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3 <title>MayaChemTools:Documentation:TopologicalPharmacophoreAtomPairsFingerprints.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="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalPharmacophoreAtomPairsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalPharmacophoreAtomPairsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalPharmacophoreAtomPairsFingerprints.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>TopologicalPharmacophoreAtomPairsFingerprints.pl - Generate topological pharmacophore atom pairs fingerprints for SD files</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>TopologicalPharmacophoreAtomPairsFingerprints.pl SDFile(s)...</p>
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26 <p>TopologicalPharmacophoreAtomPairsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
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27 [<strong>--AtomPairsSetSizeToUse</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>-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>--FuzzifyAtomPairsCount</strong> <em>Yes | No</em>] [<strong>--FuzzificationMode</strong> <em>FuzzyBinning | FuzzyBinSmoothing</em>]
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35 [<strong>--FuzzificationMethodology</strong> <em>FuzzyBinning | FuzzyBinSmoothing</em>] [<strong>--FuzzFactor</strong> <em>number</em>]
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36 [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>] [<strong>--MinDistance</strong> <em>number</em>]
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37 [<strong>--MaxDistance</strong> <em>number</em>] [<strong>-n, --NormalizationMethodology</strong> <em>None | ByHeavyAtomsCount | ByAtomTypesCount</em>]
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38 [<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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39 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>--ValuesPrecision</strong> <em>number</em>]
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40 [<strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>]
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41 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
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42 <p>
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43 </p>
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44 <h2>DESCRIPTION</h2>
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45 <p>Generate topological pharmacophore atom pairs fingerprints [ Ref 60-62, Ref 65, Ref 68 ] for
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46 <em>SDFile(s)</em> and create appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector
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47 strings corresponding to molecular fingerprints.</p>
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48 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
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49 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
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50 can be specified either by <em>*.sdf</em> or the current directory name.</p>
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51 <p>Based on the values specified for <strong>--AtomTypesToUse</strong>, pharmacophore atom types are
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52 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
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53 A pharmacophore atom pairs basis set is initialized for all unique possible pairs within
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54 <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> range.</p>
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55 <div class="OptionsBox">
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56 Let:</div>
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57 <div class="OptionsBox">
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58 P = Valid pharmacophore atom type</div>
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59 <div class="OptionsBox">
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60 Px = Pharmacophore atom type x
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61 <br/> Py = Pharmacophore atom type y</div>
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62 <div class="OptionsBox">
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63 Dmin = Minimum distance corresponding to number of bonds between
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64 two atoms
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65 <br/> Dmax = Maximum distance corresponding to number of bonds between
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66 two atoms
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67 <br/> D = Distance corresponding to number of bonds between two atoms</div>
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68 <div class="OptionsBox">
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69 Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at
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70 distance Dn</div>
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71 <div class="OptionsBox">
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72 P = Number of pharmacophore atom types to consider
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73 <br/> PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn</div>
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74 <div class="OptionsBox">
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75 PPT = Total number of possible pharmacophore atom pairs at all distances
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76 between Dmin and Dmax</div>
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77 <div class="OptionsBox">
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78 Then:</div>
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79 <div class="OptionsBox">
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80 PPD = (P * (P - 1))/2 + P</div>
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81 <div class="OptionsBox">
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82 PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P)
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83 <br/> = ((Dmax - Dmin) + 1) * PPD</div>
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84 <div class="OptionsBox">
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85 So for default values of Dmin = 1, Dmax = 10 and P = 5,</div>
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86 <div class="OptionsBox">
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87 PPD = (5 * (5 - 1))/2 + 5 = 15
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88 <br/> PPT = ((10 - 1) + 1) * 15 = 150</div>
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89 <div class="OptionsBox">
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90 The pharmacophore atom pairs bais set includes 150 values.</div>
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91 <div class="OptionsBox">
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92 The atom pair IDs correspond to:</div>
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93 <div class="OptionsBox">
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94 Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at
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95 distance Dn</div>
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96 <div class="OptionsBox">
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97 For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on</div>
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98 <p>Using distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom
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99 pairs is counted. The contribution of each atom type to atom pair interaction is optionally
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100 weighted by specified <strong>--AtomTypesWeight</strong> before assigning its count to appropriate distance
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101 bin. Based on <strong>--NormalizationMethodology</strong> option, pharmacophore atom pairs count is optionally
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102 normalized. Additionally, pharmacohore atom pairs count is optionally fuzzified before or after
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103 the normalization controlled by values of <strong>--FuzzifyAtomPairsCount</strong>, <strong>--FuzzificationMode</strong>,
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104 <strong>--FuzzificationMethodology</strong> and <strong>--FuzzFactor</strong> options.</p>
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105 <p>The final pharmacophore atom pairs count along with atom pair identifiers involving all non-hydrogen
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106 atoms, with optional normalization and fuzzification, constitute pharmacophore topological atom pairs
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107 fingerprints of the molecule.</p>
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108 <p>For <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option, the fingerprint vector correspond to
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109 only those topological pharmacophore atom pairs which are present and have non-zero count. However,
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110 for <em>FixedSize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option, the fingerprint vector contains all possible
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111 valid topological pharmacophore atom pairs with both zero and non-zero count values.</p>
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112 <p>Example of <em>SD</em> file containing topological pharmacophore atom pairs fingerprints string data:</p>
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113 <div class="OptionsBox">
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114 ... ...
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115 <br/> ... ...
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116 <br/> $$$$
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117 <br/> ... ...
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118 <br/> ... ...
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119 <br/> ... ...
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120 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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121 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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122 <br/> ... ...
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123 <br/> 2 3 1 0 0 0 0
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124 <br/> ... ...
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125 <br/> M END
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126 <br/> > <CmpdID>
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127 <br/> Cmpd1</div>
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128 <div class="OptionsBox">
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129 > <TopologicalPharmacophoreAtomPairsFingerprints>
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130 <br/> FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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131 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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132 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
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133 <br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D...;
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134 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3
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135 <br/> 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
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136 <div class="OptionsBox">
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137 $$$$
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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 pairs 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 15:32:48 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 = TopologicalPharmacophoreAtomPairs:ArbitrarySize:MinDistance1:MaxDistance10
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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 54;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;18 1 2...
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155 <br/> Cmpd2 61;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;5 1 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 pairs fingerprints string data:</p>
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159 <div class="OptionsBox">
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160 "CompoundID","TopologicalPharmacophoreAtomPairsFingerprints"
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161 <br/> "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomPairs:Arbitrary
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162 <br/> Size:MinDistance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H
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163 <br/> -D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA H
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164 <br/> BA-D2-HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4...;
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165 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3
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166 <br/> 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1"
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167 <br/> ... ...
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168 <br/> ... ...</div>
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169 <p>The current release of MayaChemTools generates the following types of topological pharmacophore
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170 atom pairs fingerprints vector strings:</p>
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171 <div class="OptionsBox">
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172 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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173 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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174 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
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175 <br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
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176 <br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
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177 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
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178 <br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
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179 <div class="OptionsBox">
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180 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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181 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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182 <br/> 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
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183 <br/> 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
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184 <br/> 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
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185 <br/> 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...</div>
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186 <div class="OptionsBox">
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187 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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188 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1
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189 <br/> -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H
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190 <br/> BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D
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191 <br/> 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...;
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192 <br/> 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
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193 <br/> 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
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194 <br/> 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0</div>
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195 <p>
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196 </p>
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197 <h2>OPTIONS</h2>
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198 <dl>
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199 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
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200 <dd>
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201 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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202 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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203 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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204 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
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205 <p>The supported aromaticity model names along with model specific control parameters
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206 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
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207 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
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208 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
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209 for detecting aromaticity corresponding to a specific model.</p>
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210 </dd>
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211 <dt><strong><strong>--AtomPairsSetSizeToUse</strong> <em>ArbitrarySize | FixedSize</em></strong></dt>
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212 <dd>
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213 <p>Atom pairs set size to use during generation of topological pharmacophore atom pairs
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214 fingerprints.</p>
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215 <p>Possible values: <em>ArbitrarySize | FixedSize</em>; Default value: <em>ArbitrarySize</em>.</p>
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216 <p>For <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option, the fingerprint vector
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217 correspond to only those topological pharmacophore atom pairs which are present and
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218 have non-zero count. However, for <em>FixedSize</em> value of <strong>--AtomPairsSetSizeToUse</strong>
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219 option, the fingerprint vector contains all possible valid topological pharmacophore atom
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220 pairs with both zero and non-zero count values.</p>
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221 </dd>
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222 <dt><strong><strong>-a, --AtomTypesToUse</strong> <em>"AtomType1,AtomType2,..."</em></strong></dt>
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223 <dd>
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224 <p>Pharmacophore atom types to use during generation of topological phramacophore
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225 atom pairs. It's a list of comma separated valid pharmacophore atom types.</p>
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226 <p>Possible values for pharmacophore atom types are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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227 Default value [ Ref 60-62 ] : <em>HBD,HBA,PI,NI,H</em>.</p>
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228 <p>The pharmacophore atom types abbreviations correspond to:</p>
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229 <div class="OptionsBox">
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230 HBD: HydrogenBondDonor
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231 <br/> HBA: HydrogenBondAcceptor
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232 <br/> PI : PositivelyIonizable
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233 <br/> NI : NegativelyIonizable
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234 <br/> Ar : Aromatic
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235 <br/> Hal : Halogen
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236 <br/> H : Hydrophobic
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237 <br/> RA : RingAtom
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238 <br/> CA : ChainAtom</div>
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239 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign pharmacophore atom
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240 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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241 <div class="OptionsBox">
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242 HydrogenBondDonor: NH, NH2, OH
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243 <br/> HydrogenBondAcceptor: N[!H], O
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244 <br/> PositivelyIonizable: +, NH2
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245 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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246 </dd>
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247 <dt><strong><strong>--AtomTypesWeight</strong> <em>"AtomType1,Weight1,AtomType2,Weight2..."</em></strong></dt>
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248 <dd>
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249 <p>Weights of specified pharmacophore atom types to use during calculation of their contribution
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250 to atom pair count. Default value: <em>None</em>. Valid values: real numbers greater than 0. In general
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251 it's comma delimited list of valid atom type and its weight.</p>
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252 <p>The weight values allow to increase the importance of specific pharmacophore atom type
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253 in the generated fingerprints. A weight value of 0 for an atom type eliminates its contribution to
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254 atom pair count where as weight value of 2 doubles its contribution.</p>
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255 </dd>
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256 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
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257 <dd>
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258 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
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259 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
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260 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
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261 IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which
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262 look like Cmpd<Number>.</p>
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263 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
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264 <div class="OptionsBox">
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265 MolID
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266 <br/> ExtReg</div>
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267 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
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268 <div class="OptionsBox">
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269 Compound</div>
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270 <p>The value specified above generates compound IDs which correspond to Compound<Number>
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271 instead of default value of Cmpd<Number>.</p>
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272 </dd>
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273 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
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274 <dd>
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275 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
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276 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
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277 </dd>
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278 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
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279 <dd>
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280 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
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281 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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282 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
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283 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
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284 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
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285 Default value: <em>LabelPrefix</em>.</p>
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286 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
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287 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
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288 values are replaced with sequential compound IDs.</p>
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289 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
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290 </dd>
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291 <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt>
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292 <dd>
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293 <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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294 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
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295 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
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296 <p>Examples:</p>
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297 <div class="OptionsBox">
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298 Extreg
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299 <br/> MolID,CompoundName</div>
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300 </dd>
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301 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
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302 <dd>
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303 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
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304 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
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305 data field; transfer SD data files common to all compounds; extract specified data fields;
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306 generate a compound ID using molname line, a compound prefix, or a combination of both.
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307 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
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308 </dd>
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309 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
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310 <dd>
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311 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
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312 Default value: <em>Yes</em>.</p>
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313 <p>By default, compound data is checked before calculating fingerprints and compounds containing
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314 atom data corresponding to non-element symbols or no atom data are ignored.</p>
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315 </dd>
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316 <dt><strong><strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em></strong></dt>
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317 <dd>
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318 <p>Specify how fingerprints label is generated in conjunction with <strong>--FingerprintsLabel</strong> option value:
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319 use fingerprints label generated only by <strong>--FingerprintsLabel</strong> option value or append topological
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320 atom pair count value IDs to <strong>--FingerprintsLabel</strong> option value.</p>
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321 <p>Possible values: <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>. Default value:
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322 <em>FingerprintsLabelOnly</em>.</p>
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323 <p>Topological atom pairs IDs appended to <strong>--FingerprintsLabel</strong> value during <em>FingerprintsLabelWithIDs</em>
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324 values of <strong>--FingerprintsLabelMode</strong> correspond to atom pair count values in fingerprint vector string.</p>
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325 <p><em>FingerprintsLabelWithIDs</em> value of <strong>--FingerprintsLabelMode</strong> is ignored during <em>ArbitrarySize</em> value
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326 of <strong>--AtomPairsSetSizeToUse</strong> option and topological atom pairs IDs not appended to the label.</p>
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327 </dd>
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328 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
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329 <dd>
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330 <p>SD data label or text file column label to use for fingerprints string in output SD or
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331 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>TopologicalPharmacophoreAtomPairsFingerprints</em>.</p>
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332 </dd>
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333 <dt><strong><strong>--FuzzifyAtomPairsCount</strong> <em>Yes | No</em></strong></dt>
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334 <dd>
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335 <p>To fuzzify or not to fuzzify atom pairs count. Possible values: <em>Yes or No</em>. Default value:
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336 <em>No</em>.</p>
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337 </dd>
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338 <dt><strong><strong>--FuzzificationMode</strong> <em>BeforeNormalization | AfterNormalization</em></strong></dt>
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339 <dd>
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340 <p>When to fuzzify atom pairs count. Possible values: <em>BeforeNormalization | AfterNormalizationYes</em>.
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341 Default value: <em>AfterNormalization</em>.</p>
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342 </dd>
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343 <dt><strong><strong>--FuzzificationMethodology</strong> <em>FuzzyBinning | FuzzyBinSmoothing</em></strong></dt>
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344 <dd>
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345 <p>How to fuzzify atom pairs count. Possible values: <em>FuzzyBinning | FuzzyBinSmoothing</em>.
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346 Default value: <em>FuzzyBinning</em>.</p>
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347 <p>In conjunction with values for options <strong>--FuzzifyAtomPairsCount</strong>, <strong>--FuzzificationMode</strong> and
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348 <strong>--FuzzFactor</strong>, <strong>--FuzzificationMethodology</strong> option is used to fuzzify pharmacophore atom
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349 pairs count.</p>
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350 <p>Let:</p>
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351 <div class="OptionsBox">
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352 Px = Pharmacophore atom type x
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353 <br/> Py = Pharmacophore atom type y
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354 <br/> PPxy = Pharmacophore atom pair between atom type Px and Py</div>
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355 <div class="OptionsBox">
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356 PPxyDn = Pharmacophore atom pairs count between atom type Px and Py
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357 at distance Dn
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358 <br/> PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py
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359 at distance Dn - 1
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360 <br/> PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py
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361 at distance Dn + 1</div>
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362 <div class="OptionsBox">
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363 FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing</div>
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364 <p>Then:</p>
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365 <p>For <em>FuzzyBinning</em>:</p>
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366 <div class="OptionsBox">
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367 PPxyDn = PPxyDn (Unchanged)</div>
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368 <div class="OptionsBox">
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369 PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
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370 <br/> PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</div>
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371 <p>For <em>FuzzyBinSmoothing</em>:</p>
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372 <div class="OptionsBox">
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373 PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax
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374 <br/> PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax</div>
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375 <div class="OptionsBox">
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376 PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
|
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377 <br/> PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</div>
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|
|
378 <p>In both fuzzification schemes, a value of 0 for FF implies no fuzzification of occurrence counts.
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379 A value of 1 during <em>FuzzyBinning</em> corresponds to maximum fuzzification of occurrence counts;
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380 however, a value of 1 during <em>FuzzyBinSmoothing</em> ends up completely distributing the value over
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381 the previous and next distance bins.</p>
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382 <p>So for default value of <strong>--FuzzFactor</strong> (FF) 0.15, the occurrence count of pharmacohore atom pairs
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383 at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn -1 and Dn + 1
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384 are incremented by PPxyDn * 0.15.</p>
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385 <p>And during <em>FuzzyBinSmoothing</em> the occurrence counts at Distance Dn is scaled back using multiplicative
|
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386 factor of (1 - 2*0.15) and the occurrence counts at distances Dn -1 and Dn + 1 are incremented by
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387 PPxyDn * 0.15. In otherwords, occurrence bin count is smoothed out by distributing it over the
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388 previous and next distance value.</p>
|
|
|
389 </dd>
|
|
|
390 <dt><strong><strong>--FuzzFactor</strong> <em>number</em></strong></dt>
|
|
|
391 <dd>
|
|
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392 <p>Specify by how much to fuzzify atom pairs count. Default value: <em>0.15</em>. Valid values: For
|
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393 <em>FuzzyBinning</em> value of <strong>--FuzzificationMethodology</strong> option: <em>between 0 and 1.0</em>; For
|
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394 <em>FuzzyBinSmoothing</em> value of <strong>--FuzzificationMethodology</strong> option: <em>between 0 and 0.5</em>.</p>
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|
|
395 </dd>
|
|
|
396 <dt><strong><strong>-h, --help</strong></strong></dt>
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397 <dd>
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398 <p>Print this help message.</p>
|
|
|
399 </dd>
|
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400 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
|
|
|
401 <dd>
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|
402 <p>Generate fingerprints for only the largest component in molecule. Possible values:
|
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403 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
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|
|
404 <p>For molecules containing multiple connected components, fingerprints can be generated
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|
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405 in two different ways: use all connected components or just the largest connected
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|
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406 component. By default, all atoms except for the largest connected component are
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407 deleted before generation of fingerprints.</p>
|
|
|
408 </dd>
|
|
|
409 <dt><strong><strong>--MinDistance</strong> <em>number</em></strong></dt>
|
|
|
410 <dd>
|
|
|
411 <p>Minimum bond distance between atom pairs for generating topological pharmacophore atom
|
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412 pairs. Default value: <em>1</em>. Valid values: positive integers including 0 and less than <strong>--MaxDistance</strong>.</p>
|
|
|
413 </dd>
|
|
|
414 <dt><strong><strong>--MaxDistance</strong> <em>number</em></strong></dt>
|
|
|
415 <dd>
|
|
|
416 <p>Maximum bond distance between atom pairs for generating topological pharmacophore atom
|
|
|
417 pairs. Default value: <em>10</em>. Valid values: positive integers and greater than <strong>--MinDistance</strong>.</p>
|
|
|
418 </dd>
|
|
|
419 <dt><strong><strong>-n, --NormalizationMethodology</strong> <em>None | ByHeavyAtomsCount | ByAtomTypesCount</em></strong></dt>
|
|
|
420 <dd>
|
|
|
421 <p>Normalization methodology to use for scaling the occurrence count of pharmacophore atom
|
|
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422 pairs within specified distance range. Possible values: <em>None, ByHeavyAtomsCount or
|
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423 ByAtomTypesCount</em>. Default value: <em>None</em>.</p>
|
|
|
424 </dd>
|
|
|
425 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
|
|
|
426 <dd>
|
|
|
427 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
|
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|
428 Default value: <em>comma</em>.</p>
|
|
|
429 </dd>
|
|
|
430 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
|
|
|
431 <dd>
|
|
|
432 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
|
|
|
433 </dd>
|
|
|
434 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
|
|
|
435 <dd>
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|
436 <p>Overwrite existing files.</p>
|
|
|
437 </dd>
|
|
|
438 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
|
|
|
439 <dd>
|
|
|
440 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
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441 <em>Yes or No</em>. Default value: <em>Yes</em></p>
|
|
|
442 </dd>
|
|
|
443 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
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|
444 <dd>
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|
|
445 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file names:
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446 <SDFileName><TopologicalPharmacophoreAtomPairsFP>.<Ext>. The file type determines <Ext> value.
|
|
|
447 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
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448 delimited text files, respectively.This option is ignored for multiple input files.</p>
|
|
|
449 </dd>
|
|
|
450 <dt><strong><strong>--ValuesPrecision</strong> <em>number</em></strong></dt>
|
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|
451 <dd>
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452 <p>Precision of atom pairs count real values which might be generated after normalization
|
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453 or fuzzification. Default value: up to <em>2</em> decimal places. Valid values: positive integers.</p>
|
|
|
454 </dd>
|
|
|
455 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
|
|
|
456 <dd>
|
|
|
457 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
458 <strong>--output</strong> option. Possible values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString
|
|
|
459 | ValuesAndIDsString | ValuesAndIDsPairsString</em>.</p>
|
|
|
460 <p>Default value during <em>FixedSize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option: <em>ValuesString</em>. Default
|
|
|
461 value during <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option: <em>IDsAndValuesString</em>.</p>
|
|
|
462 <p><em>ValuesString</em> option value is not allowed for <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong>
|
|
|
463 option.</p>
|
|
|
464 <p>Examples:</p>
|
|
|
465 <div class="OptionsBox">
|
|
|
466 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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|
|
467 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
|
|
|
468 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
|
|
|
469 <br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
|
|
|
470 <br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
|
|
|
471 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
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|
472 <br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
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|
473 <div class="OptionsBox">
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|
474 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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|
|
475 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
|
|
|
476 <br/> 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
|
|
|
477 <br/> 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
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|
478 <br/> 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
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|
479 <br/> 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...</div>
|
|
|
480 <div class="OptionsBox">
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|
|
481 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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|
|
482 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1
|
|
|
483 <br/> -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H
|
|
|
484 <br/> BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D
|
|
|
485 <br/> 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...;
|
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|
486 <br/> 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
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|
|
487 <br/> 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
|
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|
488 <br/> 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0</div>
|
|
|
489 </dd>
|
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|
490 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
|
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|
491 <dd>
|
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|
492 <p>Location of working directory. Default value: current directory.</p>
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|
|
493 </dd>
|
|
|
494 </dl>
|
|
|
495 <p>
|
|
|
496 </p>
|
|
|
497 <h2>EXAMPLES</h2>
|
|
|
498 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
|
|
|
499 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
|
|
|
500 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
|
|
|
501 with fingerprints vector strings data in ValuesString format, type:</p>
|
|
|
502 <div class="ExampleBox">
|
|
|
503 % TopologicalPharmacophoreAtomPairsFingerprints.pl -r SampleTPAPFP
|
|
|
504 -o Sample.sdf</div>
|
|
|
505 <p>To generate topological pharmacophore atom pairs fingerprints of fixed size corresponding to distances
|
|
|
506 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
|
|
|
507 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
|
|
|
508 with fingerprints vector strings data in ValuesString format, type:</p>
|
|
|
509 <div class="ExampleBox">
|
|
|
510 % TopologicalPharmacophoreAtomPairsFingerprints.pl
|
|
|
511 --AtomPairsSetSizeToUse FixedSize -r SampleTPAPFP-o Sample.sdf</div>
|
|
|
512 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
|
|
|
513 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
|
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514 of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf and SampleTPAPFP.csv files containing
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515 sequential compound IDs in CSV file along with fingerprints vector strings data in ValuesString
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516 format, type:</p>
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517 <div class="ExampleBox">
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518 % TopologicalPharmacophoreAtomPairsFingerprints.pl --output all
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519 -r SampleTPAPFP -o Sample.sdf</div>
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520 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
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521 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
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522 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
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523 with fingerprints vector strings data in IDsAndValuesPairsString format, type:</p>
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524 <div class="ExampleBox">
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525 % TopologicalPharmacophoreAtomPairsFingerprints.pl --VectorStringFormat
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526 IDsAndValuesPairsString -r SampleTPAPFP -o Sample.sdf</div>
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527 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
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528 from 1 through 6 using default atom types with no weighting, normalization, and fuzzification
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529 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
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530 with fingerprints vector strings data in ValuesString format, type:</p>
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531 <div class="ExampleBox">
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532 % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
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533 -MaxDistance 6 -r SampleTPAPFP -o Sample.sdf</div>
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534 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
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535 from 1 through 10 using "HBD,HBA,PI,NI" atom types with double the weighting for "HBD,HBA" and
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536 normalization by HeavyAtomCount but no fuzzification of atom pairs count and create a
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537 SampleTPAPFP.csv file containing sequential compound IDs along with fingerprints vector strings
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538 data in ValuesString format, type:</p>
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539 <div class="ExampleBox">
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540 % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
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541 -MaxDistance 10 --AtomTypesToUse "HBD,HBA,PI, NI" --AtomTypesWeight
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542 "HBD,2,HBA,2,PI,1,NI,1" --NormalizationMethodology ByHeavyAtomsCount
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543 --FuzzifyAtomPairsCount No -r SampleTPAPFP -o Sample.sdf</div>
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544 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to
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545 distances from 1 through 10 using "HBD,HBA,PI,NI,H" atom types with no weighting of atom types and
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546 normalization but with fuzzification of atom pairs count using FuzzyBinning methodology
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547 with FuzzFactor value 0.15 and create a SampleTPAPFP.csv file containing sequential compound
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548 IDs along with fingerprints vector strings data in ValuesString format, type:</p>
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549 <div class="ExampleBox">
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550 % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
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551 --MaxDistance 10 --AtomTypesToUse "HBD,HBA,PI, NI,H" --AtomTypesWeight
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552 "HBD,1,HBA,1,PI,1,NI,1,H,1" --NormalizationMethodology None
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553 --FuzzifyAtomPairsCount Yes --FuzzificationMethodology FuzzyBinning
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554 --FuzzFactor 0.5 -r SampleTPAPFP -o Sample.sdf</div>
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555 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
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556 distances from 1 through 10 using default atom types with no weighting,
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557 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
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558 file containing compound ID from molecule name line along with fingerprints vector strings
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559 data, type:</p>
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560 <div class="ExampleBox">
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561 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
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562 CompoundID -CompoundIDMode MolName -r SampleTPAPFP -o Sample.sdf</div>
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563 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
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564 to distances from 1 through 10 using default atom types with no weighting,
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565 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
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566 file containing compound IDs using specified data field along with fingerprints vector strings
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567 data, type:</p>
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568 <div class="ExampleBox">
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569 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
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570 CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
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571 -r SampleTPAPFP -o Sample.sdf</div>
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572 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
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573 to distances from 1 through 10 using default atom types with no weighting,
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574 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
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575 file containing compound ID using combination of molecule name line and an explicit compound
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576 prefix along with fingerprints vector strings data, type:</p>
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577 <div class="ExampleBox">
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578 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
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579 CompoundID -CompoundIDMode MolnameOrLabelPrefix
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580 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTPAPFP -o Sample.sdf</div>
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581 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
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582 to distances from 1 through 10 using default atom types with no weighting,
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583 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
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584 file containing specific data fields columns along with fingerprints vector strings
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585 data, type:</p>
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586 <div class="ExampleBox">
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587 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
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588 Specify --DataFields Mol_ID -r SampleTPAPFP -o Sample.sdf</div>
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589 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
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590 to distances from 1 through 10 using default atom types with no weighting,
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591 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
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592 file containing common data fields columns along with fingerprints vector strings
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593 data, type:</p>
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594 <div class="ExampleBox">
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595 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
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596 Common -r SampleTPAPFP -o Sample.sdf</div>
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597 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
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598 to distances from 1 through 10 using default atom types with no weighting,
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599 normalization, and fuzzification of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf,
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600 and SampleTPAPFP.csv files containing all data fields columns in CSV file along with fingerprints
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601 data, type:</p>
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602 <div class="ExampleBox">
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603 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
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604 All --output all -r SampleTPAPFP -o Sample.sdf</div>
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605 <p>
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606 </p>
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607 <h2>AUTHOR</h2>
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608 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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609 <p>
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610 </p>
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611 <h2>SEE ALSO</h2>
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612 <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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613 <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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614 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>, 
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615 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
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616 </p>
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617 <p>
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618 </p>
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619 <h2>COPYRIGHT</h2>
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620 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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621 <p>This file is part of MayaChemTools.</p>
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622 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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623 the terms of the GNU Lesser General Public License as published by the Free
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624 Software Foundation; either version 3 of the License, or (at your option)
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625 any later version.</p>
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626 <p> </p><p> </p><div class="DocNav">
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627 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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628 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalPharmacophoreAtomPairsFingerprints.pl</strong></td></tr>
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629 </table>
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630 </div>
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631 <br />
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632 <center>
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633 <img src="../../images/h2o2.png">
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634 </center>
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635 </body>
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636 </html>
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