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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./CyclesDetection.html" title="CyclesDetection.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/TopologicalPharmacophoreAtomTripletsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>TopologicalPharmacophoreAtomTripletsFingerprints</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints;</p>
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26 <p>use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints qw(:all);</p>
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27 <p>
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28 </p>
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29 <h2>DESCRIPTION</h2>
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30 <p><strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong> [ Ref 66, Ref 68-71 ] class provides
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31 the following methods:</p>
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32 <p>new, GenerateFingerprints, , GetDescription, GetAtomTripletIDs,
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33 SetAtomTypesToUse, SetDistanceBinSize, SetMaxDistance, SetMinDistance,
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34 StringifyTopologicalPharmacophoreAtomTripletsFingerprints</p>
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35 <p><strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong> is derived from <strong>Fingerprints</strong> class
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36 which in turn is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly
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37 defined in <strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong>
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38 classes using Perl's AUTOLOAD functionality. These methods are generated on-the-fly for a specified
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39 object property:</p>
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40 <div class="OptionsBox">
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41 Set<PropertyName>(<PropertyValue>);
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42 <br/> $PropertyValue = Get<PropertyName>();
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43 <br/> Delete<PropertyName>();</div>
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44 <p>Based on the values specified for <strong>AtomTypesToUse</strong>, pharmacophore atom types are
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45 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
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46 Using <strong>MinDistance</strong>, <strong>MaxDistance</strong>, and <strong>DistanceBinSize</strong> values, a
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47 binned distance matrix is generated with lower bound on the distance bin as the distance
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48 in distance matrix; the lower bound on the distance bin is also used as the distance between
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49 atom pairs for generation of atom triplet identifiers.</p>
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50 <p>A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting
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51 atom pairs binned distances between <strong>--MinDistance</strong> and <strong>--MaxDistance</strong>. The value
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52 of <strong>--UseTriangleInequality</strong> determines whether the triangle inequality test is applied during
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53 generation of atom triplets basis set. The lower distance bound, along with specified pharmacophore
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54 types, is used during generation of atom triplet IDs.</p>
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55 <div class="OptionsBox">
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56 Let:</div>
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57 <div class="OptionsBox">
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58 P = Valid pharmacophore atom type</div>
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59 <div class="OptionsBox">
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60 Px = Pharmacophore atom x
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61 <br/> Py = Pharmacophore atom y
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62 <br/> Pz = Pharmacophore atom z</div>
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63 <div class="OptionsBox">
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64 Dmin = Minimum distance corresponding to number of bonds between two atoms
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65 <br/> Dmax = Maximum distance corresponding to number of bonds between two atoms
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66 <br/> D = Distance corresponding to number of bonds between two atom</div>
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67 <div class="OptionsBox">
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68 Bsize = Distance bin size
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69 <br/> Nbins = Number of distance bins</div>
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70 <div class="OptionsBox">
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71 Dxy = Distance or lower bound of binned distance between Px and Py
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72 <br/> Dxz = Distance or lower bound of binned distance between Px and Pz
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73 <br/> Dyz = Distance or lower bound of binned distance between Py and Pz</div>
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74 <div class="OptionsBox">
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75 Then:</div>
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76 <div class="OptionsBox">
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77 PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet IDs for atom types Px,
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78 Py, and Pz</div>
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79 <div class="OptionsBox">
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80 For example: H1-H1-H1, H2-HBA-H2 and so on.</div>
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81 <div class="OptionsBox">
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82 For default values of Dmin = 1 , Dmax = 10 and Bsize = 2, the number of
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83 <br/> distance bins, Nbins = 5, are:</div>
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84 <div class="OptionsBox">
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85 [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</div>
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86 <div class="OptionsBox">
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87 and atom triplet basis set size is 2692.</div>
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88 <div class="OptionsBox">
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89 Atom triplet basis set size for various values of Dmin, Dmax and Bsize in
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90 <br/> conjunction with usage of triangle inequality is:</div>
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91 <div class="OptionsBox">
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92 Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize
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93 <br/> 1 10 2 No 4960
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94 <br/> 1 10 2 Yes 2692 [ Default ]
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95 <br/> 2 12 2 No 8436
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96 <br/> 2 12 2 Yes 4494</div>
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97 <p>Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore
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98 atom triplets is counted.</p>
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99 <p>The final pharmacophore atom triples count along with atom pair identifiers involving all non-hydrogen
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100 atoms constitute pharmacophore topological atom triplets fingerprints of the molecule.</p>
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101 <p>For <em>ArbitrarySize</em> value of <strong>AtomTripletsSetSizeToUse</strong>, the fingerprint vector correspond to
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102 only those topological pharmacophore atom triplets which are present and have non-zero count. However,
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103 for <em>FixedSize</em> value of <strong>AtomTripletsSetSizeToUse</strong>, the fingerprint vector contains all possible
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104 valid topological pharmacophore atom triplets with both zero and non-zero count values.</p>
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105 <p>The current release of MayaChemTools generates the following types of topological pharmacophore
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106 atom triplets fingerprints vector strings:</p>
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107 <div class="OptionsBox">
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108 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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109 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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110 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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111 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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112 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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113 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
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114 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
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115 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
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116 <div class="OptionsBox">
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117 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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118 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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119 <br/> 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
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120 <br/> 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
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121 <br/> 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
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122 <br/> 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...</div>
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123 <div class="OptionsBox">
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124 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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125 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString;
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126 <br/> Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-Ar1-NI1 Ar1-Ar1-P
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127 <br/> I1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1-H1-HBD1 Ar1-H1-NI1 Ar1-H1-PI1 Ar1-HBA1-HB
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128 <br/> A1 Ar1-HBA1-HBD1 Ar1-HBA1-NI1 Ar1-HBA1-PI1 Ar1-HBD1-HBD1 Ar1-HBD1-...;
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129 <br/> 46 106 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1
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130 <br/> 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145
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131 <br/> 132 26 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 ...</div>
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132 <p>
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133 </p>
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134 <h2>METHODS</h2>
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135 <dl>
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136 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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137 <dd>
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138 <div class="OptionsBox">
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139 $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
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140 %NamesAndValues);</div>
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141 <p>Using specified <em>TopologicalPharmacophoreAtomTripletsFingerprints</em> property names and values hash, <strong>new</strong>
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142 method creates a new object and returns a reference to newly created <strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong>
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143 object. By default, the following properties are initialized:</p>
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144 <div class="OptionsBox">
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145 Molecule = ''
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146 <br/> Type = 'TopologicalPharmacophoreAtomTriplets'
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147 <br/> MinDistance = 1
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148 <br/> MaxDistance = 10
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149 <br/> DistanceBinSize = 2
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150 <br/> UseTriangleInequality = 1
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151 <br/> AtomTypesToUse = ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar']</div>
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152 <p>Examples:</p>
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153 <div class="OptionsBox">
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154 $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
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155 'Molecule' => $Molecule);</div>
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156 <div class="OptionsBox">
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157 $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
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158 'Molecule' => $Molecule,
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159 'AtomTripletsSetSizeToUse' => 'ArbitrarySize';
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160 'MinDistance' => 1,
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161 'MaxDistance' => 10,
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162 'DistanceBinSize' => 2,
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163 'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar'],
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164 'UseTriangleInequality' => 1);</div>
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165 <div class="OptionsBox">
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166 $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
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167 'Molecule' => $Molecule,
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168 'AtomTripletsSetSizeToUse' => 'FixedSize';
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169 'MinDistance' => 1,
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170 'MaxDistance' => 10,
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171 'DistanceBinSize' => 2,
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172 'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar'],
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173 'UseTriangleInequality' => 1);</div>
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174 <div class="OptionsBox">
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175 $TPATFP->GenerateFingerprints();
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176 <br/> print "$TPATFP\n";</div>
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177 </dd>
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178 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
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179 <dd>
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180 <div class="OptionsBox">
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181 $Description = $TopologicalPharmacophoreAtomTripletsFP->GetDescription();</div>
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182 <p>Returns a string containing description of topological pharmacophore atom triplets fingerprints.</p>
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183 </dd>
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184 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
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185 <dd>
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186 <div class="OptionsBox">
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187 $TopologicalPharmacophoreAtomTripletsFP->GenerateFingerprints();</div>
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188 <p>Generates topological pharmacophore atom triplets fingerprints and returns
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189 <em>TopologicalPharmacophoreAtomTripletsFP</em>.</p>
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190 </dd>
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191 <dt><strong><a name="getatomtripletids" class="item"><strong>GetAtomTripletIDs</strong></a></strong></dt>
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192 <dd>
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193 <div class="OptionsBox">
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194 $AtomTripletsIDsRef = $TopologicalPharmacophoreATFP->GetAtomTripletIDs();
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195 <br/> @AtomTripletIDs = $TopologicalPharmacophoreATFP->GetAtomTripletIDs();</div>
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196 <p>Returns atom triplet IDs corresponding to atom pairs count values in topological pharmacophore
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197 atom triplet fingerprints vector as an array or reference to an array.</p>
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198 </dd>
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199 <dt><strong><a name="atomtripletssetsizetouse" class="item"><strong>AtomTripletsSetSizeToUse</strong></a></strong></dt>
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200 <dd>
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201 <div class="OptionsBox">
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202 $TPAFP->AtomTripletsSetSizeToUse($Values);</div>
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203 <p>Sets pharmacophore atom triplets set size to use for topological pharmacophore fingerprints
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204 generation and returns <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.</p>
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205 <p>Possible values for pharmacophore atom triplets set size are: <em>ArbitrarySize, FizedSize</em>.
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206 Default value: <em>ArbitrarySize</em>.</p>
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207 <p>For <em>ArbitrarySize</em> value of <strong>AtomTripletsSetSizeToUse</strong>, the fingerprint vector correspond to
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208 only those topological pharmacophore atom triplets which are present and have non-zero count. However,
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209 for <em>FixedSize</em> value of <strong>AtomTripletsSetSizeToUse</strong>, the fingerprint vector contains all possible
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210 valid topological pharmacophore atom triplets with both zero and non-zero count values.</p>
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211 </dd>
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212 <dt><strong><a name="setatomtypestouse" class="item"><strong>SetAtomTypesToUse</strong></a></strong></dt>
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213 <dd>
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214 <div class="OptionsBox">
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215 $TopologicalPharmacophoreAtomTripletsFP->SetAtomTypesToUse($ValuesRef);
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216 <br/> $TopologicalPharmacophoreAtomTripletsFP->SetAtomTypesToUse(@Values);</div>
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217 <p>Sets pharmacophore atom types to use for topological pharmacophore fingerprints
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218 generation and returns <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.</p>
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219 <p>Possible values for pharmacophore atom types are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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220 Default value [ Ref 71 ] : <em>HBD,HBA,PI,NI,H,Ar</em>.</p>
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221 <p>The pharmacophore atom types abbreviations correspond to:</p>
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222 <div class="OptionsBox">
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223 HBD: HydrogenBondDonor
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224 <br/> HBA: HydrogenBondAcceptor
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225 <br/> PI : PositivelyIonizable
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226 <br/> NI : NegativelyIonizable
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227 <br/> Ar : Aromatic
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228 <br/> Hal : Halogen
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229 <br/> H : Hydrophobic
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230 <br/> RA : RingAtom
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231 <br/> CA : ChainAtom</div>
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232 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign pharmacophore atom
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233 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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234 <div class="OptionsBox">
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235 HydrogenBondDonor: NH, NH2, OH
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236 <br/> HydrogenBondAcceptor: N[!H], O
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237 <br/> PositivelyIonizable: +, NH2
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238 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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239 </dd>
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240 <dt><strong><a name="setdistancebinsize" class="item"><strong>SetDistanceBinSize</strong></a></strong></dt>
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241 <dd>
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242 <div class="OptionsBox">
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243 $TopologicalPharmacophoreAtomTripletsFP->SetDistanceBinSize($Value);</div>
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244 <p>Sets distance bin size used to bin distances between atom pairs in atom triplets and returns
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245 <em>TopologicalPharmacophoreAtomTriplesFP</em>.</p>
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246 <p>For default <strong>MinDistance</strong> and <strong>MaxDistance</strong> values of 1 and 10 with <strong>DistanceBinSize</strong>
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247 of 2 [ Ref 70 ], the following 5 distance bins are generated:</p>
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248 <div class="OptionsBox">
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249 [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</div>
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250 <p>The lower distance bound on the distance bin is uses to bin the distance between atom pairs in
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251 atom triplets. So in the previous example, atom pairs with distances 1 and 2 fall in first distance
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252 bin, atom pairs with distances 3 and 4 fall in second distance bin and so on.</p>
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253 <p>In order to distribute distance bins of equal size, the last bin is allowed to go past <strong>MaxDistance</strong>
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254 by up to distance bin size. For example, <strong>MinDistance</strong> and <strong>MaxDistance</strong> values of 2 and 10
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255 with <strong>DistanceBinSize</strong> of 2 generates the following 6 distance bins:</p>
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256 <div class="OptionsBox">
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257 [2, 3] [4, 5] [6, 7] [8, 9] [10 11]</div>
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258 </dd>
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259 <dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt>
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260 <dd>
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261 <div class="OptionsBox">
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262 $TopologicalPharmacophoreAtomTriplesFP->SetMaxDistance($Value);</div>
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263 <p>Sets maximum bond distance between atom pairs corresponding to atom triplets for
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264 generating topological pharmacophore atom triplets fingerprints and returns
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265 <em>TopologicalPharmacophoreAtomTriplesFP</em>.</p>
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266 </dd>
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267 <dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt>
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268 <dd>
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269 <div class="OptionsBox">
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270 $TopologicalPharmacophoreAtomTriplesFP->SetMinDistance($Value);</div>
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271 <p>Sets minimum bond distance between atom pairs corresponding to atom triplets for
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272 generating topological pharmacophore atom triplets fingerprints and returns
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273 <em>TopologicalPharmacophoreAtomTriplesFP</em>.</p>
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274 </dd>
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275 <dt><strong><a name="stringifytopologicalpharmacophoreatomtripletsfingerprints" class="item"><strong>StringifyTopologicalPharmacophoreAtomTripletsFingerprints</strong></a></strong></dt>
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276 <dd>
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277 <div class="OptionsBox">
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278 $String = $TopologicalPharmacophoreAtomTripletsFingerprints->
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279 StringifyTopologicalPharmacophoreAtomTripletsFingerprints();</div>
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280 <p>Returns a string containing information about <em>TopologicalPharmacophoreAtomTripletsFingerprints</em> object.</p>
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281 </dd>
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282 </dl>
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283 <p>
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284 </p>
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285 <h2>AUTHOR</h2>
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286 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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287 <p>
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288 </p>
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289 <h2>SEE ALSO</h2>
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290 <p><a href="./Fingerprints.html">Fingerprints.pm</a>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>, 
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291 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>, 
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292 <a href="./MACCSKeys.html">MACCSKeys.pm</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, 
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293 <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, 
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294 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>
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295 </p>
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296 <p>
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297 </p>
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298 <h2>COPYRIGHT</h2>
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299 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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300 <p>This file is part of MayaChemTools.</p>
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301 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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302 the terms of the GNU Lesser General Public License as published by the Free
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303 Software Foundation; either version 3 of the License, or (at your option)
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304 any later version.</p>
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305 <p> </p><p> </p><div class="DocNav">
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306 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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307 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./CyclesDetection.html" title="CyclesDetection.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints.pm</strong></td></tr>
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308 </table>
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309 </div>
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310 <br />
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311 <center>
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312 <img src="../../images/h2o2.png">
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313 </center>
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314 </body>
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315 </html>
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