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3 <title>MayaChemTools:Documentation:Fingerprints::TopologicalAtomPairsFingerprints.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="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalAtomPairsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomPairsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalAtomPairsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalAtomPairsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalAtomPairsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalAtomPairsFingerprints.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>TopologicalAtomPairsFingerprints</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::TopologicalAtomPairsFingerprints;</p>
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26 <p>use Fingerprints::TopologicalAtomPairsFingerprints 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>TopologicalAtomPairsFingerprints</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="#getatompairids">GetAtomPairIDs</a>, <a href="#getdescription">GetDescription</a>, <a href="#setatomidentifiertype">SetAtomIdentifierType</a>
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32 , <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a>, <a href="#setmaxdistance">SetMaxDistance</a>
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33 , <a href="#setmindistance">SetMinDistance</a>, <a href="#stringifytopologicalatompairsfingerprints">StringifyTopologicalAtomPairsFingerprints</a>
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34 </p><p><strong>TopologicalAtomPairsFingerprints</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>TopologicalAtomPairsFingerprints</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>AtomTypesFingerpritns</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 pairs within <strong>MinDistance</strong> and <strong>MaxDistance</strong> are identified and counted. An atom pair
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53 identifier is generated for each unique atom pair; the format of atom pair identifier is:</p>
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54 <div class="OptionsBox">
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55 <AtomType1>-D<n>-<AtomType2></div>
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56 <div class="OptionsBox">
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57 AtomType1, AtomType2: Atom types assigned to atom1 and atom2
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58 <br/> D: Distance between atom1 and atom2</div>
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59 <div class="OptionsBox">
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60 where AtomType1 <= AtomType2</div>
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61 <p>The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute
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62 topological atom pairs fingerprints of the molecule.</p>
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63 <p>The current release of MayaChemTools generates the following types of topological atom pairs
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64 fingerprints vector strings:</p>
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65 <div class="OptionsBox">
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66 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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67 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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68 <br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
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69 <br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
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70 <br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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71 <br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...</div>
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72 <div class="OptionsBox">
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73 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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74 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
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75 <br/> 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
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76 <br/> C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2
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77 <br/> .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
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78 <br/> 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...</div>
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79 <div class="OptionsBox">
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80 FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
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81 <br/> :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D
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82 <br/> 1-C_R C_2-D1-N_3 C_2-D1-O_2 C_2-D1-O_3 C_3-D1-C_3 C_3-D1-C_R C_3-D1-N_
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83 <br/> R C_3-D1-O_3 C_R-D1-C_R C_R-D1-F_ C_R-D1-N_3 C_R-D1-N_R C_2-D2-C_3 C_2
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84 <br/> 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
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85 <br/> 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...</div>
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86 <div class="OptionsBox">
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87 FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
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88 <br/> axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH-
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89 <br/> D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH
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90 <br/> aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...;
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91 <br/> 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
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92 <br/> 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...</div>
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93 <div class="OptionsBox">
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94 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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95 <br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
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96 <br/> Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
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97 <br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
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98 <br/> 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
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99 <br/> 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...</div>
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100 <div class="OptionsBox">
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101 FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
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102 <br/> axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2
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103 <br/> C5A-D1-CB 1 C5A-D1-CR 1 C5A-D1-N5 2 C5B-D1-C5B 1 C5B-D1-C=ON 1 C5B-D1-
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104 <br/> CB 1 C=ON-D1-NC=O 1 C=ON-D1-O=CN 1 CB-D1-CB 18 CB-D1-F 1 CB-D1-NC=O 1
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105 <br/> COO-D1-CR 1 COO-D1-O=CO 1 COO-D1-OC=O 1 CR-D1-CR 7 CR-D1-N5 1 CR-D1-OR
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106 <br/> 2 C5A-D2-C5A 1 C5A-D2-C5B 2 C5A-D2-C=ON 1 C5A-D2-CB 3 C5A-D2-CR 4 ...</div>
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107 <div class="OptionsBox">
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108 FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
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109 <br/> xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1
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110 <br/> -D1-C11 2 C1-D1-C5 1 C1-D1-CS 4 C10-D1-N11 1 C11-D1-C21 1 C14-D1-C18 2
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111 <br/> C14-D1-F 1 C18-D1-C18 10 C18-D1-C20 4 C18-D1-C22 2 C20-D1-C20 3 C20-D
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112 <br/> 1-C21 1 C20-D1-N11 1 C21-D1-C21 1 C21-D1-C5 1 C21-D1-N11 1 C22-D1-N4 1
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113 <br/> C5-D1-N4 1 C5-D1-O10 1 C5-D1-O2 1 C5-D1-O9 1 CS-D1-O2 2 C1-D2-C1 3...</div>
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114 <div class="OptionsBox">
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115 FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
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116 <br/> xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C
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117 <br/> .2-D1-C.ar 1 C.2-D1-N.am 1 C.2-D1-O.2 1 C.2-D1-O.co2 2 C.3-D1-C.3 7 C.
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118 <br/> 3-D1-C.ar 1 C.3-D1-N.ar 1 C.3-D1-O.3 2 C.ar-D1-C.ar 23 C.ar-D1-F 1 C.a
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119 <br/> r-D1-N.am 1 C.ar-D1-N.ar 2 C.2-D2-C.3 1 C.2-D2-C.ar 3 C.3-D2-C.3 5 C.3
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120 <br/> -D2-C.ar 5 C.3-D2-N.ar 2 C.3-D2-O.3 4 C.3-D2-O.co2 2 C.ar-D2-C.ar 2...</div>
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121 <div class="OptionsBox">
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122 FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
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123 <br/> Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7
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124 <br/> -D1-None 2 None-D1-None 34 None-D1-O3 2 None-D1-O4 3 N21-D2-None 5 N7-
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125 <br/> D2-None 3 N7-D2-O3 1 None-D2-None 44 None-D2-O3 2 None-D2-O4 5 O3-D2-O
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126 <br/> 4 1 N21-D3-None 7 N7-D3-None 4 None-D3-None 45 None-D3-O3 4 None-D3-O4
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127 <br/> 5 N21-D4-N7 1 N21-D4-None 5 N21-D4-O3 1 N21-D4-O4 1 N7-D4-None 4 N...</div>
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128 <div class="OptionsBox">
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129 FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
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130 <br/> istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2
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131 <br/> -D1-C_R 1 C_2-D1-N_3 1 C_2-D1-O_2 2 C_2-D1-O_3 1 C_3-D1-C_3 7 C_3-D1-C
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132 <br/> _R 1 C_3-D1-N_R 1 C_3-D1-O_3 2 C_R-D1-C_R 23 C_R-D1-F_ 1 C_R-D1-N_3 1
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133 <br/> C_R-D1-N_R 2 C_2-D2-C_3 1 C_2-D2-C_R 3 C_3-D2-C_3 5 C_3-D2-C_R 5 C_3-D
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134 <br/> 2-N_R 2 C_3-D2-O_2 1 C_3-D2-O_3 5 C_R-D2-C_R 28 C_R-D2-F_ 2 C_R-D2-...</div>
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135 <p>
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136 </p>
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137 <h2>METHODS</h2>
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138 <dl>
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139 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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140 <dd>
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141 <div class="OptionsBox">
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142 $NewTopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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143 %NamesAndValues);</div>
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144 <p>Using specified <em>TopologicalAtomPairsFingerprints</em> property names and values hash, <strong>new</strong>
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145 method creates a new object and returns a reference to newly created <strong>TopologicalAtomPairsFingerprints</strong>
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146 object. By default, the following properties are initialized:</p>
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147 <div class="OptionsBox">
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148 Molecule = ''
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149 <br/> Type = 'TopologicalAtomPairs'
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150 <br/> MinDistance = 1
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151 <br/> MaxDistance = 10
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152 <br/> AtomIdentifierType = ''
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153 <br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC']
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154 <br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div>
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155 <p>Examples:</p>
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156 <div class="OptionsBox">
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157 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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158 'Molecule' => $Molecule,
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159 'AtomIdentifierType' =>
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160 'AtomicInvariantsAtomTypes');</div>
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161 <div class="OptionsBox">
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162 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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163 'Molecule' => $Molecule,
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164 'MinDistance' => 1,
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165 'MaxDistance' => 10,
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166 'AtomIdentifierType' =>
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167 'AtomicInvariantsAtomTypes',
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168 'AtomicInvariantsToUse' =>
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169 ['AS', 'X', 'BO', 'H', 'FC'] );</div>
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170 <div class="OptionsBox">
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171 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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172 'Molecule' => $Molecule,
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173 'AtomIdentifierType' =>
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174 'EStateAtomTypes');</div>
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175 <div class="OptionsBox">
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176 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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177 'Molecule' => $Molecule,
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178 'AtomIdentifierType' =>
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179 'SLogPAtomTypes');</div>
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180 <div class="OptionsBox">
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181 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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182 'Molecule' => $Molecule,
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183 'MinDistance' => 1,
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184 'MaxDistance' => 10,
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185 'AtomIdentifierType' =>
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186 'FunctionalClassAtomTypes',
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187 'FunctionalClassesToUse' =>
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188 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']);</div>
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189 <div class="OptionsBox">
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190 $TopologicalAtomPairsFingerprints->GenerateFingerprints();
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191 <br/> print "$TopologicalAtomPairsFingerprints\n";</div>
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192 </dd>
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193 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
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194 <dd>
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195 <div class="OptionsBox">
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196 $Description = $TopologicalAtomPairsFingerprints->GetDescription();</div>
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197 <p>Returns a string containing description of topological atom pairs fingerprints fingerprints.</p>
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198 </dd>
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199 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
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200 <dd>
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201 <div class="OptionsBox">
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202 $TopologicalAtomPairsFingerprints->GenerateFingerprints();</div>
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203 <p>Generates topological atom pairs fingerprints and returns <em>TopologicalAtomPairsFingerprints</em>.</p>
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204 </dd>
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205 <dt><strong><a name="getatompairids" class="item"><strong>GetAtomPairIDs</strong></a></strong></dt>
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206 <dd>
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207 <div class="OptionsBox">
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208 $AtomPairIDsRef = $TopologicalAtomPairsFingerprints->GetAtomPairIDs();
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209 <br/> @AtomPairIDs = $TopologicalAtomPairsFingerprints->GetAtomPairIDs();</div>
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210 <p>Returns atom pair IDs corresponding to atom pairs count values in topological atom pairs
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211 fingerprints vector as an array or reference to an array.</p>
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212 </dd>
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213 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
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214 <dd>
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215 <div class="OptionsBox">
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216 $TopologicalAtomPairsFingerprints->SetAtomIdentifierType($IdentifierType);</div>
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217 <p>Sets atom <em>IdentifierType</em> to use during atom pairs fingerprints generation and
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218 returns <em>TopologicalAtomPairsFingerprints</em>.</p>
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219 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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220 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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221 TPSAAtomTypes, UFFAtomTypes</em>.</p>
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222 </dd>
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223 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
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224 <dd>
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225 <div class="OptionsBox">
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226 $TopologicalAtomPairsFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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227 <br/> $TopologicalAtomPairsFingerprints->SetAtomicInvariantsToUse(@Values);</div>
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228 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
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229 for topological atom pairs fingerprints generation and returns <em>TopologicalAtomPairsFingerprints</em>.</p>
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230 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
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231 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
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232 <p>The atomic invariants abbreviations correspond to:</p>
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233 <div class="OptionsBox">
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234 AS = Atom symbol corresponding to element symbol</div>
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235 <div class="OptionsBox">
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236 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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237 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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238 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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239 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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240 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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241 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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242 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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243 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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244 <br/> RA = Ring atom annotation indicating whether atom is a ring
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245 <br/> FC<+n/-n> = Formal charge assigned to atom
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246 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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247 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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248 3 (triplet)</div>
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249 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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250 <div class="OptionsBox">
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251 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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252 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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253 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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254 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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255 are also allowed:</p>
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256 <div class="OptionsBox">
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257 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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258 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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259 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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260 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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261 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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262 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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263 <br/> H : NumOfImplicitAndExplicitHydrogens
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264 <br/> Ar : Aromatic
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265 <br/> RA : RingAtom
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266 <br/> FC : FormalCharge
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267 <br/> MN : MassNumber
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268 <br/> SM : SpinMultiplicity</div>
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269 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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270 atom types.</p>
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271 </dd>
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272 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
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273 <dd>
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274 <div class="OptionsBox">
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275 $TopologicalAtomPairsFingerprints->SetFunctionalClassesToUse($ValuesRef);
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276 <br/> $TopologicalAtomPairsFingerprints->SetFunctionalClassesToUse(@Values);</div>
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277 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
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278 for topological atom pairs fingerprints generation and returns <em>TopologicalAtomPairsFingerprints</em>.</p>
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279 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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280 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
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281 <p>The functional class abbreviations correspond to:</p>
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282 <div class="OptionsBox">
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283 HBD: HydrogenBondDonor
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284 <br/> HBA: HydrogenBondAcceptor
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285 <br/> PI : PositivelyIonizable
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286 <br/> NI : NegativelyIonizable
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287 <br/> Ar : Aromatic
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288 <br/> Hal : Halogen
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289 <br/> H : Hydrophobic
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290 <br/> RA : RingAtom
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291 <br/> CA : ChainAtom</div>
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292 <div class="OptionsBox">
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293 Functional class atom type specification for an atom corresponds to:</div>
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294 <div class="OptionsBox">
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295 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
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296 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
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297 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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298 <div class="OptionsBox">
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299 HydrogenBondDonor: NH, NH2, OH
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300 <br/> HydrogenBondAcceptor: N[!H], O
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301 <br/> PositivelyIonizable: +, NH2
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302 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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303 </dd>
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304 <dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt>
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305 <dd>
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306 <div class="OptionsBox">
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307 $TopologicalAtomPairsFingerprints->SetMaxDistance($Distance);</div>
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308 <p>Sets maximum distance to use during topological atom pairs fingerprints generation and
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309 returns <em>TopologicalAtomPairsFingerprints</em>.</p>
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310 </dd>
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311 <dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt>
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312 <dd>
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313 <div class="OptionsBox">
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314 $TopologicalAtomPairsFingerprints->SetMinDistance($Distance);</div>
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315 <p>Sets minimum distance to use during topological atom pairs fingerprints generation and
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316 returns <em>TopologicalAtomPairsFingerprints</em>.</p>
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317 </dd>
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318 <dt><strong><a name="stringifytopologicalatompairsfingerprints" class="item"><strong>StringifyTopologicalAtomPairsFingerprints</strong></a></strong></dt>
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319 <dd>
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320 <div class="OptionsBox">
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321 $String = $TopologicalAtomPairsFingerprints->
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322 StringifyTopologicalAtomPairsFingerprints();</div>
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323 <p>Returns a string containing information about <em>TopologicalAtomPairsFingerprints</em> object.</p>
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324 </dd>
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325 </dl>
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326 <p>
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327 </p>
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328 <h2>AUTHOR</h2>
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329 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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330 <p>
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331 </p>
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332 <h2>SEE ALSO</h2>
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333 <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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334 <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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335 <a href="./MACCSKeys.html">MACCSKeys.pm</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, 
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336 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>, 
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337 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
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338 </p>
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339 <p>
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340 </p>
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341 <h2>COPYRIGHT</h2>
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342 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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343 <p>This file is part of MayaChemTools.</p>
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344 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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345 the terms of the GNU Lesser General Public License as published by the Free
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346 Software Foundation; either version 3 of the License, or (at your option)
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347 any later version.</p>
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348 <p> </p><p> </p><div class="DocNav">
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349 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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350 <tr align="left" valign="top"><td width="33%" align="left"><a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalAtomPairsFingerprints.pm</strong></td></tr>
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351 </table>
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352 </div>
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353 <br />
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354 <center>
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355 <img src="../../images/h2o2.png">
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356 </center>
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357 </body>
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358 </html>
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