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3 <title>MayaChemTools:Documentation:TopologicalAtomPairsFingerprints.pl</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="./TextFilesToSDFiles.html" title="TextFilesToSDFiles.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>TopologicalAtomPairsFingerprints.pl</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.pl - Generate topological atom pairs fingerprints for SD files</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>TopologicalAtomPairsFingerprints.pl SDFile(s)...</p>
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26 <p>TopologicalAtomPairsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
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27 [<strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes</em>]
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28 [<strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em>]
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29 [<strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em>]
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30 [<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>] [<strong>--CompoundIDLabel</strong> <em>text</em>]
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31 [<strong>--CompoundIDMode</strong>] [<strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em>]
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32 [<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>]
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33 [<strong>--FingerprintsLabel</strong> <em>text</em>] [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>]
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34 [<strong>--MinDistance</strong> <em>number</em>] [<strong>--MaxDistance</strong> <em>number</em>]
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35 [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>]
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36 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>]
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37 [<strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>]
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38 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
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39 <p>
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40 </p>
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41 <h2>DESCRIPTION</h2>
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42 <p>Generate topological atom pairs fingerprints [ Ref 57, Ref 59, Ref 72 ] for <em>SDFile(s)</em> and create
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43 appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to
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44 molecular fingerprints.</p>
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45 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
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46 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
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47 can be specified either by <em>*.sdf</em> or the current directory name.</p>
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48 <p>The current release of MayaChemTools supports generation of topological atom pairs
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49 corresponding to following <strong>-a, --AtomIdentifierTypes</strong>:</p>
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50 <div class="OptionsBox">
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51 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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52 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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53 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
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54 <p>Based on the values specified for <strong>-a, --AtomIdentifierType</strong> and <strong>--AtomicInvariantsToUse</strong>,
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55 initial atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance
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56 matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom
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57 pairs within <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> are identified and counted. An atom pair
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58 identifier is generated for each unique atom pair; the format of the atom pair identifier is:</p>
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59 <div class="OptionsBox">
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60 <AtomType1>-D<n>-<AtomType2></div>
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61 <div class="OptionsBox">
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62 AtomType1, AtomType2: Atom types assigned to atom1 and atom2
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63 <br/> D: Distance between atom1 and atom2</div>
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64 <div class="OptionsBox">
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65 where AtomType1 <= AtomType2</div>
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66 <p>The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute
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67 topological atom pairs fingerprints of the molecule.</p>
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68 <p>Example of <em>SD</em> file containing topological atom pairs fingerprints string data:</p>
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69 <div class="OptionsBox">
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70 ... ...
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71 <br/> ... ...
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72 <br/> $$$$
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73 <br/> ... ...
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74 <br/> ... ...
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75 <br/> ... ...
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76 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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77 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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78 <br/> ... ...
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79 <br/> 2 3 1 0 0 0 0
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80 <br/> ... ...
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81 <br/> M END
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82 <br/> > <CmpdID>
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83 <br/> Cmpd1</div>
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84 <div class="OptionsBox">
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85 > <TopologicalAtomPairsFingerprints>
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86 <br/> FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi
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87 <br/> stance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1.H
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88 <br/> 3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.H1
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89 <br/> C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-C.X2...;
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90 <br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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91 <br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...</div>
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92 <div class="OptionsBox">
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93 $$$$
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94 <br/> ... ...
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95 <br/> ... ...</div>
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96 <p>Example of <em>FP</em> file containing topological atom pairs fingerprints string data:</p>
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97 <div class="OptionsBox">
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98 #
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99 <br/> # Package = MayaChemTools 7.4
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100 <br/> # Release Date = Oct 21, 2010
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101 <br/> #
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102 <br/> # TimeStamp = Fri Mar 11 15:04:36 2011
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103 <br/> #
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104 <br/> # FingerprintsStringType = FingerprintsVector
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105 <br/> #
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106 <br/> # Description = TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi...
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107 <br/> # VectorStringFormat = IDsAndValuesString
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108 <br/> # VectorValuesType = NumericalValues
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109 <br/> #
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110 <br/> Cmpd1 223;C.X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2...;1 1...
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111 <br/> Cmpd2 128;C.X1.BO1.H3-D1-C.X2.BO2.H2 C.X1.BO1.H3-D1-C.X3.BO4...;1 1...
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112 <br/> ... ...
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113 <br/> ... ..</div>
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114 <p>Example of CSV <em>Text</em> file containing topological atom pairs fingerprints string data:</p>
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115 <div class="OptionsBox">
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116 "CompoundID","TopologicalAtomPairsFingerprints"
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117 <br/> "Cmpd1","FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTy
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118 <br/> pes:MinDistance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C
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119 <br/> .X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X
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120 <br/> 3.BO3.H1C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1...;
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121 <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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122 <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 ...
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123 <br/> ... ...
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124 <br/> ... ...</div>
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125 <p>The current release of MayaChemTools generates the following types of topological atom pairs
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126 fingerprints vector strings:</p>
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127 <div class="OptionsBox">
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128 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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129 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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130 <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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131 <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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132 <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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133 <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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134 <div class="OptionsBox">
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135 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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136 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
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137 <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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138 <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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139 <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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140 <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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141 <div class="OptionsBox">
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142 FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
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143 <br/> :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D
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144 <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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145 <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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146 <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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147 <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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148 <div class="OptionsBox">
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149 FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
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150 <br/> axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH-
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151 <br/> D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH
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152 <br/> aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...;
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153 <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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154 <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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155 <div class="OptionsBox">
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156 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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157 <br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
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158 <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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159 <br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
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160 <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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161 <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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162 <div class="OptionsBox">
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163 FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
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164 <br/> axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2
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165 <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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166 <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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167 <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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168 <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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169 <div class="OptionsBox">
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170 FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
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171 <br/> xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1
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172 <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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173 <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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174 <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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175 <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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176 <div class="OptionsBox">
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177 FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
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178 <br/> xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C
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179 <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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180 <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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181 <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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182 <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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183 <div class="OptionsBox">
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184 FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
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185 <br/> Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7
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186 <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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187 <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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188 <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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189 <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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190 <div class="OptionsBox">
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191 FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
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192 <br/> istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2
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193 <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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194 <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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195 <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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196 <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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197 <p>
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198 </p>
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199 <h2>OPTIONS</h2>
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200 <dl>
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201 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
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202 <dd>
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203 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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204 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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205 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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206 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
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207 <p>The supported aromaticity model names along with model specific control parameters
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208 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
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209 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
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210 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
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211 for detecting aromaticity corresponding to a specific model.</p>
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212 </dd>
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213 <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt>
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214 <dd>
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215 <p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
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216 atoms during calculation of topological atom pairs fingerprints. Possible values in the current
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217 release are: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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218 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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219 TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p>
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220 </dd>
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221 <dt><strong><strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em></strong></dt>
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222 <dd>
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223 <p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
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224 option. It's a list of comma separated valid atomic invariant atom types.</p>
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225 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
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226 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
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227 <p>The atomic invariants abbreviations correspond to:</p>
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228 <div class="OptionsBox">
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229 AS = Atom symbol corresponding to element symbol</div>
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230 <div class="OptionsBox">
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231 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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232 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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233 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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234 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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235 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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236 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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237 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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238 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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239 <br/> RA = Ring atom annotation indicating whether atom is a ring
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240 <br/> FC<+n/-n> = Formal charge assigned to atom
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241 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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242 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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243 3 (triplet)</div>
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244 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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245 <div class="OptionsBox">
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246 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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247 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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248 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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249 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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250 are also allowed:</p>
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251 <div class="OptionsBox">
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252 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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253 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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254 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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255 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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256 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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257 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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258 <br/> H : NumOfImplicitAndExplicitHydrogens
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259 <br/> Ar : Aromatic
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260 <br/> RA : RingAtom
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261 <br/> FC : FormalCharge
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262 <br/> MN : MassNumber
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263 <br/> SM : SpinMultiplicity</div>
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264 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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265 atom types.</p>
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266 </dd>
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267 <dt><strong><strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em></strong></dt>
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268 <dd>
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269 <p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
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270 option. It's a list of comma separated valid functional classes.</p>
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271 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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272 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
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273 <p>The functional class abbreviations correspond to:</p>
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274 <div class="OptionsBox">
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275 HBD: HydrogenBondDonor
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276 <br/> HBA: HydrogenBondAcceptor
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277 <br/> PI : PositivelyIonizable
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278 <br/> NI : NegativelyIonizable
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279 <br/> Ar : Aromatic
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280 <br/> Hal : Halogen
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281 <br/> H : Hydrophobic
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282 <br/> RA : RingAtom
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283 <br/> CA : ChainAtom</div>
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284 <div class="OptionsBox">
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285 Functional class atom type specification for an atom corresponds to:</div>
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286 <div class="OptionsBox">
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287 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div>
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288 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
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289 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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290 <div class="OptionsBox">
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291 HydrogenBondDonor: NH, NH2, OH
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292 <br/> HydrogenBondAcceptor: N[!H], O
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293 <br/> PositivelyIonizable: +, NH2
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294 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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295 </dd>
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296 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
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297 <dd>
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298 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
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299 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
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300 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
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301 IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which
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302 look like Cmpd<Number>.</p>
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303 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
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304 <div class="OptionsBox">
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305 MolID
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306 <br/> ExtReg</div>
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307 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
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308 <div class="OptionsBox">
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309 Compound</div>
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310 <p>The value specified above generates compound IDs which correspond to Compound<Number>
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311 instead of default value of Cmpd<Number>.</p>
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312 </dd>
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313 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
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314 <dd>
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315 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
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316 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
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317 </dd>
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318 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
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319 <dd>
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320 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
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321 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
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322 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
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323 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
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324 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
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325 Default value: <em>LabelPrefix</em>.</p>
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326 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
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327 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
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328 values are replaced with sequential compound IDs.</p>
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329 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
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330 </dd>
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331 <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt>
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332 <dd>
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333 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
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334 with generated fingerprints for <em>text | both</em> values of <strong>--output</strong> option.</p>
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335 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
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336 <p>Examples:</p>
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337 <div class="OptionsBox">
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338 Extreg
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339 <br/> MolID,CompoundName</div>
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340 </dd>
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341 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
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342 <dd>
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343 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
|
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344 with generated fingerprints for <em>text | both</em> values of <strong>--output</strong> option: transfer all SD
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345 data field; transfer SD data files common to all compounds; extract specified data fields;
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346 generate a compound ID using molname line, a compound prefix, or a combination of both.
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347 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
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348 </dd>
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349 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
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350 <dd>
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351 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
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352 Default value: <em>Yes</em>.</p>
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353 <p>By default, compound data is checked before calculating fingerprints and compounds containing
|
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354 atom data corresponding to non-element symbols or no atom data are ignored.</p>
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|
355 </dd>
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356 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
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357 <dd>
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358 <p>SD data label or text file column label to use for fingerprints string in output SD or
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359 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>TopologicalAtomPairsFingerprints</em>.</p>
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|
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360 </dd>
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|
361 <dt><strong><strong>-h, --help</strong></strong></dt>
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362 <dd>
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363 <p>Print this help message.</p>
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364 </dd>
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365 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
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366 <dd>
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367 <p>Generate fingerprints for only the largest component in molecule. Possible values:
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368 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
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369 <p>For molecules containing multiple connected components, fingerprints can be generated
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370 in two different ways: use all connected components or just the largest connected
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371 component. By default, all atoms except for the largest connected component are
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372 deleted before generation of fingerprints.</p>
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373 </dd>
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374 <dt><strong><strong>--MinDistance</strong> <em>number</em></strong></dt>
|
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375 <dd>
|
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376 <p>Minimum bond distance between atom pairs for generating topological atom pairs. Default value:
|
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377 <em>1</em>. Valid values: positive integers and less than <strong>--MaxDistance</strong>.</p>
|
|
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378 </dd>
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379 <dt><strong><strong>--MaxDistance</strong> <em>number</em></strong></dt>
|
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380 <dd>
|
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381 <p>Maximum bond distance between atom pairs for generating topological atom pairs. Default value:
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382 <em>10</em>. Valid values: positive integers and greater than <strong>--MinDistance</strong>.</p>
|
|
|
383 </dd>
|
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384 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
|
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385 <dd>
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386 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
|
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387 Default value: <em>comma</em></p>
|
|
|
388 </dd>
|
|
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389 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
|
|
|
390 <dd>
|
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391 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
|
|
|
392 </dd>
|
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|
393 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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394 <dd>
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395 <p>Overwrite existing files.</p>
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|
|
396 </dd>
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397 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
|
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|
398 <dd>
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|
399 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
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|
400 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
|
401 </dd>
|
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|
402 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
|
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|
403 <dd>
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|
|
404 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file names:
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405 <SDFileName><TopologicalAtomPairsFP>.<Ext>. The file type determines <Ext> value.
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|
406 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
|
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407 delimited text files, respectively.This option is ignored for multiple input files.</p>
|
|
|
408 </dd>
|
|
|
409 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
|
|
|
410 <dd>
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|
411 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
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|
412 <strong>--output</strong> option. Possible values: <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
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|
413 ValuesAndIDsPairsString</em>. Default value: <em>IDsAndValuesString</em>.</p>
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|
|
414 <p>Examples:</p>
|
|
|
415 <div class="OptionsBox">
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|
|
416 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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|
|
417 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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|
418 <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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419 <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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|
420 <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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|
421 <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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|
422 <div class="OptionsBox">
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|
423 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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|
|
424 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
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425 <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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426 <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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427 <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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428 <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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|
|
429 </dd>
|
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|
430 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
|
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|
431 <dd>
|
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|
432 <p>Location of working directory. Default value: current directory.</p>
|
|
|
433 </dd>
|
|
|
434 </dl>
|
|
|
435 <p>
|
|
|
436 </p>
|
|
|
437 <h2>EXAMPLES</h2>
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|
|
438 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
439 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
440 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
441 <div class="ExampleBox">
|
|
|
442 % TopologicalAtomPairsFingerprints.pl -r SampleTAPFP -o Sample.sdf</div>
|
|
|
443 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
444 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf,
|
|
|
445 SampleTAPFP.fpf and SampleTAPFP.csv files containing sequential compound IDs in CSV file along
|
|
|
446 with fingerprints vector strings data, type:</p>
|
|
|
447 <div class="ExampleBox">
|
|
|
448 % TopologicalAtomPairsFingerprints.pl --output all -r SampleTAPFP
|
|
|
449 -o Sample.sdf</div>
|
|
|
450 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
451 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
452 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
453 <div class="ExampleBox">
|
|
|
454 % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
455 -r SampleTAPFP -o Sample.sdf</div>
|
|
|
456 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
457 10 using E-state types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
458 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
459 <div class="ExampleBox">
|
|
|
460 % TopologicalAtomPairsFingerprints.pl -a EStateAtomTypes
|
|
|
461 -r SampleTAPFP -o Sample.sdf</div>
|
|
|
462 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
463 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
464 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
465 <div class="ExampleBox">
|
|
|
466 % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
467 -r SampleTAPFP -o Sample.sdf</div>
|
|
|
468 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
469 10 using functional class atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
470 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
471 <div class="ExampleBox">
|
|
|
472 % TopologicalAtomPairsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
473 -r SampleTAPFP -o Sample.sdf</div>
|
|
|
474 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
475 10 using MMFF94 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
476 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
477 <div class="ExampleBox">
|
|
|
478 % TopologicalAtomPairsFingerprints.pl -a MMFF94AtomTypes
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479 -r SampleTAPFP -o Sample.sdf</div>
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480 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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481 10 using SLogP atom types in IDsAndValuesString format and create a SampleTAPFP.csv
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482 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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483 <div class="ExampleBox">
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484 % TopologicalAtomPairsFingerprints.pl -a SLogPAtomTypes
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485 -r SampleTAPFP -o Sample.sdf</div>
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486 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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487 10 using SYBYL atom types in IDsAndValuesString format and create a SampleTAPFP.csv
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488 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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489 <div class="ExampleBox">
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490 % TopologicalAtomPairsFingerprints.pl -a SYBYLAtomTypes
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491 -r SampleTAPFP -o Sample.sdf</div>
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492 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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493 10 using TPSA atom types in IDsAndValuesString format and create a SampleTAPFP.csv
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494 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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495 <div class="ExampleBox">
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496 % TopologicalAtomPairsFingerprints.pl -a TPSAAtomTypes
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497 -r SampleTAPFP -o Sample.sdf</div>
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498 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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499 10 using UFF atom types in IDsAndValuesString format and create a SampleTAPFP.csv
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500 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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501 <div class="ExampleBox">
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502 % TopologicalAtomPairsFingerprints.pl -a UFFAtomTypes
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503 -r SampleTAPFP -o Sample.sdf</div>
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504 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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505 10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTAPFP.csv
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506 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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507 <div class="ExampleBox">
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508 % TopologicalAtomPairsFingerprints.pl --VectorStringFormat
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509 IDsAndValuesPairsString -r SampleTAPFP -o Sample.sdf</div>
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510 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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511 6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
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512 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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513 <div class="ExampleBox">
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514 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
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515 --MinDistance 1 --MaxDistance 6 -r SampleTAPFP -o Sample.sdf</div>
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516 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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517 10 using only AS,X atomic invariants atom types in IDsAndValuesString format and create a
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518 SampleTAPFP.csv file containing sequential compound IDs along with fingerprints vector strings
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519 data, type:</p>
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520 <div class="ExampleBox">
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521 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
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522 --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6
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523 -r SampleTAPFP -o Sample.sdf</div>
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524 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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525 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
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526 file containing compound ID from molecule name line along with fingerprints vector strings
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527 data, type:</p>
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528 <div class="ExampleBox">
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529 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
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530 --DataFieldsMode CompoundID -CompoundIDMode MolName
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531 -r SampleTAPFP -o Sample.sdf</div>
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532 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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533 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
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534 file containing compound IDs using specified data field along with fingerprints vector strings
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535 data, type:</p>
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536 <div class="ExampleBox">
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537 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
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538 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
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539 Mol_ID -r SampleTAPFP -o Sample.sdf</div>
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540 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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541 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
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542 file containing compound ID using combination of molecule name line and an explicit compound
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543 prefix along with fingerprints vector strings data, type:</p>
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544 <div class="ExampleBox">
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545 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
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546 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
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547 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTAPFP -o Sample.sdf</div>
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548 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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549 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
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550 file containing specific data fields columns along with fingerprints vector strings
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551 data, type:</p>
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552 <div class="ExampleBox">
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553 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
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554 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTAPFP
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555 -o Sample.sdf</div>
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556 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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557 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
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558 file containing common data fields columns along with fingerprints vector strings
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559 data, type:</p>
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560 <div class="ExampleBox">
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561 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
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562 --DataFieldsMode Common -r SampleTAPFP -o Sample.sdf</div>
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563 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
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564 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf,
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565 SampleTAPFP.fpf and SampleTAPFP.csv files containing all data fields columns in CSV file along
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566 with fingerprints data, type:</p>
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567 <div class="ExampleBox">
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568 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
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569 --DataFieldsMode All --output all -r SampleTAPFP
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570 -o Sample.sdf</div>
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571 <p>
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572 </p>
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573 <h2>AUTHOR</h2>
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574 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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575 <p>
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576 </p>
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577 <h2>SEE ALSO</h2>
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578 <p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>, <a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>, 
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579 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>, 
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580 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>, 
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581 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
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582 </p>
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583 <p>
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584 </p>
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585 <h2>COPYRIGHT</h2>
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586 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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587 <p>This file is part of MayaChemTools.</p>
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588 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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589 the terms of the GNU Lesser General Public License as published by the Free
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590 Software Foundation; either version 3 of the License, or (at your option)
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591 any later version.</p>
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592 <p> </p><p> </p><div class="DocNav">
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593 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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594 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TextFilesToSDFiles.html" title="TextFilesToSDFiles.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>TopologicalAtomPairsFingerprints.pl</strong></td></tr>
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595 </table>
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596 </div>
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597 <br />
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598 <center>
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599 <img src="../../images/h2o2.png">
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600 </center>
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601 </body>
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602 </html>
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