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3 <title>MayaChemTools:Documentation:TopologicalAtomTripletsFingerprints.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="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalAtomTripletsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomTripletsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalAtomTripletsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>TopologicalAtomTripletsFingerprints.pl - Generate topological atom triplets 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>TopologicalAtomTripletsFingerprints.pl SDFile(s)...</p>
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26 <p>TopologicalAtomTripletsFingerprints.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>] [<strong>-u, --UseTriangleInequality</strong> <em>Yes | No</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 triplets fingerprints 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 triplets
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49 fingerprints 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 triplet
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58 identifier is generated for each unique atom triplet; the format of the atom triplet identifier is:</p>
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59 <div class="OptionsBox">
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60 <ATx>-Dyz-<ATy>-Dxz-<ATz>-Dxy</div>
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61 <div class="OptionsBox">
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62 ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z
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63 <br/> Dxy: Distance between atom x and atom y
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64 <br/> Dxz: Distance between atom x and atom z
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65 <br/> Dyz: Distance between atom y and atom z</div>
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66 <div class="OptionsBox">
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67 where <AT1>-D23 <= <AT2>-D13 <= <AT3>-D12</div>
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68 <p>The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute
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69 topological atom triplets fingerprints of the molecule.</p>
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70 <p>Example of <em>SD</em> file containing topological atom triplets fingerprints string data:</p>
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71 <div class="OptionsBox">
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72 ... ...
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73 <br/> ... ...
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74 <br/> $$$$
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75 <br/> ... ...
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76 <br/> ... ...
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77 <br/> ... ...
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78 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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79 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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80 <br/> ... ...
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81 <br/> 2 3 1 0 0 0 0
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82 <br/> ... ...
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83 <br/> M END
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84 <br/> > <CmpdID>
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85 <br/> Cmpd1</div>
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86 <div class="OptionsBox">
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87 > <TopologicalAtomTripletsFingerprints>
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88 <br/> FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi
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89 <br/> nDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1.B
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90 <br/> O1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D10-C
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91 <br/> .X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1...;
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92 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2
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93 <br/> 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...</div>
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94 <div class="OptionsBox">
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95 $$$$
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96 <br/> ... ...
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97 <br/> ... ...</div>
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98 <p>Example of <em>FP</em> file containing topological atom triplets fingerprints string data:</p>
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99 <div class="OptionsBox">
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100 #
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101 <br/> # Package = MayaChemTools 7.4
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102 <br/> # Release Date = Oct 21, 2010
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103 <br/> #
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104 <br/> # TimeStamp = Fri Mar 11 15:24:01 2011
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105 <br/> #
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106 <br/> # FingerprintsStringType = FingerprintsVector
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107 <br/> #
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108 <br/> # Description = TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi...
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109 <br/> # VectorStringFormat = IDsAndValuesString
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110 <br/> # VectorValuesType = NumericalValues
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111 <br/> #
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112 <br/> Cmpd1 3096;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2...;1 2 2 2 2...
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113 <br/> Cmpd2 1093;C.X1.BO1.H3-D1-C.X1.BO1.H3-D3-C.X2.BO2.H2-D4...;2 2 2 2 2...
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114 <br/> ... ...
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115 <br/> ... ..</div>
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116 <p>Example of CSV <em>Text</em> file containing topological atom triplets fingerprints string data:</p>
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117 <div class="OptionsBox">
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118 "CompoundID","TopologicalAtomTripletsFingerprints"
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119 <br/> "Cmpd1","FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAto
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120 <br/> mTypes:MinDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesStri
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121 <br/> ng;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2
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122 <br/> .H2-D10-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1....;
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123 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2
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124 <br/> 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...
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125 <br/> ... ...
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126 <br/> ... ...</div>
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127 <p>The current release of MayaChemTools generates the following types of topological atom triplets
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128 fingerprints vector strings:</p>
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129 <div class="OptionsBox">
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130 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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131 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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132 <br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
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133 <br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
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134 <br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
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135 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
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136 <br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div>
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137 <div class="OptionsBox">
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138 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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139 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
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140 <br/> ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO
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141 <br/> 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X
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142 <br/> 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2
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143 <br/> -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...</div>
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144 <div class="OptionsBox">
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145 FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan
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146 <br/> ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D
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147 <br/> 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_
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148 <br/> 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_
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149 <br/> 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...;
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150 <br/> 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2
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151 <br/> 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...</div>
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152 <div class="OptionsBox">
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153 FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance
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154 <br/> 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D
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155 <br/> 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC
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156 <br/> H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1-
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157 <br/> aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...;
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158 <br/> 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2
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159 <br/> 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1
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160 <br/> 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...</div>
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161 <div class="OptionsBox">
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162 FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi
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163 <br/> nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1
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164 <br/> -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal
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165 <br/> -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar
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166 <br/> -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...;
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167 <br/> 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5
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168 <br/> 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3
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169 <br/> 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...</div>
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170 <div class="OptionsBox">
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171 FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance
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172 <br/> 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1-
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173 <br/> N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A
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174 <br/> -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B
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175 <br/> -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3-
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176 <br/> O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-...</div>
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177 <div class="OptionsBox">
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178 FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1
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179 <br/> :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11
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180 <br/> -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D
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181 <br/> 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C
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182 <br/> 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1
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183 <br/> -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS...</div>
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184 <div class="OptionsBox">
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185 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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186 <br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
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187 <br/> .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
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188 <br/> D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
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189 <br/> -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
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190 <br/> 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...</div>
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191 <div class="OptionsBox">
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192 FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1:
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193 <br/> MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non
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194 <br/> e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D
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195 <br/> 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5
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196 N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21-
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197 <br/> D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-...</div>
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198 <div class="OptionsBox">
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199 FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M
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200 <br/> axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3
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201 <br/> -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9
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202 <br/> C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1-
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203 <br/> C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5-
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204 <br/> C_3-D6 C_2-D1-C_3-D5-O_3-D4 C_2-D1-C_3-D6-C_3-D7 C_2-D1-C_3-D7-C_3-...</div>
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205 <p>
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206 </p>
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207 <h2>OPTIONS</h2>
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208 <dl>
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209 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
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210 <dd>
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211 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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212 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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213 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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214 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
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215 <p>The supported aromaticity model names along with model specific control parameters
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216 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
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217 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
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218 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
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219 for detecting aromaticity corresponding to a specific model.</p>
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220 </dd>
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221 <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt>
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222 <dd>
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223 <p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
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224 atoms during calculation of topological atom triplets fingerprints. Possible values in the current
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225 release are: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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226 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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227 TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p>
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228 </dd>
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229 <dt><strong><strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em></strong></dt>
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230 <dd>
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231 <p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
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232 option. It's a list of comma separated valid atomic invariant atom types.</p>
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233 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
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234 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
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235 <p>The atomic invariants abbreviations correspond to:</p>
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236 <div class="OptionsBox">
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237 AS = Atom symbol corresponding to element symbol</div>
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238 <div class="OptionsBox">
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239 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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240 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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241 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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242 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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243 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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244 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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245 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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246 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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247 <br/> RA = Ring atom annotation indicating whether atom is a ring
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248 <br/> FC<+n/-n> = Formal charge assigned to atom
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249 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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250 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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251 3 (triplet)</div>
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252 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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253 <div class="OptionsBox">
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254 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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255 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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256 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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257 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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258 are also allowed:</p>
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259 <div class="OptionsBox">
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260 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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261 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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262 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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263 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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264 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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265 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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266 <br/> H : NumOfImplicitAndExplicitHydrogens
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267 <br/> Ar : Aromatic
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268 <br/> RA : RingAtom
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269 <br/> FC : FormalCharge
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270 <br/> MN : MassNumber
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271 <br/> SM : SpinMultiplicity</div>
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272 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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273 atom types.</p>
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274 </dd>
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275 <dt><strong><strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em></strong></dt>
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276 <dd>
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277 <p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
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278 option. It's a list of comma separated valid functional classes.</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</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><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
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305 <dd>
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306 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
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307 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
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308 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
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309 IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which
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310 look like Cmpd<Number>.</p>
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311 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
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312 <div class="OptionsBox">
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313 MolID
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314 <br/> ExtReg</div>
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315 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
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316 <div class="OptionsBox">
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317 Compound</div>
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318 <p>The value specified above generates compound IDs which correspond to Compound<Number>
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319 instead of default value of Cmpd<Number>.</p>
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320 </dd>
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321 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
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322 <dd>
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323 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
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324 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
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325 </dd>
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326 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
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327 <dd>
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328 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
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329 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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330 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
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331 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
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332 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
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333 Default value: <em>LabelPrefix</em>.</p>
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334 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
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335 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
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336 values are replaced with sequential compound IDs.</p>
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337 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
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338 </dd>
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|
339 <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt>
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340 <dd>
|
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341 <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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|
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342 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
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343 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
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344 <p>Examples:</p>
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345 <div class="OptionsBox">
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|
346 Extreg
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347 <br/> MolID,CompoundName</div>
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|
348 </dd>
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|
349 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
|
|
|
350 <dd>
|
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351 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
|
|
|
352 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
|
|
|
353 data field; transfer SD data files common to all compounds; extract specified data fields;
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|
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354 generate a compound ID using molname line, a compound prefix, or a combination of both.
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355 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
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|
|
356 </dd>
|
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|
357 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
|
|
|
358 <dd>
|
|
|
359 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
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|
|
360 Default value: <em>Yes</em>.</p>
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|
361 <p>By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
362 atom data corresponding to non-element symbols or no atom data are ignored.</p>
|
|
|
363 </dd>
|
|
|
364 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
|
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365 <dd>
|
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|
366 <p>SD data label or text file column label to use for fingerprints string in output SD or
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|
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367 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>TopologicalAtomTripletsFingerprints</em>.</p>
|
|
|
368 </dd>
|
|
|
369 <dt><strong><strong>-h, --help</strong></strong></dt>
|
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|
370 <dd>
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|
371 <p>Print this help message.</p>
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|
372 </dd>
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373 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
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|
374 <dd>
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375 <p>Generate fingerprints for only the largest component in molecule. Possible values:
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|
376 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
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|
377 <p>For molecules containing multiple connected components, fingerprints can be generated
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|
|
378 in two different ways: use all connected components or just the largest connected
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|
|
379 component. By default, all atoms except for the largest connected component are
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|
|
380 deleted before generation of fingerprints.</p>
|
|
|
381 </dd>
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|
382 <dt><strong><strong>--MinDistance</strong> <em>number</em></strong></dt>
|
|
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383 <dd>
|
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384 <p>Minimum bond distance between atom triplets for generating topological atom triplets. Default value:
|
|
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385 <em>1</em>. Valid values: positive integers and less than <strong>--MaxDistance</strong>.</p>
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|
386 </dd>
|
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|
387 <dt><strong><strong>--MaxDistance</strong> <em>number</em></strong></dt>
|
|
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388 <dd>
|
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|
389 <p>Maximum bond distance between atom triplets for generating topological atom triplets. Default value:
|
|
|
390 <em>10</em>. Valid values: positive integers and greater than <strong>--MinDistance</strong>.</p>
|
|
|
391 </dd>
|
|
|
392 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
|
|
|
393 <dd>
|
|
|
394 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
|
|
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395 Default value: <em>comma</em></p>
|
|
|
396 </dd>
|
|
|
397 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
|
|
|
398 <dd>
|
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|
399 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
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|
|
400 </dd>
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|
|
401 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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|
402 <dd>
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|
403 <p>Overwrite existing files.</p>
|
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|
404 </dd>
|
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|
405 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
|
|
|
406 <dd>
|
|
|
407 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
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|
|
408 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
|
409 </dd>
|
|
|
410 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
|
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|
411 <dd>
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|
412 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file names:
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|
|
413 <SDFileName><TopologicalAtomTripletsFP>.<Ext>. The file type determines <Ext> value.
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|
|
414 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
|
|
|
415 delimited text files, respectively.This option is ignored for multiple input files.</p>
|
|
|
416 </dd>
|
|
|
417 <dt><strong><strong>-u, --UseTriangleInequality</strong> <em>Yes | No</em></strong></dt>
|
|
|
418 <dd>
|
|
|
419 <p>Specify whether to imply triangle distance inequality test to distances between atom pairs in
|
|
|
420 atom triplets during generation of atom triplets generation. Possible values: <em>Yes or No</em>.
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421 Default value: <em>No</em>.</p>
|
|
|
422 <p>Triangle distance inequality test implies that distance or binned distance between any two atom
|
|
|
423 pairs in an atom triplet must be less than the sum of distances or binned distances between other
|
|
|
424 two atoms pairs and greater than the difference of their distances.</p>
|
|
|
425 <div class="OptionsBox">
|
|
|
426 For atom triplet ATx-Dyz-ATy-Dxz-ATz-Dxy to satisfy triangle inequality:</div>
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|
|
427 <div class="OptionsBox">
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|
|
428 Dyz > |Dxz - Dxy| and Dyz < Dxz + Dxy
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|
429 <br/> Dxz > |Dyz - Dxy| and Dyz < Dyz + Dxy
|
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|
430 <br/> Dxy > |Dyz - Dxz| and Dxy < Dyz + Dxz</div>
|
|
|
431 </dd>
|
|
|
432 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
|
|
|
433 <dd>
|
|
|
434 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
435 <strong>--output</strong> option. Possible values: <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
436 ValuesAndIDsPairsString</em>. Default value: <em>IDsAndValuesString</em>.</p>
|
|
|
437 <p>Examples:</p>
|
|
|
438 <div class="OptionsBox">
|
|
|
439 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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|
|
440 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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|
|
441 <br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
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|
|
442 <br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
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|
|
443 <br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
|
|
|
444 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
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|
445 <br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div>
|
|
|
446 <div class="OptionsBox">
|
|
|
447 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
|
|
|
448 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
|
|
|
449 <br/> ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO
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|
|
450 <br/> 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X
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|
|
451 <br/> 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2
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|
|
452 <br/> -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...</div>
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|
453 </dd>
|
|
|
454 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
|
|
|
455 <dd>
|
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456 <p>Location of working directory. Default value: current directory.</p>
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457 </dd>
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458 </dl>
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459 <p>
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460 </p>
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461 <h2>EXAMPLES</h2>
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462 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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463 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
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464 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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465 <div class="ExampleBox">
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466 % TopologicalAtomTripletsFingerprints.pl -r SampleTATFP -o Sample.sdf</div>
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467 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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468 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf,
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469 SampleTATFP.fpf and SampleTATFP.csv files containing sequential compound IDs in CSV file along
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470 with fingerprints vector strings data, type:</p>
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471 <div class="ExampleBox">
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472 % TopologicalAtomTripletsFingerprints.pl --output all -r SampleTATFP
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473 -o Sample.sdf</div>
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474 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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475 10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTATFP.csv
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476 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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477 <div class="ExampleBox">
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478 % TopologicalAtomTripletsFingerprints.pl --VectorStringFormat
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479 IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf</div>
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480 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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481 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTATFP.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 % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes
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485 -r SampleTATFP -o Sample.sdf</div>
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486 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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487 10 using E-state atom types in IDsAndValuesString format and create a SampleTATFP.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 % TopologicalAtomTripletsFingerprints.pl -a EStateAtomTypes
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491 -r SampleTATFP -o Sample.sdf</div>
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492 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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493 10 using functional class atom types in IDsAndValuesString format and create a SampleTATFP.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 % TopologicalAtomTripletsFingerprints.pl -a FunctionalClassAtomTypes
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497 -r SampleTATFP -o Sample.sdf</div>
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498 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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499 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTATFP.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 % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes
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503 -r SampleTATFP -o Sample.sdf</div>
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504 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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505 10 using MM94 atom types in IDsAndValuesString format and create a SampleTATFP.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 % TopologicalAtomTripletsFingerprints.pl -a MMFF94AtomTypes
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509 -r SampleTATFP -o Sample.sdf</div>
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510 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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511 10 using SLogP atom types in IDsAndValuesString format and create a SampleTATFP.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 % TopologicalAtomTripletsFingerprints.pl -a SLogPAtomTypes
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515 -r SampleTATFP -o Sample.sdf</div>
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516 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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517 10 using SYBYL atom types in IDsAndValuesString format and create a SampleTATFP.csv
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518 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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519 <div class="ExampleBox">
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520 % TopologicalAtomTripletsFingerprints.pl -a SYBYLAtomTypes
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521 -r SampleTATFP -o Sample.sdf</div>
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522 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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523 10 using TPSA atom types in IDsAndValuesString format and create a SampleTATFP.csv
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524 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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525 <div class="ExampleBox">
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526 % TopologicalAtomTripletsFingerprints.pl -a TPSAAtomTypes
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527 -r SampleTATFP -o Sample.sdf</div>
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528 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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529 10 using UFF atom types in IDsAndValuesString format and create a SampleTATFP.csv
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530 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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531 <div class="ExampleBox">
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532 % TopologicalAtomTripletsFingerprints.pl -a UFFAtomTypes
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533 -r SampleTATFP -o Sample.sdf</div>
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534 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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535 6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
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536 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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537 <div class="ExampleBox">
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538 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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539 --MinDistance 1 --MaxDistance 6 -r SampleTATFP -o Sample.sdf</div>
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540 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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541 10 using only AS,X atomic invariants atom types in IDsAndValuesString format and create a
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542 SampleTATFP.csv file containing sequential compound IDs along with fingerprints vector strings
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543 data, type:</p>
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544 <div class="ExampleBox">
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545 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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546 --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6
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547 -r SampleTATFP -o Sample.sdf</div>
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548 <p>To generate topological atom triplets 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 SampleTATFP.csv
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550 file containing compound ID from molecule name line 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 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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554 --DataFieldsMode CompoundID -CompoundIDMode MolName
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555 -r SampleTATFP -o Sample.sdf</div>
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556 <p>To generate topological atom triplets 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 SampleTATFP.csv
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558 file containing compound IDs using specified data field 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 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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562 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
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563 Mol_ID -r SampleTATFP -o Sample.sdf</div>
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564 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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565 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
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566 file containing compound ID using combination of molecule name line and an explicit compound
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567 prefix along with fingerprints vector strings data, type:</p>
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568 <div class="ExampleBox">
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569 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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570 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
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571 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf</div>
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572 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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573 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
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574 file containing specific data fields columns along with fingerprints vector strings
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575 data, type:</p>
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576 <div class="ExampleBox">
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577 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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578 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP
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579 -o Sample.sdf</div>
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580 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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581 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
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582 file containing common data fields columns along with fingerprints vector strings
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583 data, type:</p>
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584 <div class="ExampleBox">
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585 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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586 --DataFieldsMode Common -r SampleTATFP -o Sample.sdf</div>
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587 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
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588 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf,
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589 SampleTATFP.fpf and SampleTATFP.csv files containing all data fields columns in CSV file along with
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590 fingerprints data, type:</p>
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591 <div class="ExampleBox">
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592 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
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593 --DataFieldsMode All --output all -r SampleTATFP
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594 -o Sample.sdf</div>
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595 <p>
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596 </p>
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597 <h2>AUTHOR</h2>
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598 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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599 <p>
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600 </p>
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601 <h2>SEE ALSO</h2>
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602 <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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603 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>, 
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604 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>, 
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605 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
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606 </p>
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607 <p>
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608 </p>
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609 <h2>COPYRIGHT</h2>
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610 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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611 <p>This file is part of MayaChemTools.</p>
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612 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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613 the terms of the GNU Lesser General Public License as published by the Free
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614 Software Foundation; either version 3 of the License, or (at your option)
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615 any later version.</p>
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616 <p> </p><p> </p><div class="DocNav">
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617 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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618 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalAtomTripletsFingerprints.pl</strong></td></tr>
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619 </table>
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620 </div>
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621 <br />
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622 <center>
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623 <img src="../../images/h2o2.png">
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624 </center>
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625 </body>
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626 </html>
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