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3 <title>MayaChemTools:Documentation:Fingerprints::TopologicalAtomTripletsFingerprints.pm</title>
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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="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalAtomTripletsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomTripletsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalAtomTripletsFingerprints.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>TopologicalAtomTripletsFingerprints</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::TopologicalAtomTripletsFingerprints;</p>
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26 <p>use Fingerprints::TopologicalAtomTripletsFingerprints 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>TopologicalAtomTripletsFingerprints</strong> [ Ref 57, Ref 59, Ref 72 ] class provides the following methods:</p>
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31 <p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getatomtripletids">GetAtomTripletIDs</a>, <a href="#getdescription">GetDescription</a>
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32 , <a href="#setatomidentifiertype">SetAtomIdentifierType</a>, <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a>
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33 , <a href="#setmaxdistance">SetMaxDistance</a>, <a href="#setmindistance">SetMinDistance</a>, <a href="#stringifytopologicalatomtripletsfingerprints">StringifyTopologicalAtomTripletsFingerprints</a>
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34 </p><p><strong>TopologicalAtomTripletsFingerprints</strong> is derived from <strong>Fingerprints</strong> class which in turn
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35 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
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36 in <strong>TopologicalAtomTripletsFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes using Perl's
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37 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
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38 <div class="OptionsBox">
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39 Set<PropertyName>(<PropertyValue>);
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40 <br/> $PropertyValue = Get<PropertyName>();
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41 <br/> Delete<PropertyName>();</div>
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42 <p>The current release of MayaChemTools supports generation of <strong>TopologicalAtomTripletsFingerprints</strong>
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43 corresponding to following <strong>AtomtomIdentifierTypes</strong>:</p>
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44 <div class="OptionsBox">
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45 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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46 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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47 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
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48 <p>Based on the values specified for <strong>AtomIdentifierType</strong> along with other specified
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49 parameters such as <strong>AtomicInvariantsToUse</strong> and <strong>FunctionalClassesToUse</strong>, initial
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50 atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance
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51 matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom
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52 triplets within <strong>MinDistance</strong> and <strong>MaxDistance</strong> are identified and counted. An atom triplet
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53 identifier is generated for each unique atom triplet; the format of atom triplet identifier is:</p>
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54 <div class="OptionsBox">
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55 <ATx>-Dyz-<ATy>-Dxz-<ATz>-Dxy</div>
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56 <div class="OptionsBox">
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57 ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z
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58 <br/> Dxy: Distance between atom x and atom y
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59 <br/> Dxz: Distance between atom x and atom z
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60 <br/> Dyz: Distance between atom y and atom z</div>
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61 <div class="OptionsBox">
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62 where <AT1>-D23 <= <AT2>-D13 <= <AT3>-D12</div>
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63 <p>The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute
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64 topological atom triplets fingerprints of the molecule.</p>
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65 <p>The current release of MayaChemTools generates the following types of topological atom triplets
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66 fingerprints vector strings:</p>
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67 <div class="OptionsBox">
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68 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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69 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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70 <br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
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71 <br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
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72 <br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
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73 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
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74 <br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div>
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75 <div class="OptionsBox">
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76 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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77 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
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78 <br/> ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO
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79 <br/> 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X
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80 <br/> 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2
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81 <br/> -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...</div>
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82 <div class="OptionsBox">
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83 FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan
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84 <br/> ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D
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85 <br/> 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_
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86 <br/> 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_
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87 <br/> 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...;
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88 <br/> 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2
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89 <br/> 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...</div>
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90 <div class="OptionsBox">
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91 FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance
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92 <br/> 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D
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93 <br/> 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC
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94 <br/> H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1-
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95 <br/> aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...;
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96 <br/> 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2
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97 <br/> 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1
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98 <br/> 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...</div>
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99 <div class="OptionsBox">
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100 FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi
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101 <br/> nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1
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102 <br/> -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal
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103 <br/> -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar
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104 <br/> -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...;
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105 <br/> 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5
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106 <br/> 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3
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107 <br/> 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...</div>
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108 <div class="OptionsBox">
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109 FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance
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110 <br/> 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1-
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111 <br/> N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A
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112 <br/> -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B
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113 <br/> -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3-
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114 <br/> O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-...</div>
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115 <div class="OptionsBox">
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116 FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1
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117 <br/> :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11
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118 <br/> -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D
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119 <br/> 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C
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120 <br/> 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1
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121 <br/> -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS...</div>
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122 <div class="OptionsBox">
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123 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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124 <br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
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125 <br/> .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
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126 <br/> D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
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127 <br/> -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
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128 <br/> 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...</div>
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129 <div class="OptionsBox">
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130 FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1:
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131 <br/> MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non
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132 <br/> e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D
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133 <br/> 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5
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134 N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21-
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135 <br/> D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-...</div>
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136 <div class="OptionsBox">
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137 FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M
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138 <br/> axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3
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139 <br/> -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9
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140 <br/> C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1-
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141 <br/> C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5-
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142 <br/> C_3-D6 C_2-D1-C_3-D5-O_3-D4 C_2-D1-C_3-D6-C_3-D7 C_2-D1-C_3-D7-C_3-...</div>
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143 <p>
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144 </p>
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145 <h2>METHODS</h2>
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146 <dl>
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147 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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148 <dd>
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149 <div class="OptionsBox">
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150 $NewTopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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151 %NamesAndValues);</div>
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152 <p>Using specified <em>TopologicalAtomTripletsFingerprints</em> property names and values hash, <strong>new</strong>
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153 method creates a new object and returns a reference to newly created <strong>TopologicalAtomTripletsFingerprints</strong>
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154 object. By default, the following properties are initialized:</p>
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155 <div class="OptionsBox">
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156 Molecule = ''
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157 <br/> Type = 'TopologicalAtomTriplets'
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158 <br/> MinDistance = 1
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159 <br/> MaxDistance = 10
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160 <br/> UseTriangleInequality = 1
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161 <br/> AtomIdentifierType = ''
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162 <br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC']
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163 <br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div>
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164 <p>Examples:</p>
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165 <div class="OptionsBox">
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166 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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167 'Molecule' => $Molecule,
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168 'AtomIdentifierType' =>
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169 'AtomicInvariantsAtomTypes');</div>
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170 <div class="OptionsBox">
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171 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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172 'Molecule' => $Molecule,
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173 'MinDistance' => 1,
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174 'MaxDistance' => 10,
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175 'AtomIdentifierType' =>
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176 'AtomicInvariantsAtomTypes',
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177 'AtomicInvariantsToUse' =>
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178 ['AS', 'X', 'BO', 'H', 'FC'] );</div>
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179 <div class="OptionsBox">
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180 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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181 'Molecule' => $Molecule,
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182 'AtomIdentifierType' =>
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183 'DREIDINGAtomTypes');</div>
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184 <div class="OptionsBox">
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185 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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186 'Molecule' => $Molecule,
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187 'AtomIdentifierType' =>
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188 'MMFF94AtomTypes');</div>
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189 <div class="OptionsBox">
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190 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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191 'Molecule' => $Molecule,
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192 'AtomIdentifierType' =>
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193 'TPSAAtomTypes');</div>
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194 <div class="OptionsBox">
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195 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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196 'Molecule' => $Molecule,
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197 'MinDistance' => 1,
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198 'MaxDistance' => 10,
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199 'AtomIdentifierType' =>
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200 'FunctionalClassAtomTypes',
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201 'FunctionalClassesToUse' =>
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202 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']);</div>
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203 <div class="OptionsBox">
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204 $TopologicalAtomTripletsFingerprints->GenerateFingerprints();
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205 <br/> print "$TopologicalAtomTripletsFingerprints\n";</div>
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206 </dd>
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207 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
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208 <dd>
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209 <div class="OptionsBox">
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210 $Return = $TopologicalAtomTripletsFingerprints->GetDescription();</div>
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211 <p>Returns a string containing description of topological atom triplets fingerprints.</p>
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212 </dd>
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213 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
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214 <dd>
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215 <div class="OptionsBox">
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216 $TopologicalAtomTripletsFingerprints->GenerateFingerprints();</div>
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217 <p>Generates topological atom triplets fingerprints and returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
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218 </dd>
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219 <dt><strong><a name="getatomtripletids" class="item"><strong>GetAtomTripletIDs</strong></a></strong></dt>
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220 <dd>
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221 <div class="OptionsBox">
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222 $AtomTripletIDsRef = $TopologicalAtomTripletsFingerprints->GetAtomTripletIDs();
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223 <br/> @AtomTripletIDs = $TopologicalAtomTripletsFingerprints->GetAtomTripletIDs();</div>
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224 <p>Returns atom triplet IDs corresponding to atom triplets count values in topological atom triplets
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225 fingerprints vector as an array or reference to an array.</p>
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226 </dd>
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227 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
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228 <dd>
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229 <div class="OptionsBox">
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230 $TopologicalAtomTripletsFingerprints->SetAtomIdentifierType($IdentifierType);</div>
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231 <p>Sets atom <em>IdentifierType</em> to use during atom triplets fingerprints generation and
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232 returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
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233 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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234 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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235 TPSAAtomTypes, UFFAtomTypes</em>.</p>
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236 </dd>
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237 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
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238 <dd>
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239 <div class="OptionsBox">
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240 $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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241 <br/> $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse(@Values);</div>
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242 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
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243 for topological atom triplets fingerprints generation and returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
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244 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
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245 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
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246 <p>The atomic invariants abbreviations correspond to:</p>
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247 <div class="OptionsBox">
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248 AS = Atom symbol corresponding to element symbol</div>
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249 <div class="OptionsBox">
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250 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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251 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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252 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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253 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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254 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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255 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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256 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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257 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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258 <br/> RA = Ring atom annotation indicating whether atom is a ring
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259 <br/> FC<+n/-n> = Formal charge assigned to atom
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260 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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261 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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262 3 (triplet)</div>
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263 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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264 <div class="OptionsBox">
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265 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></div>
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266 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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267 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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268 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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269 are also allowed:</p>
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270 <div class="OptionsBox">
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271 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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272 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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273 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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274 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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275 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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276 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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277 <br/> H : NumOfImplicitAndExplicitHydrogens
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278 <br/> Ar : Aromatic
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279 <br/> RA : RingAtom
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280 <br/> FC : FormalCharge
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281 <br/> MN : MassNumber
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282 <br/> SM : SpinMultiplicity</div>
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283 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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284 atom types.</p>
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285 </dd>
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286 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
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287 <dd>
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288 <div class="OptionsBox">
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289 $TopologicalTripletsFingerprints->SetFunctionalClassesToUse($ValuesRef);
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290 <br/> $TopologicalTripletsFingerprints->SetFunctionalClassesToUse(@Values);</div>
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291 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
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292 for topological atom triplets fingerprints generation and returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
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293 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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294 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
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295 <p>The functional class abbreviations correspond to:</p>
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296 <div class="OptionsBox">
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297 HBD: HydrogenBondDonor
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298 <br/> HBA: HydrogenBondAcceptor
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299 <br/> PI : PositivelyIonizable
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300 <br/> NI : NegativelyIonizable
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301 <br/> Ar : Aromatic
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302 <br/> Hal : Halogen
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303 <br/> H : Hydrophobic
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304 <br/> RA : RingAtom
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305 <br/> CA : ChainAtom</div>
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306 <div class="OptionsBox">
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307 Functional class atom type specification for an atom corresponds to:</div>
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308 <div class="OptionsBox">
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309 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
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310 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
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311 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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312 <div class="OptionsBox">
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313 HydrogenBondDonor: NH, NH2, OH
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314 <br/> HydrogenBondAcceptor: N[!H], O
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315 <br/> PositivelyIonizable: +, NH2
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316 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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317 </dd>
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318 <dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt>
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319 <dd>
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320 <div class="OptionsBox">
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321 $TopologicalAtomTripletsFingerprints->SetMaxDistance($Distance);</div>
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322 <p>Sets maximum distance to use during topological atom triplets fingerprints generation and
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323 returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
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324 </dd>
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325 <dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt>
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326 <dd>
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327 <div class="OptionsBox">
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328 $TopologicalAtomTripletsFingerprints->SetMinDistance($Distance);</div>
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329 <p>Sets minimum distance to use during topological atom triplets fingerprints generation and
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330 returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
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331 </dd>
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332 <dt><strong><a name="stringifytopologicalatomtripletsfingerprints" class="item"><strong>StringifyTopologicalAtomTripletsFingerprints</strong></a></strong></dt>
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333 <dd>
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334 <div class="OptionsBox">
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335 $String = $TopologicalAtomTripletsFingerprints->
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336 StringifyTopologicalAtomTripletsFingerprints();</div>
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337 <p>Returns a string containing information about <em>TopologicalAtomTripletsFingerprints</em> object.</p>
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338 </dd>
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339 </dl>
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340 <p>
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341 </p>
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342 <h2>AUTHOR</h2>
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343 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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344 <p>
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345 </p>
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346 <h2>SEE ALSO</h2>
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347 <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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348 <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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349 <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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350 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>, 
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351 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
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352 </p>
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353 <p>
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354 </p>
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355 <h2>COPYRIGHT</h2>
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356 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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357 <p>This file is part of MayaChemTools.</p>
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358 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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359 the terms of the GNU Lesser General Public License as published by the Free
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360 Software Foundation; either version 3 of the License, or (at your option)
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361 any later version.</p>
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362 <p> </p><p> </p><div class="DocNav">
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363 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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364 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalAtomTripletsFingerprints.pm</strong></td></tr>
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365 </table>
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366 </div>
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367 <br />
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368 <center>
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369 <img src="../../images/h2o2.png">
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370 </center>
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371 </body>
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372 </html>
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