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3 <title>MayaChemTools:Documentation:ExtendedConnectivityFingerprints.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="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtractFromPDBFiles.html" title="ExtractFromPDBFiles.html">Next</a></td><td width="34%" align="middle"><strong>ExtendedConnectivityFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/ExtendedConnectivityFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/ExtendedConnectivityFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ExtendedConnectivityFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ExtendedConnectivityFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ExtendedConnectivityFingerprints.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>ExtendedConnectivityFingerprints.pl - Generate extended connectivity 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>ExtendedConnectivityFingerprints.pl SDFile(s)...</p>
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26 <p>ExtendedConnectivityFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
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27 [<strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes</em>]
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28 [<strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em>]
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29 [<strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em>]
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30 [<strong>--BitsOrder</strong> <em>Ascending | Descending</em>] [<strong>-b, --BitStringFormat</strong> <em>BinaryString | HexadecimalString</em>]
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31 [<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>] [<strong>--CompoundIDLabel</strong> <em>text</em>]
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32 [<strong>--CompoundIDMode</strong>] [<strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em>]
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33 [<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>]
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34 [<strong>--FingerprintsLabel</strong> <em>text</em>] [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>]
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35 [<strong>-m, --mode</strong> <em>ExtendedConnectivity | ExtendedConnecticityCount | ExtendedConnecticityBits</em>]
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36 [<strong>-n, --NeighborhoodRadius</strong> <em>number</em>] [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>]
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37 [<strong>-o, --overwrite</strong>] [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-s, --size</strong> <em>number</em>]
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38 [<strong>--UsePerlCoreRandom</strong> <em>Yes | No</em>]
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39 [<strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>]
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40 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
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41 <p>
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42 </p>
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43 <h2>DESCRIPTION</h2>
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44 <p>Generate extended connectivity fingerprints [ Ref 48, Ref 52 ] for <em>SDFile(s)</em> and create appropriate
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45 SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to molecular fingerprints.</p>
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46 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
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47 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
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48 can be specified either by <em>*.sdf</em> or the current directory name.</p>
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49 <p>The current release of MayaChemTools supports generation of extended connectivity fingerprints
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50 corresponding to following <strong>-a, --AtomIdentifierTypes</strong>:</p>
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51 <div class="OptionsBox">
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52 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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53 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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54 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
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55 <p>Based on values specified for <strong>-a, --AtomIdentifierType</strong>, <strong>--AtomicInvariantsToUse</strong>
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56 and <strong>--FunctionalClassesToUse</strong>, initial atom types are assigned to all non-hydrogen atoms in
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57 a molecule and these atom types strings are converted into initial atom identifier integers using
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58 <strong>TextUtil::HashCode</strong> function. The duplicate atom identifiers are removed.</p>
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59 <p>For <strong>-n, --NeighborhoodRadius</strong> value of <em>0</em>, the initial set of unique atom identifiers comprises
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60 the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen
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61 atom up to specified <strong>-n, --NeighborhoodRadius</strong> value. For each non-hydrogen central atom
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62 at a specific radius, its neighbors at next radius level along with their bond orders and previously
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63 calculated atom identifiers are collected which in turn are used to generate a new integer
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64 atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order
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65 followed by atom identifiers to make these values graph invariant.</p>
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66 <p>After integer atom identifiers have been generated for all non-hydrogen atoms at all specified
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67 neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code
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68 value generated using <strong>TextUtil::HashCode</strong> are tracked by keeping the atom identifiers at
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69 lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified
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70 radius are also tracked by identifying equivalent atoms and bonds corresponding to substructures
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71 used for generating atom identifier and keeping integer atom identifier with lowest value.</p>
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72 <p>For <em>ExtendedConnnectivity</em> value of fingerprints <strong>-m, --mode</strong>, the duplicate identifiers are
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73 removed from the list and the unique atom identifiers constitute the extended connectivity
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74 fingerprints of a molecule.</p>
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75 <p>For <em>ExtendedConnnectivityCount</em> value of fingerprints <strong>-m, --mode</strong>, the occurrence of each
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76 unique atom identifiers appears is counted and the unique atom identifiers along with their
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77 count constitute the extended connectivity fingerprints of a molecule.</p>
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78 <p>For <em>ExtendedConnectivityBits</em> value of fingerprints <strong>-m, --mode</strong>, the unique atom identifiers
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79 are used as a random number seed to generate a random integer value between 0 and <strong>--Size</strong> which
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80 in turn is used to set corresponding bits in the fingerprint bit-vector string.</p>
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81 <p>Example of <em>SD</em> file containing extended connectivity fingerprints string data:</p>
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82 <div class="OptionsBox">
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83 ... ...
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84 <br/> ... ...
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85 <br/> $$$$
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86 <br/> ... ...
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87 <br/> ... ...
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88 <br/> ... ...
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89 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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90 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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91 <br/> ... ...
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92 <br/> 2 3 1 0 0 0 0
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93 <br/> ... ...
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94 <br/> M END
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95 <br/> > <CmpdID>
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96 <br/> Cmpd1</div>
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97 <div class="OptionsBox">
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98 > <ExtendedConnectivityFingerprints>
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99 <br/> FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radiu
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100 <br/> s2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 66
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101 <br/> 6191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414087
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102 <br/> 99 49532520 64643108 79385615 96062769 273726379 564565671 855141035 90
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103 <br/> 6706094 988546669 1018231313 1032696425 1197507444 1331250018 133853...</div>
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104 <div class="OptionsBox">
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105 $$$$
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106 <br/> ... ...
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107 <br/> ... ...</div>
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108 <p>Example of <em>FP</em> file containing extended connectivity fingerprints string data:</p>
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109 <div class="OptionsBox">
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110 #
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111 <br/> # Package = MayaChemTools 7.4
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112 <br/> # Release Date = Oct 21, 2010
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113 <br/> #
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114 <br/> # TimeStamp = Fri Mar 11 14:43:57 2011
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115 <br/> #
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116 <br/> # FingerprintsStringType = FingerprintsVector
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117 <br/> #
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118 <br/> # Description = ExtendedConnectivity:AtomicInvariantsAtomTypes:Radius2
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119 <br/> # VectorStringFormat = ValuesString
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120 <br/> # VectorValuesType = AlphaNumericalValues
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121 <br/> #
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122 <br/> Cmpd1 60;73555770 333564680 352413391 666191900 1001270906 137167432...
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123 <br/> Cmpd2 41;73555770 333564680 666191900 1142173602 1363635752 14814699...
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124 <br/> ... ...
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125 <br/> ... ..</div>
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126 <p>Example of CSV <em>Text</em> file containing extended connectivity fingerprints string data:</p>
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127 <div class="OptionsBox">
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128 "CompoundID","ExtendedConnectivityFingerprints"
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129 <br/> "Cmpd1","FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTy
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130 <br/> pes:Radius2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352
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131 <br/> 413391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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132 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671 8551
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133 <br/> 41035 906706094 988546669 1018231313 1032696425 1197507444 13312500..."
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134 <br/> ... ...
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135 <br/> ... ...</div>
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136 <p>The current release of MayaChemTools generates the following types of extended connectivity
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137 fingerprints vector strings:</p>
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138 <div class="OptionsBox">
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139 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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140 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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141 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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142 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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143 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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144 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
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145 <div class="OptionsBox">
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146 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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147 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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148 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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149 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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150 <br/> 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
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151 <br/> 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1</div>
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152 <div class="OptionsBox">
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153 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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154 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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155 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
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156 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
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157 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
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158 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
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159 <div class="OptionsBox">
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160 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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161 <br/> es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
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162 <br/> 0300000091000004000000020000100000000124008200020000000040020000000000
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163 <br/> 2080000000820040010020000000008040000000000080001000000000400000000000
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164 <br/> 4040000090000061010000000800200000000000001400000000020080000000000020
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165 <br/> 00008020200000408000</div>
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166 <div class="OptionsBox">
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167 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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168 <br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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169 <br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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170 <br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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171 <br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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172 <br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div>
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173 <div class="OptionsBox">
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174 FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
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175 <br/> Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
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176 <br/> 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
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177 <br/> 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
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178 <br/> 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
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179 <br/> 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1</div>
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180 <div class="OptionsBox">
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181 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
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182 <br/> s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
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183 <br/> 0000000001000100000000001000000000000000000000000000000000101000000010
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184 <br/> 0000001000000000010000000000000000000000000000000000000000000000000100
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185 <br/> 0000000000001000000000000001000000000001001000000000000000000000000000
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186 <br/> 0000000000000000100000000000001000000000000000000000000000000000000...</div>
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187 <div class="OptionsBox">
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188 FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
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189 <br/> lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
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190 <br/> 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
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191 <br/> 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
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192 <br/> 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
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193 <br/> 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...</div>
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194 <div class="OptionsBox">
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195 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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196 <br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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197 <br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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198 <br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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199 <br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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200 <br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div>
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201 <div class="OptionsBox">
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202 FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
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203 <br/> haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
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204 <br/> 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
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205 <br/> 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
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206 <br/> 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
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207 <br/> 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...</div>
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208 <div class="OptionsBox">
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209 FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
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210 <br/> aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
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211 <br/> 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
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212 <br/> 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
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213 <br/> 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
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214 <br/> 41915747 679881756 721736571 794256218 908276640 992898760 10987549...</div>
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215 <div class="OptionsBox">
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216 FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
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217 <br/> aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
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218 <br/> 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
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219 <br/> 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
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220 <br/> 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
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221 <br/> 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...</div>
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222 <div class="OptionsBox">
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223 FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
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224 <br/> NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
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225 <br/> 700688206 265614156 363161397 681332588 810600886 885767127 950172500
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226 <br/> 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
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227 <br/> 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
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228 <br/> 654 256360355 279492740 291251259 317592700 333763396 972105960 101...</div>
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229 <div class="OptionsBox">
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230 FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
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231 <br/> umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
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232 <br/> 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
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233 <br/> 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
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234 <br/> 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
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235 <br/> 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...</div>
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236 <p>
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237 </p>
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238 <h2>OPTIONS</h2>
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239 <dl>
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240 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
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241 <dd>
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242 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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243 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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244 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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245 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
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246 <p>The supported aromaticity model names along with model specific control parameters
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247 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
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248 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
|
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249 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
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250 for detecting aromaticity corresponding to a specific model.</p>
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251 </dd>
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252 <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt>
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253 <dd>
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254 <p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
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255 atoms during calculation of extended connectivity fingerprints [ Ref 48, Ref 52]. Possible values
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256 in the current release are: <em>AtomicInvariantsAtomTypes, FunctionalClassAtomTypes,
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257 DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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258 TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p>
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259 </dd>
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260 <dt><strong><strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em></strong></dt>
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261 <dd>
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262 <p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
|
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263 option. It's a list of comma separated valid atomic invariant atom types.</p>
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264 <p>Possible values for atomic invarians are: <em>AS, X, BO, LBO, SB, DB, TB,
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265 H, Ar, RA, FC, MN, SM</em>. Default value [ Ref 24 ]: <em>AS,X,BO,H,FC,MN</em>.</p>
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266 <p>The atomic invariants abbreviations correspond to:</p>
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267 <div class="OptionsBox">
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268 AS = Atom symbol corresponding to element symbol</div>
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269 <div class="OptionsBox">
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270 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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271 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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272 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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273 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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274 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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275 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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276 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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277 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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278 <br/> RA = Ring atom annotation indicating whether atom is a ring
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279 <br/> FC<+n/-n> = Formal charge assigned to atom
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280 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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281 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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282 3 (triplet)</div>
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283 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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284 <div class="OptionsBox">
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285 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></div>
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286 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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287 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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288 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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289 are also allowed:</p>
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290 <div class="OptionsBox">
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291 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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292 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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293 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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294 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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295 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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296 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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297 <br/> H : NumOfImplicitAndExplicitHydrogens
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298 <br/> Ar : Aromatic
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299 <br/> RA : RingAtom
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300 <br/> FC : FormalCharge
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301 <br/> MN : MassNumber
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302 <br/> SM : SpinMultiplicity</div>
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303 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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304 atom types.</p>
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305 </dd>
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306 <dt><strong><strong>--BitsOrder</strong> <em>Ascending | Descending</em></strong></dt>
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307 <dd>
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308 <p>Bits order to use during generation of fingerprints bit-vector string for <em>ExtendedConnectivityBits</em>
|
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309 value of <strong>-m, --mode</strong> option. Possible values: <em>Ascending, Descending</em>. Default: <em>Ascending</em>.</p>
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310 <p><em>Ascending</em> bit order which corresponds to first bit in each byte as the lowest bit as
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311 opposed to the highest bit.</p>
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312 <p>Internally, bits are stored in <em>Ascending</em> order using Perl vec function. Regardless
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313 of machine order, big-endian or little-endian, vec function always considers first
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314 string byte as the lowest byte and first bit within each byte as the lowest bit.</p>
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315 </dd>
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316 <dt><strong><strong>-b, --BitStringFormat</strong> <em>BinaryString | HexadecimalString</em></strong></dt>
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317 <dd>
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318 <p>Format of fingerprints bit-vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
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319 <strong>--output</strong> used during <em>ExtendedConnectivityBits</em> value of <strong>-m, --mode</strong> option. Possible
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320 values: <em>BinaryString, HexadecimalString</em>. Default value: <em>BinaryString</em>.</p>
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321 <p><em>BinaryString</em> corresponds to an ASCII string containing 1s and 0s. <em>HexadecimalString</em>
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322 contains bit values in ASCII hexadecimal format.</p>
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323 <p>Examples:</p>
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324 <div class="OptionsBox">
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325 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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326 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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327 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
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328 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
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329 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
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330 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
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331 <div class="OptionsBox">
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332 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
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333 <br/> s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
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334 <br/> 0000000001000100000000001000000000000000000000000000000000101000000010
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335 <br/> 0000001000000000010000000000000000000000000000000000000000000000000100
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336 <br/> 0000000000001000000000000001000000000001001000000000000000000000000000
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337 <br/> 0000000000000000100000000000001000000000000000000000000000000000000...</div>
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|
338 </dd>
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339 <dt><strong><strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em></strong></dt>
|
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340 <dd>
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341 <p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
|
|
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342 option. It's a list of comma separated valid functional classes.</p>
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343 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
|
|
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344 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
|
|
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345 <p>The functional class abbreviations correspond to:</p>
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346 <div class="OptionsBox">
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347 HBD: HydrogenBondDonor
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348 <br/> HBA: HydrogenBondAcceptor
|
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349 <br/> PI : PositivelyIonizable
|
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350 <br/> NI : NegativelyIonizable
|
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351 <br/> Ar : Aromatic
|
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|
352 <br/> Hal : Halogen
|
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|
353 <br/> H : Hydrophobic
|
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354 <br/> RA : RingAtom
|
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|
355 <br/> CA : ChainAtom</div>
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356 <div class="OptionsBox">
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357 Functional class atom type specification for an atom corresponds to:</div>
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358 <div class="OptionsBox">
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359 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div>
|
|
|
360 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
|
|
|
361 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
|
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362 <div class="OptionsBox">
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|
363 HydrogenBondDonor: NH, NH2, OH
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|
364 <br/> HydrogenBondAcceptor: N[!H], O
|
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|
365 <br/> PositivelyIonizable: +, NH2
|
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|
366 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
|
|
|
367 </dd>
|
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368 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
|
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369 <dd>
|
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|
370 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
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|
|
371 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
|
|
|
372 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
|
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373 IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which
|
|
|
374 look like Cmpd<Number>.</p>
|
|
|
375 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
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|
376 <div class="OptionsBox">
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|
|
377 MolID
|
|
|
378 <br/> ExtReg</div>
|
|
|
379 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
|
|
|
380 <div class="OptionsBox">
|
|
|
381 Compound</div>
|
|
|
382 <p>The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
383 instead of default value of Cmpd<Number>.</p>
|
|
|
384 </dd>
|
|
|
385 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
|
|
|
386 <dd>
|
|
|
387 <p>Specify compound ID column label for FP or CSV/TSV text file(s) used during <em>CompoundID</em> value
|
|
|
388 of <strong>--DataFieldsMode</strong> option. Default: <em>CompoundID</em>.</p>
|
|
|
389 </dd>
|
|
|
390 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
|
|
|
391 <dd>
|
|
|
392 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
|
|
|
393 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
|
|
|
394 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
|
|
|
395 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
|
|
|
396 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
|
|
|
397 Default: <em>LabelPrefix</em>.</p>
|
|
|
398 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
|
|
|
399 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
|
|
|
400 values are replaced with sequential compound IDs.</p>
|
|
|
401 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
|
|
|
402 </dd>
|
|
|
403 <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt>
|
|
|
404 <dd>
|
|
|
405 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
|
|
|
406 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
|
|
|
407 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
|
|
|
408 <p>Examples:</p>
|
|
|
409 <div class="OptionsBox">
|
|
|
410 Extreg
|
|
|
411 <br/> MolID,CompoundName</div>
|
|
|
412 </dd>
|
|
|
413 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
|
|
|
414 <dd>
|
|
|
415 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
|
|
|
416 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
|
|
|
417 data field; transfer SD data files common to all compounds; extract specified data fields;
|
|
|
418 generate a compound ID using molname line, a compound prefix, or a combination of both.
|
|
|
419 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
|
|
|
420 </dd>
|
|
|
421 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
|
|
|
422 <dd>
|
|
|
423 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
|
|
|
424 Default value: <em>Yes</em>.</p>
|
|
|
425 <p>By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
426 atom data corresponding to non-element symbols or no atom data are ignored.</p>
|
|
|
427 </dd>
|
|
|
428 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
|
|
|
429 <dd>
|
|
|
430 <p>SD data label or text file column label to use for fingerprints string in output SD or
|
|
|
431 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>ExtendedConnectivityFingerprints</em>.</p>
|
|
|
432 </dd>
|
|
|
433 <dt><strong><strong>-h, --help</strong></strong></dt>
|
|
|
434 <dd>
|
|
|
435 <p>Print this help message.</p>
|
|
|
436 </dd>
|
|
|
437 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
|
|
|
438 <dd>
|
|
|
439 <p>Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
440 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
|
441 <p>For molecules containing multiple connected components, fingerprints can be generated
|
|
|
442 in two different ways: use all connected components or just the largest connected
|
|
|
443 component. By default, all atoms except for the largest connected component are
|
|
|
444 deleted before generation of fingerprints.</p>
|
|
|
445 </dd>
|
|
|
446 <dt><strong><strong>-m, --mode</strong> <em>ExtendedConnectivity | ExtendedConnectivityCount | ExtendedConnectivityBits</em></strong></dt>
|
|
|
447 <dd>
|
|
|
448 <p>Specify type of extended connectivity fingerprints to generate for molecules in <em>SDFile(s)</em>.
|
|
|
449 Possible values: <em>ExtendedConnectivity, ExtendedConnecticityCount or
|
|
|
450 ExtendedConnectivityBits</em>. Default value: <em>ExtendedConnectivity</em>.</p>
|
|
|
451 <p>For <em>ExtendedConnnectivity</em> value of fingerprints <strong>-m, --mode</strong>, a fingerprint vector
|
|
|
452 containing unique atom identifiers constitute the extended connectivity fingerprints
|
|
|
453 of a molecule.</p>
|
|
|
454 <p>For <em>ExtendedConnnectivityCount</em> value of fingerprints <strong>-m, --mode</strong>, a fingerprint vector
|
|
|
455 containing unique atom identifiers along with their count constitute the extended connectivity
|
|
|
456 fingerprints of a molecule.</p>
|
|
|
457 <p>For <em>ExtendedConnnectivityBits</em> value of fingerprints <strong>-m, --mode</strong>, a fingerprint bit vector
|
|
|
458 indicating presence/absence of structurally unique atom identifiers constitute the extended
|
|
|
459 connectivity fingerprints of a molecule.</p>
|
|
|
460 </dd>
|
|
|
461 <dt><strong><strong>-n, --NeighborhoodRadius</strong> <em>number</em></strong></dt>
|
|
|
462 <dd>
|
|
|
463 <p>Atomic neighborhood radius for generating extended connectivity neighborhoods. Default
|
|
|
464 value: <em>2</em>. Valid values: >= 0. Neighborhood radius of zero correspond to just the list
|
|
|
465 of non-hydrogen atoms.</p>
|
|
|
466 <p>Default value of <em>2</em> for atomic neighborhood radius generates extended connectivity
|
|
|
467 fingerprints corresponding to path length or diameter value of <em>4</em> [ Ref 52b ].</p>
|
|
|
468 </dd>
|
|
|
469 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
|
|
|
470 <dd>
|
|
|
471 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
|
|
|
472 Default value: <em>comma</em>.</p>
|
|
|
473 </dd>
|
|
|
474 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
|
|
|
475 <dd>
|
|
|
476 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
|
|
|
477 </dd>
|
|
|
478 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
|
|
|
479 <dd>
|
|
|
480 <p>Overwrite existing files.</p>
|
|
|
481 </dd>
|
|
|
482 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
|
|
|
483 <dd>
|
|
|
484 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
485 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
|
486 </dd>
|
|
|
487 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
|
|
|
488 <dd>
|
|
|
489 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file names:
|
|
|
490 <SDFileName><ExtendedConnectivityFP>.<Ext>. The file type determines <Ext>
|
|
|
491 value. The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
|
|
|
492 delimited text files, respectively.This option is ignored for multiple input files.</p>
|
|
|
493 </dd>
|
|
|
494 <dt><strong><strong>-s, --size</strong> <em>number</em></strong></dt>
|
|
|
495 <dd>
|
|
|
496 <p>Size of bit-vector to use during generation of fingerprints bit-vector string for
|
|
|
497 <em>ExtendedConnectivityBits</em> value of <strong>-m, --mode</strong>. Default value: <em>1024</em>.
|
|
|
498 Valid values correspond to any positive integer which satisfies the following criteria:
|
|
|
499 power of 2, >= 32 and <= 2 ** 32.</p>
|
|
|
500 <p>Examples:</p>
|
|
|
501 <div class="OptionsBox">
|
|
|
502 512
|
|
|
503 1024
|
|
|
504 2048</div>
|
|
|
505 </dd>
|
|
|
506 <dt><strong><strong>--UsePerlCoreRandom</strong> <em>Yes | No</em></strong></dt>
|
|
|
507 <dd>
|
|
|
508 <p>Specify whether to use Perl CORE::rand or MayaChemTools MathUtil::random function
|
|
|
509 during random number generation for setting bits in fingerprints bit-vector strings. Possible
|
|
|
510 values: <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
|
511 <p><em>No</em> value option for <strong>--UsePerlCoreRandom</strong> allows the generation of fingerprints
|
|
|
512 bit-vector strings which are same across different platforms.</p>
|
|
|
513 <p>The random number generator implemented in MayaChemTools is a variant of
|
|
|
514 linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].
|
|
|
515 It is also referred to as Lehmer random number generator or Park-Miller
|
|
|
516 random number generator.</p>
|
|
|
517 <p>Unlike Perl's core random number generator function rand, the random number
|
|
|
518 generator implemented in MayaChemTools, MathUtil::random, generates consistent
|
|
|
519 random values across different platforms for a specific random seed and leads
|
|
|
520 to generation of portable fingerprints bit-vector strings.</p>
|
|
|
521 </dd>
|
|
|
522 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
|
|
|
523 <dd>
|
|
|
524 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
525 <strong>--output</strong> used during <ExtendedConnectivityCount> value of <strong>-m, --mode</strong> option. Possible
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526 values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
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527 ValuesAndIDsPairsString</em>.</p>
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528 <p>Default value during <ExtendedConnectivityCount> value of <strong>-m, --mode</strong> option:
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529 <em>IDsAndValuesString</em>.</p>
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530 <p>Default value during <ExtendedConnectivity> value of <strong>-m, --mode</strong> option: <em>ValuesString</em>.</p>
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531 <p>Examples:</p>
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532 <div class="OptionsBox">
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533 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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534 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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535 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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536 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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537 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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538 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
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539 <div class="OptionsBox">
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540 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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541 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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542 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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543 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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544 <br/> 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
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545 <br/> 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1</div>
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546 </dd>
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547 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
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548 <dd>
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549 <p>Location of working directory. Default: current directory.</p>
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550 </dd>
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551 </dl>
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552 <p>
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553 </p>
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554 <h2>EXAMPLES</h2>
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555 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
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556 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
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557 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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558 <div class="ExampleBox">
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559 % ExtendedConnectivityFingerprints.pl -r SampleECAIFP -o Sample.sdf</div>
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560 <p>To generate extended connectivity count fingerprints corresponding to neighborhood radius up to
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561 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
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562 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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563 <div class="ExampleBox">
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564 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount
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565 -r SampleECAIFP -o Sample.sdf</div>
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566 <p>To generate extended connectivity bits fingerprints as hexadecimal bit-string corresponding to
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567 neighborhood radius up to 2 using atomic invariants atom types in vector string format and
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568 create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints
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569 vector strings data, type:</p>
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570 <div class="ExampleBox">
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571 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits
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572 -r SampleECAIFP -o Sample.sdf</div>
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573 <p>To generate extended connectivity bits fingerprints as binary bit-string corresponding to
|
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574 neighborhood radius up to 2 using atomic invariants atom types in vector string format and
|
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575 create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints
|
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576 vector strings data, type:</p>
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577 <div class="ExampleBox">
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578 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits
|
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579 --BitStringFormat BinaryString -r SampleECAIFP -o Sample.sdf</div>
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|
|
580 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
581 2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf
|
|
|
582 and SampleECAIFP.csv files containing sequential compound IDs in CSV file along with fingerprints
|
|
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583 vector strings data, type:</p>
|
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584 <div class="ExampleBox">
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|
585 % ExtendedConnectivityFingerprints.pl --output all -r SampleECAIFP
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586 -o Sample.sdf</div>
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|
|
587 <p>To generate extended connectivity count fingerprints corresponding to neighborhood radius up to
|
|
|
588 2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf
|
|
|
589 and SampleECAIFP.csv files containing sequential compound IDs in CSV file along with fingerprints
|
|
|
590 vector strings data, type:</p>
|
|
|
591 <div class="ExampleBox">
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592 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount
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593 --output all -r SampleECAIFP -o Sample.sdf</div>
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|
594 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
595 2 using functional class atom types in vector string format and create a SampleECFCFP.csv file
|
|
|
596 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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|
|
597 <div class="ExampleBox">
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|
598 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
|
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599 -r SampleECFCFP -o Sample.sdf</div>
|
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|
600 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
601 2 using DREIDING atom types in vector string format and create a SampleECFP.csv file
|
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|
602 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
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|
|
603 <div class="ExampleBox">
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604 % ExtendedConnectivityFingerprints.pl -a DREIDINGAtomTypes
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605 -r SampleECFP -o Sample.sdf</div>
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|
606 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
607 2 using E-state atom types in vector string format and create a SampleECFP.csv file
|
|
|
608 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
609 <div class="ExampleBox">
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610 % ExtendedConnectivityFingerprints.pl -a EStateAtomTypes
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611 -r SampleECFP -o Sample.sdf</div>
|
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612 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
613 2 using MMFF94 atom types in vector string format and create a SampleECFP.csv file
|
|
|
614 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
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|
615 <div class="ExampleBox">
|
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|
616 % ExtendedConnectivityFingerprints.pl -a MMFF94AtomTypes
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617 -r SampleECFP -o Sample.sdf</div>
|
|
|
618 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
619 2 using SLogP atom types in vector string format and create a SampleECFP.csv file
|
|
|
620 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
621 <div class="ExampleBox">
|
|
|
622 % ExtendedConnectivityFingerprints.pl -a SLogPAtomTypes
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|
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623 -r SampleECFP -o Sample.sdf</div>
|
|
|
624 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
625 2 using SYBYL atom types in vector string format and create a SampleECFP.csv file
|
|
|
626 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
627 <div class="ExampleBox">
|
|
|
628 % ExtendedConnectivityFingerprints.pl -a SYBYLAtomTypes
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|
|
629 -r SampleECFP -o Sample.sdf</div>
|
|
|
630 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
631 2 using TPSA atom types in vector string format and create a SampleECFP.csv file
|
|
|
632 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
633 <div class="ExampleBox">
|
|
|
634 % ExtendedConnectivityFingerprints.pl -a TPSAAtomTypes
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635 -r SampleECFP -o Sample.sdf</div>
|
|
|
636 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
637 2 using UFF atom types in vector string format and create a SampleECFP.csv file
|
|
|
638 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
639 <div class="ExampleBox">
|
|
|
640 % ExtendedConnectivityFingerprints.pl -a UFFAtomTypes
|
|
|
641 -r SampleECFP -o Sample.sdf</div>
|
|
|
642 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
643 3 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
|
|
|
644 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
645 <div class="ExampleBox">
|
|
|
646 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes -n 3
|
|
|
647 -r SampleECAIFP -o Sample.sdf</div>
|
|
|
648 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
649 3 using functional class atom types in vector string format and create a SampleECFCFP.csv file
|
|
|
650 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
651 <div class="ExampleBox">
|
|
|
652 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes -n 3
|
|
|
653 -r SampleECFCFP -o Sample.sdf</div>
|
|
|
654 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
655 2 using only AS,X atomic invariants atom types in vector string format and create a
|
|
|
656 SampleECAIFP.csv file containing sequential compound IDs along with fingerprints vector
|
|
|
657 strings data, type:</p>
|
|
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658 <div class="ExampleBox">
|
|
|
659 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
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|
|
660 --AtomicInvariantsToUse "AS,X" -r SampleECAIFP -o Sample.sdf</div>
|
|
|
661 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
662 2 using only HBD,HBA functional class atom types in vector string format and create a
|
|
|
663 SampleECFCFP.csv file containing sequential compound IDs along with fingerprints vector
|
|
|
664 strings data, type:</p>
|
|
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665 <div class="ExampleBox">
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666 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
|
|
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667 --FunctionalClassesToUse "HBD,HBA" -r SampleECFCFP -o Sample.sdf</div>
|
|
|
668 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
669 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
|
|
|
670 file containing compound ID from molecule name line along with fingerprints vector strings
|
|
|
671 data, type:</p>
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|
|
672 <div class="ExampleBox">
|
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673 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
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|
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674 --DataFieldsMode CompoundID -CompoundIDMode MolName
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|
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675 -r SampleECAIFP -o Sample.sdf</div>
|
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676 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
677 2 using functional class atom types in vector string format and create a SampleECFCFP.csv
|
|
|
678 file containing compound IDs using specified data field along with fingerprints vector strings
|
|
|
679 data, type:</p>
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|
|
680 <div class="ExampleBox">
|
|
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681 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
|
|
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682 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
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|
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683 -r SampleECFCFP -o Sample.sdf</div>
|
|
|
684 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
685 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv
|
|
|
686 file containing compound ID using combination of molecule name line and an explicit compound
|
|
|
687 prefix along with fingerprints vector strings data, type:</p>
|
|
|
688 <div class="ExampleBox">
|
|
|
689 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
690 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
|
|
|
691 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleECAIFP -o Sample.sdf</div>
|
|
|
692 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
693 2 using functional class atom types in vector string format and create a SampleECFCFP.csv
|
|
|
694 file containing specific data fields columns along with fingerprints vector strings
|
|
|
695 data, type:</p>
|
|
|
696 <div class="ExampleBox">
|
|
|
697 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
698 --DataFieldsMode Specify --DataFields Mol_ID -r SampleECFCFP
|
|
|
699 -o Sample.sdf</div>
|
|
|
700 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
701 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv
|
|
|
702 file containing common data fields columns along with fingerprints vector strings data, type:</p>
|
|
|
703 <div class="ExampleBox">
|
|
|
704 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
705 --DataFieldsMode Common -r SampleECAIFP -o Sample.sdf</div>
|
|
|
706 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
707 2 using functional class atom types in vector string format and create SampleECFCFP.sdf, SampleECFCFP.fpf
|
|
|
708 and SampleECFCFP.csv files containing all data fields columns in CSV file along with fingerprints
|
|
|
709 vector strings data, type:</p>
|
|
|
710 <div class="ExampleBox">
|
|
|
711 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
712 --DataFieldsMode All --output all -r SampleECFCFP
|
|
|
713 -o Sample.sdf</div>
|
|
|
714 <p>
|
|
|
715 </p>
|
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716 <h2>AUTHOR</h2>
|
|
|
717 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
|
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|
718 <p>
|
|
|
719 </p>
|
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720 <h2>SEE ALSO</h2>
|
|
|
721 <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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|
|
722 <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>, 
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|
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723 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>, 
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|
|
724 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
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|
|
725 </p>
|
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|
726 <p>
|
|
|
727 </p>
|
|
|
728 <h2>COPYRIGHT</h2>
|
|
|
729 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
|
|
|
730 <p>This file is part of MayaChemTools.</p>
|
|
|
731 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
732 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
733 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
734 any later version.</p>
|
|
|
735 <p> </p><p> </p><div class="DocNav">
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|
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736 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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737 <tr align="left" valign="top"><td width="33%" align="left"><a href="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtractFromPDBFiles.html" title="ExtractFromPDBFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ExtendedConnectivityFingerprints.pl</strong></td></tr>
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738 </table>
|
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739 </div>
|
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740 <br />
|
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741 <center>
|
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742 <img src="../../images/h2o2.png">
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743 </center>
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744 </body>
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745 </html>
|
