	523 510 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	524 511
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	525 512 <span class="c"># Set final descriptor values...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	526 513 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	527 514
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	528 515 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	529 516 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	530 517
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	531 518 <span class="c"># Calculate molecular complexity value...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	532 519 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	533 <a name="_CalculateDescriptorValues-"></a> 520 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	534 521 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	535 522 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	536 523
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	537 524 <span class="c"># Setup fingerprints object and generate fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	538 525 <span class="i">$MethodName</span> = <span class="q">"_Setup"</span> . <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	539 526 <span class="i">$FingerprintsObject</span> = <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	540 527
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	541 528 <span class="i">$FingerprintsObject</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	542 529
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	543 530 <span class="c"># Make sure atom types fingerprints generation is successful...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	544 531 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsObject</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	545 532 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	546 533 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	547 534
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	548 535 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	549 536 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	550 537 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	551 538
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	552 539 <span class="c"># Normalize molecular complexity...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	553 540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	554 541 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_NormalizeMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	555 542 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	556 543 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	557 544 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	558 545
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	559 546 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	560 547 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	561 548
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	562 549 <span class="c"># Setup atom types fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	563 550 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	564 <a name="_SetupAtomTypesFingerprints-"></a> 551 <span class="k">sub </span><span class="m">_SetupAtomTypesFingerprints</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	565 552 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	566 553 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	567 554
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	568 555 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::AtomTypesFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'AtomTypesCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	569 556 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	570 557
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	571 558 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	572 559 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	573 560
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	574 561 <span class="c"># Setup extended connectivity fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	575 562 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	576 <a name="_SetupExtendedConnectivityFingerprints-"></a> 563 <span class="k">sub </span><span class="m">_SetupExtendedConnectivityFingerprints</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	577 564 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	578 565 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	579 566
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	580 567 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'ExtendedConnectivity'</span><span class="cm">,</span> <span class="q">'NeighborhoodRadius'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	581 568 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	582 569
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	583 570 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	584 571 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	585 572
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	586 573 <span class="c"># Setup MACCS keys...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	587 574 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	588 <a name="_SetupMACCSKeys-"></a> 575 <span class="k">sub </span><span class="m">_SetupMACCSKeys</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	589 576 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	590 577 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	591 578
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	592 579 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::MACCSKeys</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'MACCSKeyBits'</span><span class="cm">,</span> <span class="q">'Size'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	593 580
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	594 581 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	595 582 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	596 583
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	597 584 <span class="c"># Set up path length fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	598 585 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	599 <a name="_SetupPathLengthFingerprints-"></a> 586 <span class="k">sub </span><span class="m">_SetupPathLengthFingerprints</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	600 587 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	601 588 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	602 589
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	603 590 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::PathLengthFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'PathLengthCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'MinLength'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinPathLength</span>}<span class="cm">,</span> <span class="q">'MaxLength'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxPathLength</span>}<span class="cm">,</span> <span class="q">'AllowRings'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'AllowSharedBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'UseBondSymbols'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="cm">,</span> <span class="q">'UseUniquePaths'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	604 591 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	605 592
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	606 593 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	607 594 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	608 595
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	609 596 <span class="c"># Setup topological atom pairs fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	610 597 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	611 <a name="_SetupTopologicalAtomPairsFingerprints-"></a> 598 <span class="k">sub </span><span class="m">_SetupTopologicalAtomPairsFingerprints</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	612 599 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	613 600 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	614 601
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	615 602 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	616 603 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	617 604
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	618 605 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	619 606 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	620 607
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	621 608 <span class="c"># Setup topological atom triplets fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	622 609 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	623 <a name="_SetupTopologicalAtomTripletsFingerprints-"></a> 610 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTripletsFingerprints</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	624 611 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	625 612 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	626 613
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	627 614 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	628 615 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	629 616
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	630 617 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	631 618 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	632 619
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	633 620 <span class="c"># Setup topological atom torsions fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	634 621 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	635 <a name="_SetupTopologicalAtomTorsionsFingerprints-"></a> 622 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTorsionsFingerprints</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	636 623 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	637 624 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	638 625
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	639 626 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	640 627
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	641 628 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	642 629
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	643 630 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	644 631 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	645 632
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	646 633 <span class="c"># Setup TopologicalPharmacophoreAtomPairsFingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	647 634 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	648 <a name="_SetupTopologicalPharmacophoreAtomPairsFingerprints-"></a> 635 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	649 636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	650 637 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$AtomPairsSetSizeToUse</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	651 638
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	652 639 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	653 640 <span class="i">$AtomPairsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	654 641
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	655 642 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomPairsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$AtomPairsSetSizeToUse</span><span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">'NormalizationMethodology'</span> <span class="cm">=></span> <span class="q">'None'</span><span class="cm">,</span> <span class="q">'ValuesPrecision'</span> <span class="cm">=></span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	656 643
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	657 644 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	658 645 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	659 646
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	660 647 <span class="c"># Setup TopologicalPharmacophoreAtomTripletsFingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	661 648 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	662 <a name="_SetupTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 649 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	663 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	664 651 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	665 652
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	666 653 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	667 654 <span class="i">$AtomTripletsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	668 655
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	669 656 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomTripletsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'DistanceBinSize'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	670 657
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	671 658 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	672 659 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	673 660
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	674 661 <span class="c"># Normalize molecular complexity value...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	675 662 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	676 <a name="_NormalizeMolecularComplexity-"></a> 663 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexity</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	677 664 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	678 665
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	679 666 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span> && <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByHeavyAtomsCount$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	680 667 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByHeavyAtomsCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	681 668 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	682 669 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints\|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span> && <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	683 670 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByPossibleKeysCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	684 671 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	685 672 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	686 673 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_NormalizeMolecularComplexity: NormalizationMethodology value, $This->{NormalizationMethodology}, is not valid. Supported values: ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	687 674 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	688 675 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	689 676 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	690 677
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	691 678 <span class="c"># Normalize molecular complexity value by heavy atom count...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	692 679 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	693 <a name="_NormalizeMolecularComplexityByHeavyAtomsCount-"></a> 680 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByHeavyAtomsCount</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	694 681 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	695 682 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfHeavyAtoms</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	696 683
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	697 684 <span class="i">$NumOfHeavyAtoms</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetNumOfHeavyAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	698 685 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfHeavyAtoms</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	699 686 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	700 687 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	701 688
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	702 689 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfHeavyAtoms</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	703 690 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$NormalizedComplexity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	704 691
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	705 692 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	706 693 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	707 694
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	708 695 <span class="c"># Normalize molecular complexity value by possible keys count...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	709 696 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	710 <a name="_NormalizeMolecularComplexityByPossibleKeysCount-"></a> 697 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByPossibleKeysCount</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	711 698 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	712 699 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfPossibleKeys</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	713 700
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	714 701 <span class="i">$NumOfPossibleKeys</span> = <span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	715 702 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfPossibleKeys</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	716 703 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	717 704 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	718 705
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	719 706 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfPossibleKeys</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	720 707 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$NormalizedComplexity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	721 708
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	722 709 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	723 710 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	724 711
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	725 712 <span class="c"># Calculate molecular complexity value using fingerprints objects...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	726 713 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	727 <a name="_CalculateMolecularComplexity-"></a> 714 <span class="k">sub </span><span class="m">_CalculateMolecularComplexity</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	728 715 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	729 716
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	730 717 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	731 718 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsBitVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	732 719 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	733 720 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsVector$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	734 721 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	735 722 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	736 723 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	737 724 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_CalculateMolecularComplexity: Fingerprints vector type is not valid. Supported values: FingerprintsBitVector or FingerprintsVector..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	738 725 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	739 726
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	740 727 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	741 728 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	742 729
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	743 730 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	744 731 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	745 <a name="_CalculateMolecularComplexityUsingFingerprintsVector-"></a> 732 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsVector</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	746 733 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	747 734
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	748 735 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="s">(</span><span class="i">$FingerprintsVector</span><span class="i">->GetType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^(OrderedNumericalValues\|NumericalValues)$/i</span><span class="s">)</span> ? <span class="i">$FingerprintsVector</span><span class="i">->GetNumOfNonZeroValues</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="i">$FingerprintsVector</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	749 736
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	750 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	751 738 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	752 739
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	753 740 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	754 741 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	755 <a name="_CalculateMolecularComplexityUsingFingerprintsBitVector-"></a> 742 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsBitVector</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	756 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	757 744
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	758 745 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">$FingerprintsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	759 746
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	760 747 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	761 748 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	762 749
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	763 750 <span class="c"># Setup final descriptor values...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	764 751 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	765 <a name="_SetFinalDescriptorValues-"></a> 752 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	766 753 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	767 754
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	768 755 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	769 756
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	770 757 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexity</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	771 758
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	772 759 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	773 760 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	774 761
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	775 762 <span class="c"># Set atom identifier type to use for generating fingerprints...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	776 763 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	777 <a name="_SetAtomIdentifierTypeValuesToUse-"></a> 764 <span class="k">sub </span><span class="m">_SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	778 765 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	779 766
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	780 767 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	781 768 <span class="i">$FingerprintsObject</span><span class="i">->SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	782 769 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	783 770 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	784 771 <span class="i">$FingerprintsObject</span><span class="i">->SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	785 772 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	786 773 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes\|EStateAtomTypes\|MMFF94AtomTypes\|SLogPAtomTypes\|SYBYLAtomTypes\|TPSAAtomTypes\|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	787 774 <span class="c"># Nothing to do for now...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	788 775 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	789 776 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	790 777 <span class="w">croak</span> <span class="q">"Error: The value specified, $This->{AtomIdentifierType}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	791 778 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	792 779 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	793 780
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	794 781 <span class="c"># Initialize atom indentifier type information...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	795 782 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	796 783 <span class="c"># Current supported values:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	797 784 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	798 785 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	799 786 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	800 787 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	801 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 788 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	802 789 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	803 790
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	804 791 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	805 792 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	806 793 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	807 794 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	808 795 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	809 796 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	810 797 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	811 798 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	812 799 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	813 800 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes\|EStateAtomTypes\|MMFF94AtomTypes\|SLogPAtomTypes\|SYBYLAtomTypes\|TPSAAtomTypes\|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	814 801 <span class="c"># Nothing to do for now...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	815 802 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	816 803 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	817 804 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	818 805 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	819 806 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	820 807 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	821 808
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	822 809 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	823 810 <span class="c"># class, to use for generating initial atom identifiers...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	824 811 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	825 812 <span class="c"># Let:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	826 813 <span class="c"># AS = Atom symbol corresponding to element symbol</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	827 814 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	828 815 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	829 816 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	830 817 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	831 818 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	832 819 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	833 820 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	834 821 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	835 822 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	836 823 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	837 824 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	838 825 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	839 826 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	840 827 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	841 828 <span class="c"># Then:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	842 829 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	843 830 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	844 831 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	845 832 <span class="c"># AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	846 833 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	847 834 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	848 835 <span class="c"># optional.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	849 836 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	850 837 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	851 838 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	852 839 <span class="c"># AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n></span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	853 840 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	854 841 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	855 842 <span class="c"># are also allowed:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	856 843 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	857 844 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	858 845 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	859 846 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	860 847 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	861 848 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	862 849 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	863 850 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	864 851 <span class="c"># Ar : Aromatic</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	865 852 <span class="c"># RA : RingAtom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	866 853 <span class="c"># FC : FormalCharge</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	867 854 <span class="c"># MN : MassNumber</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	868 855 <span class="c"># SM : SpinMultiplicity</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	869 856 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	870 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 857 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	871 858 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	872 859
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	873 860 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	874 861
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	875 862 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints\|TopologicalAtomPairsFingerprints\|TopologicalAtomTripletsFingerprints\|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	876 863 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	877 864 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	878 865 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	879 866 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="cm">,</span> <span class="q">'MN'</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	880 867 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	881 868 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	882 869 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	883 870 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	884 871
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	885 872 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	886 873 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	887 874
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	888 875 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	889 876 <span class="c"># class, to use for generating initial atom identifiers...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	890 877 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	891 878 <span class="c"># Let:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	892 879 <span class="c"># HBD: HydrogenBondDonor</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	893 880 <span class="c"># HBA: HydrogenBondAcceptor</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	894 881 <span class="c"># PI : PositivelyIonizable</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	895 882 <span class="c"># NI : NegativelyIonizable</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	896 883 <span class="c"># Ar : Aromatic</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	897 884 <span class="c"># Hal : Halogen</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	898 885 <span class="c"># H : Hydrophobic</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	899 886 <span class="c"># RA : RingAtom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	900 887 <span class="c"># CA : ChainAtom</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	901 888 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	902 889 <span class="c"># Then:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	903 890 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	904 891 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	905 892 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	906 893 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	907 894 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	908 895 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	909 896 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	910 897 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	911 898 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	912 899 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	913 900 <span class="c"># HydrogenBondAcceptor: N[!H], O</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	914 901 <span class="c"># PositivelyIonizable: +, NH2</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	915 902 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	916 903 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	917 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 904 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	918 905 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	919 906
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	920 907 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	921 908
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	922 909 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints\|ExtendedConnectivityFingerprints\|PathLengthFingerprints\|TopologicalAtomPairsFingerprints\|TopologicalAtomTripletsFingerprints\|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	923 910 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	924 911 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	925 912 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	926 913 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	927 914 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	928 915 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	929 916 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	930 917 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	931 918
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	932 919 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	933 920 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	934 921
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	935 922 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	936 923 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	937 <a name="SetAtomicInvariantsToUse-"></a> 924 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	938 925 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	939 926 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$SpecifiedAtomicInvariant</span><span class="cm">,</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	940 927
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	941 928 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	942 929 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	943 930 <span class="k">return</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	944 931 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	945 932
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	946 933 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	947 934 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	948 935 <span class="k">return</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	949 936 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	950 937
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	951 938 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	952 939 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	953 940
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	954 941 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	955 942 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	956 943
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	957 944 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	958 945 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	959 946 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	960 947 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	961 948 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	962 949 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	963 950
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	964 951 <span class="c"># Make sure specified AtomicInvariants are valid...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	965 952 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	966 953 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	967 954 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	968 955 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	969 956 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	970 957 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	971 958 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	972 959
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	973 960 <span class="c"># Set atomic invariants to use...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	974 961 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	975 962 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	976 963
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	977 964 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	978 965 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	979 966
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	980 967 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	981 968 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	982 <a name="SetFunctionalClassesToUse-"></a> 969 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	983 970 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	984 971 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="cm">,</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	985 972
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	986 973 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	987 974 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	988 975 <span class="k">return</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	989 976 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	990 977
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	991 978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	992 979 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	993 980 <span class="k">return</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	994 981 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	995 982
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	996 983 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	997 984 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	998 985
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	999 986 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1000 987 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1001 988
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1002 989 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1003 990 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1004 991 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1005 992 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1006 993 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1007 994 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1008 995
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1009 996 <span class="c"># Make sure specified FunctionalClasses are valid...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1010 997 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1011 998 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedFunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1012 999 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1013 1000 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1014 1001 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1015 1002 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1016 1003
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1017 1004 <span class="c"># Set functional classes to use...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1018 1005 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1019 1006 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1020 1007
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1021 1008 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1022 1009 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1023 1010
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1024 1011 <span class="c"># Return a string containg data for MolecularComplexityDescriptors object...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1025 1012 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1026 <a name="StringifyMolecularComplexityDescriptors-"></a>1013 <span class="k">sub </span><span class="m">StringifyMolecularComplexityDescriptors</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1027 1014 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1028 1015 <span class="k">my</span><span class="s">(</span><span class="i">$ComplexityDescriptorsString</span><span class="cm">,</span> <span class="i">$Nothing</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1029 1016
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1030 1017 <span class="i">$ComplexityDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; MolecularComplexityType: $This->{MolecularComplexityType}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1031 1018
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1032 1019 <span class="c"># Setup fingerprints specific information...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1033 1020 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1034 1021 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MACCSKeysSize = $This->{MACCSKeysSize}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1035 1022 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1036 1023 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1037 1024 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; NeighborhoodRadius = $This->{NeighborhoodRadius}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1038 1025 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1039 1026 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1040 1027 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinPathLength = $This->{MinPathLength}; MaxPathLength = $This->{MaxPathLength}; UseBondSymbols: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1041 1028 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1042 1029 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1043 1030 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1044 1031 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1045 1032 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1046 1033 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1047 1034 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1048 1035 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTorsionsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1049 1036 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1050 1037 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1051 1038 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1052 1039 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1053 1040 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1054 1041 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1055 1042 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}; DistanceBinSize: $This->{DistanceBinSize}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1056 1043 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1057 1044
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1058 1045 <span class="c"># Setup atom identifier information...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1059 1046 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints\|ExtendedConnectivityFingerprints\|PathLengthFingerprints\|TopologicalAtomPairsFingerprints\|TopologicalAtomTripletsFingerprints\|TopologicalAtomTorsionsFingerprints\|TopologicalPharmacophoreAtomPairsFingerprints\|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1060 1047 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomIdentifierType = $This->{AtomIdentifierType}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1061 1048
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1062 1049 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1063 1050 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomicInvariants</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1064 1051
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1065 1052 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1066 1053 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1067 1054
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1068 1055 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1069 1056 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1070 1057 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1071 1058
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1072 1059 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1073 1060 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1074 1061 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AvailableAtomicInvariants: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1075 1062 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1076 1063 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1077 1064 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1078 1065
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1079 1066 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1080 1067 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1081 1068
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1082 1069 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1083 1070 <span class="k">push</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">"$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1084 1071 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1085 1072
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1086 1073 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1087 1074 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1088 1075 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AvailableFunctionalClasses: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1089 1076 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1090 1077 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1091 1078 <span class="k">return</span> <span class="i">$ComplexityDescriptorsString</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1092 1079 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1093 1080
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1094 1081 <span class="c"># Is it a MolecularComplexityDescriptors object?</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1095 <a name="_IsMolecularComplexityDescriptors-"></a>1082 <span class="k">sub </span><span class="m">_IsMolecularComplexityDescriptors</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1096 1083 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1097 1084
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1098 1085 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1099 1086 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1100 1087
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1101 <a name="EOF-"></a></pre>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1102 <p> </p>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1103 <br />
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1104 <center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1105 <img src="../../../images/h2o2.png">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1106 </center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1107 </body>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1108 </html>

Mercurial > repos > deepakjadmin > mayatool3_test2

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