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3 <title>MayaChemTools:Documentation:TopologicalAtomTorsionsFingerprints.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="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalAtomTorsionsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomTorsionsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalAtomTorsionsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalAtomTorsionsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalAtomTorsionsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalAtomTorsionsFingerprints.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>TopologicalAtomTorsionsFingerprints.pl - Generate topological atom torsions 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>TopologicalAtomTorsionsFingerprints.pl SDFile(s)...</p>
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26 <p>TopologicalAtomTorsionsFingerprints.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>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>]
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35 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-v, --VectorStringFormat</strong>]
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36 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
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37 <p>
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38 </p>
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39 <h2>DESCRIPTION</h2>
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40 <p>Generate topological atom torsions fingerprints [ Ref 58, Ref 72 ] for <em>SDFile(s)</em> and create
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41 appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to
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42 molecular fingerprints.</p>
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43 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
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44 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
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45 can be specified either by <em>*.sdf</em> or the current directory name.</p>
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46 <p>The current release of MayaChemTools supports generation of topological atom torsions
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47 fingerprints corresponding to following <strong>-a, --AtomIdentifierTypes</strong>:</p>
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48 <div class="OptionsBox">
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49 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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50 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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51 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
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52 <p>Based on the values specified for <strong>-a, --AtomIdentifierType</strong> and <strong>--AtomicInvariantsToUse</strong>,
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53 initial atom types are assigned to all non-hydrogen atoms in a molecule. All unique atom torsions
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54 are identified and an atom torsion identifier is generated; the format of atom torsion identifier is:</p>
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55 <div class="OptionsBox">
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56 <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4></div>
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57 <div class="OptionsBox">
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58 AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types</div>
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59 <div class="OptionsBox">
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60 where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4</div>
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61 <p>The atom torsion identifiers for all unique atom torsions corresponding to non-hydrogen atoms constitute
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62 topological atom torsions fingerprints of the molecule.</p>
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63 <p>Example of <em>SD</em> file containing topological atom torsions fingerprints string data:</p>
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64 <div class="OptionsBox">
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65 ... ...
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66 <br/> ... ...
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67 <br/> $$$$
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68 <br/> ... ...
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69 <br/> ... ...
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70 <br/> ... ...
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71 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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72 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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73 <br/> ... ...
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74 <br/> 2 3 1 0 0 0 0
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75 <br/> ... ...
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76 <br/> M END
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77 <br/> > <CmpdID>
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78 <br/> Cmpd1</div>
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79 <div class="OptionsBox">
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80 > <TopologicalAtomTorsionsFingerprints>
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81 <br/> FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;33
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82 <br/> ;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.
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83 <br/> X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO2.H
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84 <br/> 2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O.X1....;
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85 <br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div>
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86 <div class="OptionsBox">
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87 $$$$
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88 <br/> ... ...
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89 <br/> ... ...</div>
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90 <p>Example of <em>FP</em> file containing topological atom torsions fingerprints string data:</p>
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91 <div class="OptionsBox">
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92 #
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93 <br/> # Package = MayaChemTools 7.4
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94 <br/> # Release Date = Oct 21, 2010
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95 <br/> #
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96 <br/> # TimeStamp = Fri Mar 11 15:17:20 2011
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97 <br/> #
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98 <br/> # FingerprintsStringType = FingerprintsVector
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99 <br/> #
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100 <br/> # Description = TopologicalAtomTorsions:AtomicInvariantsAtomTypes
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101 <br/> # VectorStringFormat = IDsAndValuesString
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102 <br/> # VectorValuesType = NumericalValues
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103 <br/> #
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104 <br/> Cmpd1 33;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.X3.BO4...;2 2 1 1 2 2 ...
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105 <br/> Cmpd2 23;C.X1.BO1.H3-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2...;2 2 1 5 ...
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106 <br/> ... ...
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107 <br/> ... ..</div>
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108 <p>Example of CSV <em>Text</em> file containing topological atom torsions fingerprints string data:</p>
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109 <div class="OptionsBox">
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110 "CompoundID","TopologicalAtomTorsionsFingerprints"
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111 <br/> "Cmpd1","FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAto
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112 <br/> mTypes;33;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.
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113 <br/> X3.BO4-C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C
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114 <br/> .X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3....;
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115 <br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
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116 <br/> ... ...
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117 <br/> ... ...</div>
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118 <p>The current release of MayaChemTools generates the following types of topological atom torsions
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119 fingerprints vector strings:</p>
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120 <div class="OptionsBox">
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121 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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122 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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123 <br/> C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
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124 <br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
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125 <br/> ;2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div>
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126 <div class="OptionsBox">
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127 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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128 <br/> 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
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129 <br/> .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
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130 <br/> 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
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131 <br/> O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
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132 <br/> O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...</div>
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133 <div class="OptionsBox">
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134 FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
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135 <br/> calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C
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136 <br/> _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2
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137 <br/> C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...;
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138 <br/> 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1</div>
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139 <div class="OptionsBox">
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140 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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141 <br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
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142 <br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
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143 <br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
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144 <br/> 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2</div>
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145 <div class="OptionsBox">
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146 FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
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147 <br/> ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar-
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148 <br/> Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar
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149 <br/> -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...;
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150 <br/> 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3</div>
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151 <div class="OptionsBox">
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152 FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
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153 <br/> lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5
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154 <br/> B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5
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155 <br/> A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...;
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156 <br/> 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
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157 <br/> 1 1 2 1 1 3 1 3</div>
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158 <div class="OptionsBox">
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159 FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
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160 <br/> Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1
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161 <br/> 1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS
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162 <br/> 2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1
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163 <br/> C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20
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164 <br/> 2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C...</div>
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165 <div class="OptionsBox">
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166 FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
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167 <br/> Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2
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168 <br/> -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C.
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169 <br/> ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3
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170 <br/> -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C.
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171 <br/> ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ...</div>
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172 <div class="OptionsBox">
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173 FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
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174 <br/> lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4
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175 <br/> None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None-
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176 <br/> None-None 44 None-None-None-O3 3 None-None-None-O4 5</div>
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177 <div class="OptionsBox">
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178 FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
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179 <br/> lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C
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180 <br/> _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3
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181 <br/> -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C
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182 <br/> _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2
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183 C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-...</div>
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184 <p>
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185 </p>
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186 <h2>OPTIONS</h2>
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187 <dl>
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188 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
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189 <dd>
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190 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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191 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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192 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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193 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
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194 <p>The supported aromaticity model names along with model specific control parameters
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195 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
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196 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
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197 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
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198 for detecting aromaticity corresponding to a specific model.</p>
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199 </dd>
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200 <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt>
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201 <dd>
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202 <p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
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203 atoms during calculation of topological atom torsions fingerprints. Possible values in the current
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204 release are: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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205 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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206 TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p>
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207 </dd>
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208 <dt><strong><strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em></strong></dt>
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209 <dd>
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210 <p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
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211 option. It's a list of comma separated valid atomic invariant atom types.</p>
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212 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
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213 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
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214 <p>The atomic invariants abbreviations correspond to:</p>
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215 <div class="OptionsBox">
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216 AS = Atom symbol corresponding to element symbol</div>
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217 <div class="OptionsBox">
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218 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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219 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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220 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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221 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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222 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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223 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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224 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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225 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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226 <br/> RA = Ring atom annotation indicating whether atom is a ring
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227 <br/> FC<+n/-n> = Formal charge assigned to atom
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228 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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229 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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230 3 (triplet)</div>
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231 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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232 <div class="OptionsBox">
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233 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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234 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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235 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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236 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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237 are also allowed:</p>
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238 <div class="OptionsBox">
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239 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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240 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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241 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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242 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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243 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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244 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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245 <br/> H : NumOfImplicitAndExplicitHydrogens
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246 <br/> Ar : Aromatic
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247 <br/> RA : RingAtom
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248 <br/> FC : FormalCharge
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249 <br/> MN : MassNumber
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250 <br/> SM : SpinMultiplicity</div>
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251 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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252 atom types.</p>
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253 </dd>
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254 <dt><strong><strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em></strong></dt>
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255 <dd>
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256 <p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
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257 option. It's a list of comma separated valid functional classes.</p>
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258 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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259 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
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260 <p>The functional class abbreviations correspond to:</p>
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261 <div class="OptionsBox">
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262 HBD: HydrogenBondDonor
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263 <br/> HBA: HydrogenBondAcceptor
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264 <br/> PI : PositivelyIonizable
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265 <br/> NI : NegativelyIonizable
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266 <br/> Ar : Aromatic
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267 <br/> Hal : Halogen
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268 <br/> H : Hydrophobic
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269 <br/> RA : RingAtom
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270 <br/> CA : ChainAtom</div>
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271 <div class="OptionsBox">
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272 Functional class atom type specification for an atom corresponds to:</div>
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273 <div class="OptionsBox">
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274 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div>
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275 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
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276 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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277 <div class="OptionsBox">
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278 HydrogenBondDonor: NH, NH2, OH
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279 <br/> HydrogenBondAcceptor: N[!H], O
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280 <br/> PositivelyIonizable: +, NH2
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281 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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282 </dd>
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283 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
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284 <dd>
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285 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
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286 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
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287 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
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288 IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which
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289 look like Cmpd<Number>.</p>
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290 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
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291 <div class="OptionsBox">
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292 MolID
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293 <br/> ExtReg</div>
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294 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
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295 <div class="OptionsBox">
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296 Compound</div>
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297 <p>The value specified above generates compound IDs which correspond to Compound<Number>
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298 instead of default value of Cmpd<Number>.</p>
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299 </dd>
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300 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
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301 <dd>
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302 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
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303 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
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304 </dd>
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305 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
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306 <dd>
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307 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
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308 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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309 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
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310 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
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311 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
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312 Default value: <em>LabelPrefix</em>.</p>
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313 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
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314 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
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315 values are replaced with sequential compound IDs.</p>
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316 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
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317 </dd>
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318 <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt>
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319 <dd>
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320 <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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321 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
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322 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
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323 <p>Examples:</p>
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324 <div class="OptionsBox">
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325 Extreg
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326 <br/> MolID,CompoundName</div>
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327 </dd>
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328 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
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329 <dd>
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330 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
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331 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
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332 data field; transfer SD data files common to all compounds; extract specified data fields;
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333 generate a compound ID using molname line, a compound prefix, or a combination of both.
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334 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
|
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335 </dd>
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336 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
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337 <dd>
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338 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
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339 Default value: <em>Yes</em>.</p>
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340 <p>By default, compound data is checked before calculating fingerprints and compounds containing
|
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341 atom data corresponding to non-element symbols or no atom data are ignored.</p>
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342 </dd>
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343 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
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344 <dd>
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345 <p>SD data label or text file column label to use for fingerprints string in output SD or
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346 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>TopologicalAtomTorsionsFingerprints</em>.</p>
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347 </dd>
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348 <dt><strong><strong>-h, --help</strong></strong></dt>
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349 <dd>
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350 <p>Print this help message.</p>
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351 </dd>
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352 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
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353 <dd>
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354 <p>Generate fingerprints for only the largest component in molecule. Possible values:
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355 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
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356 <p>For molecules containing multiple connected components, fingerprints can be generated
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357 in two different ways: use all connected components or just the largest connected
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358 component. By default, all atoms except for the largest connected component are
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359 deleted before generation of fingerprints.</p>
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360 </dd>
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361 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
|
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362 <dd>
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363 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
|
|
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364 Default value: <em>comma</em>.</p>
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|
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365 </dd>
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366 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
|
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367 <dd>
|
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368 <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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|
|
369 </dd>
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370 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
|
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371 <dd>
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372 <p>Overwrite existing files.</p>
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|
|
373 </dd>
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374 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
|
|
|
375 <dd>
|
|
|
376 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
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|
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377 <em>Yes or No</em>. Default value: <em>Yes</em></p>
|
|
|
378 </dd>
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379 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
|
|
|
380 <dd>
|
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381 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file names:
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382 <SDFileName><TopologicalAtomTorsionsFP>.<Ext>. The file type determines <Ext> value.
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|
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383 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
|
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|
384 delimited text files, respectively.This option is ignored for multiple input files.</p>
|
|
|
385 </dd>
|
|
|
386 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
|
|
|
387 <dd>
|
|
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388 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
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389 <strong>--output</strong> option. Possible values: <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
390 ValuesAndIDsPairsString</em>. Defaultvalue: <em>IDsAndValuesString</em>.</p>
|
|
|
391 <p>Examples:</p>
|
|
|
392 <div class="OptionsBox">
|
|
|
393 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
394 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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|
395 <br/> C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
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396 <br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
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|
397 <br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div>
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|
|
398 <div class="OptionsBox">
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399 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
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400 <br/> 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
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|
401 <br/> .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
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|
402 <br/> 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
|
|
|
403 <br/> O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
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|
|
404 <br/> O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...</div>
|
|
|
405 </dd>
|
|
|
406 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
|
|
|
407 <dd>
|
|
|
408 <p>Location of working directory. Default value: current directory.</p>
|
|
|
409 </dd>
|
|
|
410 </dl>
|
|
|
411 <p>
|
|
|
412 </p>
|
|
|
413 <h2>EXAMPLES</h2>
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|
414 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
415 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
416 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
417 <div class="ExampleBox">
|
|
|
418 % TopologicalAtomTorsionsFingerprints.pl -r SampleTATFP -o Sample.sdf</div>
|
|
|
419 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
420 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv
|
|
|
421 files containing sequential compound IDs in CSV file along with fingerprints vector strings
|
|
|
422 data, type:</p>
|
|
|
423 <div class="ExampleBox">
|
|
|
424 % TopologicalAtomTorsionsFingerprints.pl --output all -r SampleTATFP
|
|
|
425 -o Sample.sdf</div>
|
|
|
426 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
427 IDsAndValuesPairsString format and create a SampleTATFP.csv file containing sequential
|
|
|
428 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
429 <div class="ExampleBox">
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|
|
430 % TopologicalAtomTorsionsFingerprints.pl --VectorStringFormat
|
|
|
431 IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf</div>
|
|
|
432 <p>To generate topological atom torsions fingerprints using DREIDING atom types in
|
|
|
433 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
434 compound IDs along with fingerprints vector strings data, type:</p>
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|
|
435 <div class="ExampleBox">
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|
|
436 % TopologicalAtomTorsionsFingerprints.pl -a DREIDINGAtomTypes
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|
|
437 -r SampleTATFP -o Sample.sdf</div>
|
|
|
438 <p>To generate topological atom torsions fingerprints using E-state atom types in
|
|
|
439 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
440 compound IDs along with fingerprints vector strings data, type:</p>
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|
|
441 <div class="ExampleBox">
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|
|
442 % TopologicalAtomTorsionsFingerprints.pl -a EStateAtomTypes
|
|
|
443 -r SampleTATFP -o Sample.sdf</div>
|
|
|
444 <p>To generate topological atom torsions fingerprints using functional class atom types in
|
|
|
445 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
446 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
447 <div class="ExampleBox">
|
|
|
448 % TopologicalAtomTorsionsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
449 -r SampleTATFP -o Sample.sdf</div>
|
|
|
450 <p>To generate topological atom torsions fingerprints using MMFF94 atom types in
|
|
|
451 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
452 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
453 <div class="ExampleBox">
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|
|
454 % TopologicalAtomTorsionsFingerprints.pl -a MMFF94AtomTypes
|
|
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455 -r SampleTATFP -o Sample.sdf</div>
|
|
|
456 <p>To generate topological atom torsions fingerprints using SLogP atom types in
|
|
|
457 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
458 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
459 <div class="ExampleBox">
|
|
|
460 % TopologicalAtomTorsionsFingerprints.pl -a SLogPAtomTypes
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|
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461 -r SampleTATFP -o Sample.sdf</div>
|
|
|
462 <p>To generate topological atom torsions fingerprints using SYBYL atom types in
|
|
|
463 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
464 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
465 <div class="ExampleBox">
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|
|
466 % TopologicalAtomTorsionsFingerprints.pl -a SYBYLAtomTypes
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|
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467 -r SampleTATFP -o Sample.sdf</div>
|
|
|
468 <p>To generate topological atom torsions fingerprints using TPSA atom types in
|
|
|
469 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
470 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
471 <div class="ExampleBox">
|
|
|
472 % TopologicalAtomTorsionsFingerprints.pl -a TPSAAtomTypes
|
|
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473 -r SampleTATFP -o Sample.sdf</div>
|
|
|
474 <p>To generate topological atom torsions fingerprints using UFF atom types in
|
|
|
475 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
476 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
477 <div class="ExampleBox">
|
|
|
478 % TopologicalAtomTorsionsFingerprints.pl -a UFFAtomTypes
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|
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479 -r SampleTATFP -o Sample.sdf</div>
|
|
|
480 <p>To generate topological atom torsions fingerprints using only AS,X atomic invariants atom
|
|
|
481 types in IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
482 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
483 <div class="ExampleBox">
|
|
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484 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
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485 --AtomicInvariantsToUse "AS,X" -r SampleTATFP -o Sample.sdf</div>
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486 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
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487 IDsAndValuesString format and create a SampleTATFP.csv file containing compoundID
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488 from molecule name line along with fingerprints vector strings, type:</p>
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489 <div class="ExampleBox">
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490 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
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491 --DataFieldsMode CompoundID -CompoundIDMode MolName
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492 -r SampleTATFP -o Sample.sdf</div>
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493 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
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494 IDsAndValuesString format and create a SampleTATFP.csv file containing compound IDs
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495 using specified data field along with fingerprints vector strings, type:</p>
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496 <div class="ExampleBox">
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497 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
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498 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
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499 Mol_ID -r SampleTATFP -o Sample.sdf</div>
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500 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
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501 IDsAndValuesString format and create a SampleTATFP.csv file containing compound ID
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502 using combination of molecule name line and an explicit compound prefix along with
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503 fingerprints vector strings data, type:</p>
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504 <div class="ExampleBox">
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505 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
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506 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
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507 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf</div>
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508 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
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509 IDsAndValuesString format and create a SampleTATFP.csv file containing specific data
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510 fields columns along with fingerprints vector strings, type:</p>
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511 <div class="ExampleBox">
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512 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
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513 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP
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514 -o Sample.sdf</div>
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515 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
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516 IDsAndValuesString format and create a SampleTATFP.csv file containing common
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517 data fields columns along with fingerprints vector strings, type:</p>
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518 <div class="ExampleBox">
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519 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
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520 --DataFieldsMode Common -r SampleTATFP -o Sample.sdf</div>
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521 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
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522 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv
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523 files containing all data fields columns in CSV file along with fingerprints data, type:</p>
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524 <div class="ExampleBox">
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525 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
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526 --DataFieldsMode All --output all -r SampleTATFP
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527 -o Sample.sdf</div>
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528 <p>
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529 </p>
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530 <h2>AUTHOR</h2>
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531 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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532 <p>
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533 </p>
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534 <h2>SEE ALSO</h2>
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535 <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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536 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>, 
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537 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, 
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538 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
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539 </p>
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540 <p>
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541 </p>
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542 <h2>COPYRIGHT</h2>
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543 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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544 <p>This file is part of MayaChemTools.</p>
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545 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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546 the terms of the GNU Lesser General Public License as published by the Free
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547 Software Foundation; either version 3 of the License, or (at your option)
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548 any later version.</p>
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549 <p> </p><p> </p><div class="DocNav">
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550 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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551 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalAtomTorsionsFingerprints.pl</strong></td></tr>
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552 </table>
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553 </div>
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554 <br />
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555 <center>
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556 <img src="../../images/h2o2.png">
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557 </center>
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558 </body>
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559 </html>
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