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3 <title>MayaChemTools:Documentation:TopologicalPharmacophoreAtomTripletsFingerprints.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="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./EndPage.html" title="EndPage.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalPharmacophoreAtomTripletsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalPharmacophoreAtomTripletsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalPharmacophoreAtomTripletsFingerprints.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>TopologicalPharmacophoreAtomTripletsFingerprints.pl - Generate topological pharmacophore 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>TopologicalPharmacophoreAtomTripletsFingerprints.pl SDFile(s)...</p>
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26 <p>TopologicalPharmacophoreAtomTripletsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
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27 [<strong>--AtomTripletsSetSizeToUse</strong> <em>ArbitrarySize | FixedSize</em>]
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28 [<strong>-a, --AtomTypesToUse</strong> <em>"AtomType1, AtomType2..."</em>]
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29 [<strong>--AtomTypesWeight</strong> <em>"AtomType1, Weight1, AtomType2, Weight2..."</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>--DistanceBinSize</strong> <em>number</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>]
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33 [<strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>] [<strong>--FingerprintsLabel</strong> <em>text</em>]
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34 [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>] [<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 pharmacophore atom triplets fingerprints [ Ref 66, Ref 68-71 ] for
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43 <em>SDFile(s)</em> and create appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector
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44 strings corresponding to 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>Based on the values specified for <strong>--AtomTypesToUse</strong>, pharmacophore atom types are
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49 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
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50 Using <strong>--MinDistance</strong>, <strong>--MaxDistance</strong>, and <strong>--DistanceBinSize</strong> values, a
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51 binned distance matrix is generated with lower bound on the distance bin as the distance
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52 in distance matrix; the lower bound on the distance bin is also used as the distance between
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53 atom pairs for generation of atom triplet identifiers.</p>
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54 <p>A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting
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55 atom pairs binned distances between <strong>--MinDistance</strong> and <strong>--MaxDistance</strong>. The value
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56 of <strong>--UseTriangleInequality</strong> determines whether the triangle inequality test is applied during
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57 generation of atom triplets basis set. The lower distance bound, along with specified pharmacophore
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58 types, is used during generation of atom triplet IDs.</p>
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59 <div class="OptionsBox">
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60 Let:</div>
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61 <div class="OptionsBox">
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62 P = Valid pharmacophore atom type</div>
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63 <div class="OptionsBox">
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64 Px = Pharmacophore atom x
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65 <br/> Py = Pharmacophore atom y
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66 <br/> Pz = Pharmacophore atom z</div>
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67 <div class="OptionsBox">
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68 Dmin = Minimum distance corresponding to number of bonds between two atoms
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69 <br/> Dmax = Maximum distance corresponding to number of bonds between two atoms
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70 <br/> D = Distance corresponding to number of bonds between two atom</div>
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71 <div class="OptionsBox">
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72 Bsize = Distance bin size
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73 <br/> Nbins = Number of distance bins</div>
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74 <div class="OptionsBox">
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75 Dxy = Distance or lower bound of binned distance between Px and Py
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76 <br/> Dxz = Distance or lower bound of binned distance between Px and Pz
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77 <br/> Dyz = Distance or lower bound of binned distance between Py and Pz</div>
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78 <div class="OptionsBox">
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79 Then:</div>
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80 <div class="OptionsBox">
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81 PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet IDs for atom types Px,
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82 Py, and Pz</div>
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83 <div class="OptionsBox">
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84 For example: H1-H1-H1, H2-HBA-H2 and so on</div>
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85 <div class="OptionsBox">
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86 For default values of Dmin = 1 , Dmax = 10 and Bsize = 2:</div>
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87 <div class="OptionsBox">
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88 the number of distance bins, Nbins = 5, are:</div>
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89 <div class="OptionsBox">
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90 [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</div>
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91 <div class="OptionsBox">
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92 and atom triplet basis set size is 2692.</div>
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93 <div class="OptionsBox">
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94 Atom triplet basis set size for various values of Dmin, Dmax and Bsize in
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95 <br/> conjunction with usage of triangle inequality is:</div>
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96 <div class="OptionsBox">
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97 Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize
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98 <br/> 1 10 2 No 4960
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99 <br/> 1 10 2 Yes 2692 [ Default ]
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100 <br/> 2 12 2 No 8436
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101 <br/> 2 12 2 Yes 4494</div>
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102 <p>Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore
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103 atom triplets is counted.</p>
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104 <p>The final pharmacophore atom triples count along with atom pair identifiers involving all non-hydrogen
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105 atoms constitute pharmacophore topological atom triplets fingerprints of the molecule.</p>
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106 <p>For <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option, the fingerprint vector correspond to
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107 only those topological pharmacophore atom triplets which are present and have non-zero count. However,
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108 for <em>FixedSize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option, the fingerprint vector contains all possible
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109 valid topological pharmacophore atom triplets with both zero and non-zero count values.</p>
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110 <p>Example of <em>SD</em> file containing topological pharmacophore atom triplets fingerprints string data:</p>
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111 <div class="OptionsBox">
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112 ... ...
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113 <br/> ... ...
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114 <br/> $$$$
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115 <br/> ... ...
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116 <br/> ... ...
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117 <br/> ... ...
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118 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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119 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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120 <br/> ... ...
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121 <br/> 2 3 1 0 0 0 0
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122 <br/> ... ...
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123 <br/> M END
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124 <br/> > <CmpdID>
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125 <br/> Cmpd1</div>
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126 <div class="OptionsBox">
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127 > <TopologicalPharmacophoreAtomTripletsFingerprints>
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128 <br/> FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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129 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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130 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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131 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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132 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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133 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
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134 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
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135 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
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136 <div class="OptionsBox">
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137 $$$$
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138 <br/> ... ...
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139 <br/> ... ...</div>
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140 <p>Example of <em>FP</em> file containing topological pharmacophore atom triplets fingerprints string data:</p>
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141 <div class="OptionsBox">
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142 #
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143 <br/> # Package = MayaChemTools 7.4
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144 <br/> # Release Date = Oct 21, 2010
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145 <br/> #
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146 <br/> # TimeStamp = Fri Mar 11 15:38:58 2011
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147 <br/> #
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148 <br/> # FingerprintsStringType = FingerprintsVector
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149 <br/> #
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150 <br/> # Description = TopologicalPharmacophoreAtomTriplets:ArbitrarySize:M...
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151 <br/> # VectorStringFormat = IDsAndValuesString
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152 <br/> # VectorValuesType = NumericalValues
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153 <br/> #
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154 <br/> Cmpd1 696;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1...;;46 106...
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155 <br/> Cmpd2 251;H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-H1-NI1...;4 1 3 1 1 2 2...
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156 <br/> ... ...
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157 <br/> ... ..</div>
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158 <p>Example of CSV <em>Text</em> file containing topological pharmacophore atom triplets fingerprints string data:</p>
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159 <div class="OptionsBox">
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160 "CompoundID","TopologicalPharmacophoreAtomTripletsFingerprints"
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161 <br/> "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomTriplets:Arbitr
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162 <br/> arySize:MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesStri
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163 <br/> ng;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HB
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164 <br/> A1 Ar1-H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA
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165 <br/> 1 H1-HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 A...;
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166 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
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167 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
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168 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
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169 <br/> ... ...
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170 <br/> ... ...</div>
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171 <p>The current release of MayaChemTools generates the following types of topological pharmacophore
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172 atom triplets fingerprints vector strings:</p>
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173 <div class="OptionsBox">
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174 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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175 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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176 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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177 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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178 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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179 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
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180 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
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181 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
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182 <div class="OptionsBox">
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183 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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184 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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185 <br/> 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
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186 <br/> 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
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187 <br/> 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
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188 <br/> 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...</div>
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189 <div class="OptionsBox">
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190 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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191 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString;
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192 <br/> Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-Ar1-NI1 Ar1-Ar1-P
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193 <br/> I1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1-H1-HBD1 Ar1-H1-NI1 Ar1-H1-PI1 Ar1-HBA1-HB
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194 <br/> A1 Ar1-HBA1-HBD1 Ar1-HBA1-NI1 Ar1-HBA1-PI1 Ar1-HBD1-HBD1 Ar1-HBD1-...;
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195 <br/> 46 106 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1
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196 <br/> 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145
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197 <br/> 132 26 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 ...</div>
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198 <p>
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199 </p>
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200 <h2>OPTIONS</h2>
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201 <dl>
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202 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
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203 <dd>
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204 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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205 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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206 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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207 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
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208 <p>The supported aromaticity model names along with model specific control parameters
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209 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
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210 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
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211 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
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212 for detecting aromaticity corresponding to a specific model.</p>
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213 </dd>
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214 <dt><strong><strong>--AtomTripletsSetSizeToUse</strong> <em>ArbitrarySize | FixedSize</em></strong></dt>
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215 <dd>
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216 <p>Atom triplets set size to use during generation of topological pharmacophore atom triplets
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217 fingerprints.</p>
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218 <p>Possible values: <em>ArbitrarySize | FixedSize</em>; Default value: <em>ArbitrarySize</em>.</p>
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219 <p>For <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option, the fingerprint vector
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220 correspond to only those topological pharmacophore atom triplets which are present and
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221 have non-zero count. However, for <em>FixedSize</em> value of <strong>--AtomTripletsSetSizeToUse</strong>
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222 option, the fingerprint vector contains all possible valid topological pharmacophore atom
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223 triplets with both zero and non-zero count values.</p>
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224 </dd>
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225 <dt><strong><strong>-a, --AtomTypesToUse</strong> <em>"AtomType1,AtomType2,..."</em></strong></dt>
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226 <dd>
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227 <p>Pharmacophore atom types to use during generation of topological phramacophore
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228 atom triplets. It's a list of comma separated valid pharmacophore atom types.</p>
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229 <p>Possible values for pharmacophore atom types are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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230 Default value [ Ref 71 ] : <em>HBD,HBA,PI,NI,H,Ar</em>.</p>
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231 <p>The pharmacophore atom types abbreviations correspond to:</p>
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232 <div class="OptionsBox">
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233 HBD: HydrogenBondDonor
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234 <br/> HBA: HydrogenBondAcceptor
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235 <br/> PI : PositivelyIonizable
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236 <br/> NI : NegativelyIonizable
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237 <br/> Ar : Aromatic
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238 <br/> Hal : Halogen
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239 <br/> H : Hydrophobic
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240 <br/> RA : RingAtom
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241 <br/> CA : ChainAtom</div>
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242 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign pharmacophore atom
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243 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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244 <div class="OptionsBox">
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245 HydrogenBondDonor: NH, NH2, OH
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246 <br/> HydrogenBondAcceptor: N[!H], O
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247 <br/> PositivelyIonizable: +, NH2
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248 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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249 </dd>
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250 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
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251 <dd>
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252 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
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253 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
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254 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
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255 IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which
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256 look like Cmpd<Number>.</p>
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257 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
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258 <div class="OptionsBox">
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259 MolID
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260 <br/> ExtReg</div>
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261 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
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262 <div class="OptionsBox">
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263 Compound</div>
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264 <p>The value specified above generates compound IDs which correspond to Compound<Number>
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265 instead of default value of Cmpd<Number>.</p>
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266 </dd>
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267 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
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268 <dd>
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269 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
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270 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
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271 </dd>
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272 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
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273 <dd>
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274 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
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275 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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276 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
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277 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
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278 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
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279 Default value: <em>LabelPrefix</em>.</p>
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280 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
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281 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
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282 values are replaced with sequential compound IDs.</p>
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283 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
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284 </dd>
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285 <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt>
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286 <dd>
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287 <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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288 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
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289 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
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290 <p>Examples:</p>
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291 <div class="OptionsBox">
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292 Extreg
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293 <br/> MolID,CompoundName</div>
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294 </dd>
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295 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
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296 <dd>
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297 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
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298 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
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299 data field; transfer SD data files common to all compounds; extract specified data fields;
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300 generate a compound ID using molname line, a compound prefix, or a combination of both.
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301 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
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302 </dd>
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303 <dt><strong><strong>--DistanceBinSize</strong> <em>number</em></strong></dt>
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304 <dd>
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305 <p>Distance bin size used to bin distances between atom pairs in atom triplets. Default value: <em>2</em>.
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306 Valid values: positive integers.</p>
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307 <p>For default <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> values of 1 and 10 with <strong>--DistanceBinSize</strong>
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308 of 2 [ Ref 70 ], the following 5 distance bins are generated:</p>
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309 <div class="OptionsBox">
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310 [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</div>
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311 <p>The lower distance bound on the distance bin is uses to bin the distance between atom pairs in
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312 atom triplets. So in the previous example, atom pairs with distances 1 and 2 fall in first distance
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313 bin, atom pairs with distances 3 and 4 fall in second distance bin and so on.</p>
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314 <p>In order to distribute distance bins of equal size, the last bin is allowed to go past <strong>--MaxDistance</strong>
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315 by up to distance bin size. For example, <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> values of 2 and 10
|
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316 with <strong>--DistanceBinSize</strong> of 2 generates the following 6 distance bins:</p>
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317 <div class="OptionsBox">
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318 [2, 3] [4, 5] [6, 7] [8, 9] [10 11]</div>
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319 </dd>
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320 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
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321 <dd>
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322 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
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323 Default value: <em>Yes</em>.</p>
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324 <p>By default, compound data is checked before calculating fingerprints and compounds containing
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325 atom data corresponding to non-element symbols or no atom data are ignored.</p>
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326 </dd>
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327 <dt><strong><strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em></strong></dt>
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328 <dd>
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329 <p>Specify how fingerprints label is generated in conjunction with <strong>--FingerprintsLabel</strong> option value:
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330 use fingerprints label generated only by <strong>--FingerprintsLabel</strong> option value or append topological
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331 atom pair count value IDs to <strong>--FingerprintsLabel</strong> option value.</p>
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332 <p>Possible values: <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>. Default value:
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333 <em>FingerprintsLabelOnly</em>.</p>
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334 <p>Topological atom pairs IDs appended to <strong>--FingerprintsLabel</strong> value during <em>FingerprintsLabelWithIDs</em>
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335 values of <strong>--FingerprintsLabelMode</strong> correspond to atom pair count values in fingerprint vector string.</p>
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336 <p><em>FingerprintsLabelWithIDs</em> value of <strong>--FingerprintsLabelMode</strong> is ignored during <em>ArbitrarySize</em> value
|
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337 of <strong>--AtomTripletsSetSizeToUse</strong> option and topological atom triplets IDs not appended to the label.</p>
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338 </dd>
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339 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
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340 <dd>
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341 <p>SD data label or text file column label to use for fingerprints string in output SD or
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342 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.</p>
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343 </dd>
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344 <dt><strong><strong>-h, --help</strong></strong></dt>
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345 <dd>
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346 <p>Print this help message.</p>
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347 </dd>
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348 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
|
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349 <dd>
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350 <p>Generate fingerprints for only the largest component in molecule. Possible values:
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351 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
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352 <p>For molecules containing multiple connected components, fingerprints can be generated
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353 in two different ways: use all connected components or just the largest connected
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354 component. By default, all atoms except for the largest connected component are
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355 deleted before generation of fingerprints.</p>
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356 </dd>
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357 <dt><strong><strong>--MinDistance</strong> <em>number</em></strong></dt>
|
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358 <dd>
|
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359 <p>Minimum bond distance between atom pairs corresponding to atom triplets for generating
|
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360 topological pharmacophore atom triplets. Default value: <em>1</em>. Valid values: positive integers and
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361 less than <strong>--MaxDistance</strong>.</p>
|
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362 </dd>
|
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363 <dt><strong><strong>--MaxDistance</strong> <em>number</em></strong></dt>
|
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364 <dd>
|
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365 <p>Maximum bond distance between atom pairs corresponding to atom triplets for generating
|
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366 topological pharmacophore atom triplets. Default value: <em>10</em>. Valid values: positive integers and
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367 greater than <strong>--MinDistance</strong>.</p>
|
|
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368 </dd>
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|
369 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
|
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370 <dd>
|
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371 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
|
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372 Default value: <em>comma</em>.</p>
|
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|
373 </dd>
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374 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
|
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375 <dd>
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376 <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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377 </dd>
|
|
|
378 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
|
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379 <dd>
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380 <p>Overwrite existing files.</p>
|
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381 </dd>
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382 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
|
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383 <dd>
|
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384 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
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385 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
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386 </dd>
|
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|
387 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
|
|
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388 <dd>
|
|
|
389 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file names:
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|
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390 <SDFileName><TopologicalPharmacophoreAtomTripletsFP>.<Ext>. The file type determines <Ext> value.
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|
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391 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
|
|
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392 delimited text files, respectively.This option is ignored for multiple input files.</p>
|
|
|
393 </dd>
|
|
|
394 <dt><strong><strong>-u, --UseTriangleInequality</strong> <em>Yes | No</em></strong></dt>
|
|
|
395 <dd>
|
|
|
396 <p>Specify whether to imply triangle distance inequality test to distances between atom pairs in
|
|
|
397 atom triplets during generation of atom triplets basis set generation. Possible values:
|
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398 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
|
399 <p>Triangle distance inequality test implies that distance or binned distance between any two atom
|
|
|
400 pairs in an atom triplet must be less than the sum of distances or binned distances between other
|
|
|
401 two atoms pairs and greater than the difference of their distances.</p>
|
|
|
402 <div class="OptionsBox">
|
|
|
403 For atom triplet PxDyz-PyDxz-PzDxy to satisfy triangle inequality:</div>
|
|
|
404 <div class="OptionsBox">
|
|
|
405 Dyz > |Dxz - Dxy| and Dyz < Dxz + Dxy
|
|
|
406 <br/> Dxz > |Dyz - Dxy| and Dyz < Dyz + Dxy
|
|
|
407 <br/> Dxy > |Dyz - Dxz| and Dxy < Dyz + Dxz</div>
|
|
|
408 </dd>
|
|
|
409 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
|
|
|
410 <dd>
|
|
|
411 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
412 <strong>--output</strong> option. Possible values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString |
|
|
|
413 ValuesAndIDsString | ValuesAndIDsPairsString</em>. Defaultvalue: <em>ValuesString</em>.</p>
|
|
|
414 <p>Default value during <em>FixedSize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option: <em>ValuesString</em>. Default
|
|
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415 value during <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option: <em>IDsAndValuesString</em>.</p>
|
|
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416 <p><em>ValuesString</em> option value is not allowed for <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong>
|
|
|
417 option.</p>
|
|
|
418 <p>Examples:</p>
|
|
|
419 <div class="OptionsBox">
|
|
|
420 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
|
|
|
421 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
|
|
|
422 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
|
|
|
423 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
|
|
|
424 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
|
|
|
425 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
|
|
|
426 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
|
|
|
427 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
|
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|
428 <div class="OptionsBox">
|
|
|
429 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
|
|
|
430 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
|
|
|
431 <br/> 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
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|
432 <br/> 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
|
|
|
433 <br/> 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
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|
|
434 <br/> 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...</div>
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|
435 <div class="OptionsBox">
|
|
|
436 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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|
|
437 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesAndIDsPairsSt
|
|
|
438 <br/> ring;46 Ar1-Ar1-Ar1 106 Ar1-Ar1-H1 8 Ar1-Ar1-HBA1 3 Ar1-Ar1-HBD1 0 Ar1
|
|
|
439 <br/> -Ar1-NI1 0 Ar1-Ar1-PI1 83 Ar1-H1-H1 11 Ar1-H1-HBA1 4 Ar1-H1-HBD1 0 Ar1
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|
|
440 <br/> -H1-NI1 0 Ar1-H1-PI1 0 Ar1-HBA1-HBA1 1 Ar1-HBA1-HBD1 0 Ar1-HBA1-NI1 0
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|
|
441 <br/> Ar1-HBA1-PI1 0 Ar1-HBD1-HBD1 0 Ar1-HBD1-NI1 0 Ar1-HBD1-PI1 0 Ar1-NI...</div>
|
|
|
442 </dd>
|
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|
443 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
|
|
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444 <dd>
|
|
|
445 <p>Location of working directory. Default value: current directory.</p>
|
|
|
446 </dd>
|
|
|
447 </dl>
|
|
|
448 <p>
|
|
|
449 </p>
|
|
|
450 <h2>EXAMPLES</h2>
|
|
|
451 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
452 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
453 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
|
|
|
454 with fingerprints vector strings data in ValuesString format, type:</p>
|
|
|
455 <div class="ExampleBox">
|
|
|
456 % TopologicalPharmacophoreAtomTripletsFingerprints.pl -r SampleTPATFP
|
|
|
457 -o Sample.sdf</div>
|
|
|
458 <p>To generate topological pharmacophore atom triplets fingerprints of fixed size corresponding to 5
|
|
|
459 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
460 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
|
|
|
461 with fingerprints vector strings data in ValuesString format, type:</p>
|
|
|
462 <div class="ExampleBox">
|
|
|
463 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
464 --AtomTripletsSetSizeToUse FixedSize -r SampleTPATFP -o Sample.sdf</div>
|
|
|
465 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
466 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
467 inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files with CSV file containing
|
|
|
468 sequential compound IDs along with fingerprints vector strings data in ValuesString format, type:</p>
|
|
|
469 <div class="ExampleBox">
|
|
|
470 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --output all
|
|
|
471 -r SampleTPATFP -o Sample.sdf</div>
|
|
|
472 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
473 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
474 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
|
|
|
475 with fingerprints vector strings data in ValuesString format and atom triplets IDs in the
|
|
|
476 fingerprint data column label starting with Fingerprints, type:</p>
|
|
|
477 <div class="ExampleBox">
|
|
|
478 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
479 --FingerprintsLabelMode FingerprintsLabelWithIDs --FingerprintsLabel
|
|
|
480 Fingerprints -r SampleTPATFP -o Sample.sdf</div>
|
|
|
481 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
482 distance bins spanning distances from 1 through 10 using default atoms with distances not satisfying triangle
|
|
|
483 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
|
|
|
484 with fingerprints vector strings data in ValuesString format, type:</p>
|
|
|
485 <div class="ExampleBox">
|
|
|
486 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
487 --UseTriangleInequality No -r SampleTPATFP -o Sample.sdf</div>
|
|
|
488 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6
|
|
|
489 distance bins spanning distances from 1 through 12 using default atoms with distances satisfying triangle
|
|
|
490 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
|
|
|
491 with fingerprints vector strings data in ValuesString format, type:</p>
|
|
|
492 <div class="ExampleBox">
|
|
|
493 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
494 --UseTriangleInequality Yes --MinDistance 1 --MaxDistance 12
|
|
|
495 --DistanceBinSIze 2 -r SampleTPATFP -o Sample.sdf</div>
|
|
|
496 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6
|
|
|
497 distance bins spanning distances from 1 through 12 using "HBD,HBA,PI, NI, H, Ar" atoms with distances
|
|
|
498 satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound
|
|
|
499 IDs along with fingerprints vector strings data in ValuesString format, type:</p>
|
|
|
500 <div class="ExampleBox">
|
|
|
501 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
502 --AtomTypesToUse "HBD,HBA,PI,NI,H,Ar" --UseTriangleInequality Yes
|
|
|
503 --MinDistance 1 --MaxDistance 12 --DistanceBinSIze 2
|
|
|
504 --VectorStringFormat ValuesString -r SampleTPATFP -o Sample.sdf</div>
|
|
|
505 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
506 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
507 inequality and create a SampleTPATFP.csv file containing sequential compound IDs from
|
|
|
508 molecule name line along with fingerprints vector strings data in ValuesString format, type:</p>
|
|
|
509 <div class="ExampleBox">
|
|
|
510 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
|
|
|
511 CompoundID -CompoundIDMode MolName -r SampleTPATFP -o Sample.sdf</div>
|
|
|
512 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
513 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
514 inequality and create a SampleTPATFP.csv file containing sequential compound IDs using
|
|
|
515 specified data field along with fingerprints vector strings data in ValuesString format, type:</p>
|
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516 <div class="ExampleBox">
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517 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
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518 CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
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519 -r SampleTPATFP -o Sample.sdf</div>
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520 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
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521 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
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522 inequality and create a SampleTPATFP.csv file containing sequential compound IDs using
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523 combination of molecule name line and an explicit compound prefix along with fingerprints vector
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524 strings data, type:</p>
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525 <div class="ExampleBox">
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526 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
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527 CompoundID -CompoundIDMode MolnameOrLabelPrefix
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528 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleSampleTPATFP
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529 -o Sample.sdf</div>
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530 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
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531 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
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532 inequality and create a SampleTPATFP.csv file containing specific data fields columns along
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533 with fingerprints vector strings data, type:</p>
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534 <div class="ExampleBox">
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535 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
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536 Specify --DataFields Mol_ID -r SampleTPATFP -o Sample.sdf</div>
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537 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
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538 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
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539 inequality and create a SampleTPATFP.csv file containing common data fields columns along
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540 with fingerprints vector strings data, type:</p>
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541 <div class="ExampleBox">
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542 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
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543 Common -r SampleTPATFP -o Sample.sdf</div>
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544 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
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545 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
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546 inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files containing all
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547 data fields columns in CSV file along with fingerprints data, type:</p>
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548 <div class="ExampleBox">
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549 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
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550 All --output all -r SampleTPATFP -o Sample.sdf</div>
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551 <p>
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552 </p>
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553 <h2>AUTHOR</h2>
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554 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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555 <p>
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556 </p>
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557 <h2>SEE ALSO</h2>
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558 <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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559 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>, 
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560 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>, 
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561 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>
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562 </p>
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563 <p>
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564 </p>
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565 <h2>COPYRIGHT</h2>
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566 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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567 <p>This file is part of MayaChemTools.</p>
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568 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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569 the terms of the GNU Lesser General Public License as published by the Free
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570 Software Foundation; either version 3 of the License, or (at your option)
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571 any later version.</p>
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572 <p> </p><p> </p><div class="DocNav">
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573 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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574 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./EndPage.html" title="EndPage.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalPharmacophoreAtomTripletsFingerprints.pl</strong></td></tr>
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575 </table>
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576 </div>
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577 <br />
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578 <center>
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579 <img src="../../images/h2o2.png">
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580 </center>
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581 </body>
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582 </html>
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