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3 <title>MayaChemTools:Documentation:AtomNeighborhoodsFingerprints.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="./AnalyzeTextFilesData.html" title="AnalyzeTextFilesData.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>AtomNeighborhoodsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/AtomNeighborhoodsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/AtomNeighborhoodsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/AtomNeighborhoodsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/AtomNeighborhoodsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/AtomNeighborhoodsFingerprints.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>AtomNeighborhoodsFingerprints.pl - Generate atom neighborhoods 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>AtomNeighborhoodsFingerprints.pl SDFile(s)...</p>
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26 <p>AtomNeighborhoodsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
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27 [<strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes |
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28 DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em>]
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29 [<strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em>]
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30 [<strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</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>--MinNeighborhoodRadius</strong> <em>number</em>] [<strong>--MaxNeighborhoodRadius</strong> <em>number</em>]
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36 [<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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37 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>]
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38 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
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39 <p>
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40 </p>
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41 <h2>DESCRIPTION</h2>
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42 <p>Generate atom neighborhoods fingerprints [ Ref 53-56, Ref 73 ] for <em>SDFile(s)</em> and create appropriate
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43 SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to molecular fingerprints.</p>
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44 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
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45 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
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46 can be specified either by <em>*.sdf</em> or the current directory name.</p>
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47 <p>The current release of MayaChemTools supports generation of atom neighborhoods fingerprints
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48 corresponding to following <strong>-a, --AtomIdentifierTypes</strong>:</p>
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49 <div class="OptionsBox">
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50 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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51 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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52 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
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53 <p>Based on the values specified for <strong>-a, --AtomIdentifierType</strong> and <strong>--AtomicInvariantsToUse</strong>,
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54 initial atom types are assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods
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55 around each non-hydrogen central atom corresponding to radii between specified values
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56 <strong>--MinNeighborhoodRadius</strong> and <strong>--MaxNeighborhoodRadius</strong>, unique atom types at
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57 each radii level are counted and an atom neighborhood identifier is generated.</p>
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58 <p>The format of an atom neighborhood identifier around a central non-hydrogen atom at a
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59 specific radius is:</p>
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60 <div class="OptionsBox">
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61 NR<n>-<AtomType>-ATC<n></div>
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62 <div class="OptionsBox">
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63 NR: Neighborhood radius
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64 <br/> AtomType: Assigned atom type
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65 <br/> ATC: Atom type count</div>
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66 <p>The atom neighborhood identifier for a non-hydrogen central atom corresponding to all specified radii
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67 is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter:</p>
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68 <div class="OptionsBox">
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69 NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:...</div>
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70 <p>The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are
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71 concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule.</p>
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72 <p>Example of <em>SD</em> file containing atom neighborhood fingerprints string data:</p>
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73 <div class="OptionsBox">
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74 ... ...
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75 <br/> ... ...
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76 <br/> $$$$
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77 <br/> ... ...
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78 <br/> ... ...
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79 <br/> ... ...
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80 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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81 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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82 <br/> ... ...
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83 <br/> 2 3 1 0 0 0 0
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84 <br/> ... ...
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85 <br/> M END
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86 <br/> > <CmpdID>
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87 <br/> Cmpd1</div>
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88 <div class="OptionsBox">
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89 > <AtomNeighborhoodsFingerprints>
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90 <br/> FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu
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91 <br/> s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-ATC1
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92 <br/> :NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X1.B
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93 <br/> O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1
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94 <br/> NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C...</div>
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95 <div class="OptionsBox">
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96 $$$$
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97 <br/> ... ...
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98 <br/> ... ...</div>
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99 <p>Example of <em>FP</em> file containing atom neighborhood fingerprints string data:</p>
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100 <div class="OptionsBox">
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101 #
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102 <br/> # Package = MayaChemTools 7.4
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103 <br/> # Release Date = Oct 21, 2010
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104 <br/> #
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105 <br/> # TimeStamp = Fri Mar 11 14:15:27 2011
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106 <br/> #
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107 <br/> # FingerprintsStringType = FingerprintsVector
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108 <br/> #
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109 <br/> # Description = AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu...
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110 <br/> # VectorStringFormat = ValuesString
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111 <br/> # VectorValuesType = AlphaNumericalValues
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112 <br/> #
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113 <br/> Cmpd1 41;NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-A...
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114 <br/> Cmpd2 23;NR0-C.X1.BO1.H3-ATC1:NR1-C.X2.BO2.H2-ATC1:NR2-C.X3.BO3.H1-A...
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115 <br/> ... ...
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116 <br/> ... ..</div>
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117 <p>Example of CSV <em>Text</em> file containing atom neighborhood fingerprints string data:</p>
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118 <div class="OptionsBox">
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119 "CompoundID","AtomNeighborhoodsFingerprints"
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120 <br/> "Cmpd1","FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes
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121 <br/> :MinRadius0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.B
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122 <br/> O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1
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123 <br/> NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3
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124 <br/> .BO4-ATC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1..."
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125 <br/> ... ...
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126 <br/> ... ...</div>
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127 <p>The current release of MayaChemTools generates the following types of atom neighborhoods
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128 fingerprints vector strings:</p>
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129 <div class="OptionsBox">
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130 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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131 <br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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132 <br/> C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
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133 <br/> 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
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134 <br/> TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
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135 <br/> -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...</div>
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136 <div class="OptionsBox">
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137 FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
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138 <br/> adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:
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139 <br/> NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N
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140 <br/> _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT
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141 <br/> C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR
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142 <br/> 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...</div>
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143 <div class="OptionsBox">
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144 FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
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145 <br/> ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1:
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146 <br/> NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR
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147 <br/> 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-
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148 <br/> aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0-
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149 <br/> aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...</div>
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150 <div class="OptionsBox">
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151 FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
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152 <br/> s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar-
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153 <br/> ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT
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154 <br/> C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N
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155 <br/> R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A
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156 <br/> TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...</div>
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157 <div class="OptionsBox">
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158 FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
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159 <br/> ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR
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160 <br/> 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC
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161 <br/> 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C
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162 <br/> 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT
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163 <br/> C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...</div>
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164 <div class="OptionsBox">
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165 FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
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166 <br/> us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1-
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167 <br/> CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:
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168 <br/> NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21-
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169 <br/> ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O
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170 <br/> 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...</div>
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171 <div class="OptionsBox">
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172 FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
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173 <br/> us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1
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174 <br/> -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1-
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175 <br/> O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3-
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176 <br/> ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT
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177 <br/> C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...</div>
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178 <div class="OptionsBox">
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179 FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
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180 <br/> s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2
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181 <br/> -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non
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182 <br/> e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21-
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183 <br/> ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A
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184 <br/> TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...</div>
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185 <div class="OptionsBox">
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186 FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
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187 <br/> 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O
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188 <br/> _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT
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189 <br/> C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR
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190 <br/> 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R
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191 <br/> -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...</div>
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192 <p>
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193 </p>
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194 <h2>OPTIONS</h2>
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195 <dl>
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196 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
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197 <dd>
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198 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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199 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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200 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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201 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
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202 <p>The supported aromaticity model names along with model specific control parameters
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203 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
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204 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
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205 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
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206 for detecting aromaticity corresponding to a specific model.</p>
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207 </dd>
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208 <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt>
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209 <dd>
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210 <p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
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211 atoms during calculation of atom neighborhoods fingerprints. Possible values in the current
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212 release are: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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213 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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214 TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p>
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215 </dd>
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216 <dt><strong><strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em></strong></dt>
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217 <dd>
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218 <p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
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219 option. It's a list of comma separated valid atomic invariant atom types.</p>
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220 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
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221 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
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222 <p>The atomic invariants abbreviations correspond to:</p>
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223 <div class="OptionsBox">
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224 AS = Atom symbol corresponding to element symbol</div>
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225 <div class="OptionsBox">
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226 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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227 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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228 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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229 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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230 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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231 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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232 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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233 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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234 <br/> RA = Ring atom annotation indicating whether atom is a ring
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235 <br/> FC<+n/-n> = Formal charge assigned to atom
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236 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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237 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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238 3 (triplet)</div>
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239 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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240 <div class="OptionsBox">
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241 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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242 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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243 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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244 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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245 are also allowed:</p>
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246 <div class="OptionsBox">
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247 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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248 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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249 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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250 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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251 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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252 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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253 <br/> H : NumOfImplicitAndExplicitHydrogens
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254 <br/> Ar : Aromatic
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255 <br/> RA : RingAtom
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256 <br/> FC : FormalCharge
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257 <br/> MN : MassNumber
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258 <br/> SM : SpinMultiplicity</div>
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259 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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260 atom types.</p>
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261 </dd>
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262 <dt><strong><strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em></strong></dt>
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263 <dd>
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264 <p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
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265 option. It's a list of comma separated valid functional classes.</p>
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266 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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267 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
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268 <p>The functional class abbreviations correspond to:</p>
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269 <div class="OptionsBox">
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270 HBD: HydrogenBondDonor
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271 <br/> HBA: HydrogenBondAcceptor
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272 <br/> PI : PositivelyIonizable
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273 <br/> NI : NegativelyIonizable
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274 <br/> Ar : Aromatic
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275 <br/> Hal : Halogen
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276 <br/> H : Hydrophobic
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277 <br/> RA : RingAtom
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278 <br/> CA : ChainAtom</div>
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279 <div class="OptionsBox">
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280 Functional class atom type specification for an atom corresponds to:</div>
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281 <div class="OptionsBox">
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282 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div>
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283 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
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284 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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285 <div class="OptionsBox">
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286 HydrogenBondDonor: NH, NH2, OH
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287 <br/> HydrogenBondAcceptor: N[!H], O
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288 <br/> PositivelyIonizable: +, NH2
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289 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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290 </dd>
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291 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
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292 <dd>
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293 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
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294 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
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295 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
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296 IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which
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297 look like Cmpd<Number>.</p>
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298 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
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299 <div class="OptionsBox">
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300 MolID
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301 <br/> ExtReg</div>
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302 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
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303 <div class="OptionsBox">
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304 Compound</div>
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305 <p>The value specified above generates compound IDs which correspond to Compound<Number>
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306 instead of default value of Cmpd<Number>.</p>
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307 </dd>
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308 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
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309 <dd>
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310 <p>Specify compound ID column label for FP or CSV/TSV text file(s) used during <em>CompoundID</em> value
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311 of <strong>--DataFieldsMode</strong> option. Default: <em>CompoundID</em>.</p>
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312 </dd>
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313 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
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314 <dd>
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315 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
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316 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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317 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
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318 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
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319 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
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320 Default: <em>LabelPrefix</em>.</p>
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321 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
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322 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
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323 values are replaced with sequential compound IDs.</p>
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324 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
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325 </dd>
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326 <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt>
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327 <dd>
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328 <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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329 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
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330 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
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331 <p>Examples:</p>
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332 <div class="OptionsBox">
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333 Extreg
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334 <br/> MolID,CompoundName</div>
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335 </dd>
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336 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
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337 <dd>
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338 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
|
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339 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
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340 data field; transfer SD data files common to all compounds; extract specified data fields;
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341 generate a compound ID using molname line, a compound prefix, or a combination of both.
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342 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
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343 </dd>
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344 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
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345 <dd>
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346 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
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347 Default value: <em>Yes</em>.</p>
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348 <p>By default, compound data is checked before calculating fingerprints and compounds containing
|
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349 atom data corresponding to non-element symbols or no atom data are ignored.</p>
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350 </dd>
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351 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
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352 <dd>
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353 <p>SD data label or text file column label to use for fingerprints string in output SD or
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354 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>AtomNeighborhoodsFingerprints</em>.</p>
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|
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355 </dd>
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356 <dt><strong><strong>-h, --help</strong></strong></dt>
|
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357 <dd>
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358 <p>Print this help message.</p>
|
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359 </dd>
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360 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
|
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361 <dd>
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362 <p>Generate fingerprints for only the largest component in molecule. Possible values:
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363 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
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364 <p>For molecules containing multiple connected components, fingerprints can be generated
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365 in two different ways: use all connected components or just the largest connected
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366 component. By default, all atoms except for the largest connected component are
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367 deleted before generation of fingerprints.</p>
|
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|
368 </dd>
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369 <dt><strong><strong>--MinNeighborhoodRadius</strong> <em>number</em></strong></dt>
|
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|
370 <dd>
|
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371 <p>Minimum atom neighborhood radius for generating atom neighborhoods. Default value: <em>0</em>.
|
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372 Valid values: positive integers and less than <strong>--MaxNeighborhoodRadius</strong>. Neighborhood
|
|
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373 radius of zero corresponds to list of non-hydrogen atoms.</p>
|
|
|
374 </dd>
|
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375 <dt><strong><strong>--MaxNeighborhoodRadius</strong> <em>number</em></strong></dt>
|
|
|
376 <dd>
|
|
|
377 <p>Maximum atom neighborhood radius for generating atom neighborhoods. Default value: <em>2</em>.
|
|
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378 Valid values: positive integers and greater than <strong>--MineighborhoodRadius</strong>.</p>
|
|
|
379 </dd>
|
|
|
380 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
|
|
|
381 <dd>
|
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|
382 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
|
|
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383 Default value: <em>comma</em>.</p>
|
|
|
384 </dd>
|
|
|
385 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
|
|
|
386 <dd>
|
|
|
387 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
|
|
|
388 </dd>
|
|
|
389 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
|
|
|
390 <dd>
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|
391 <p>Overwrite existing files.</p>
|
|
|
392 </dd>
|
|
|
393 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
|
|
|
394 <dd>
|
|
|
395 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
396 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
|
397 </dd>
|
|
|
398 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
|
|
|
399 <dd>
|
|
|
400 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file names:
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|
|
401 <SDFileName><AtomNeighborhoodsFP>.<Ext>. The file type determines <Ext>
|
|
|
402 value. The sdf, fpf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab
|
|
|
403 delimited text files, respectively.This option is ignored for multiple input files.</p>
|
|
|
404 </dd>
|
|
|
405 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
|
|
|
406 <dd>
|
|
|
407 <p>Location of working directory. Default: current directory.</p>
|
|
|
408 </dd>
|
|
|
409 </dl>
|
|
|
410 <p>
|
|
|
411 </p>
|
|
|
412 <h2>EXAMPLES</h2>
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|
|
413 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
414 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
415 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
416 <div class="ExampleBox">
|
|
|
417 % AtomNeighborhoodsFingerprints.pl -r SampleANFP -o Sample.sdf</div>
|
|
|
418 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
419 2 using DREIDING atom types in vector string format and create a SampleANFP.csv
|
|
|
420 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
421 <div class="ExampleBox">
|
|
|
422 % AtomNeighborhoodsFingerprints.pl -a DREIDINGAtomTypes -r SampleANFP
|
|
|
423 -o Sample.sdf</div>
|
|
|
424 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
425 2 using EStateAtomTypes types in vector string format and create a SampleANFP.csv
|
|
|
426 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
427 <div class="ExampleBox">
|
|
|
428 % AtomNeighborhoodsFingerprints.pl -a EStateAtomTypes -r SampleANFP
|
|
|
429 -o Sample.sdf</div>
|
|
|
430 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
431 2 using SYBYL atom types in vector string format and create a SampleANFP.csv
|
|
|
432 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
433 <div class="ExampleBox">
|
|
|
434 % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP
|
|
|
435 -o Sample.sdf</div>
|
|
|
436 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
437 2 using FunctionalClass atom types in vector string format and create a SampleANFP.csv
|
|
|
438 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
439 <div class="ExampleBox">
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|
|
440 % AtomNeighborhoodsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
441 -r SampleANFP -o Sample.sdf</div>
|
|
|
442 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
443 2 using MMFF94 atom types in vector string format and create a SampleANFP.csv
|
|
|
444 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
445 <div class="ExampleBox">
|
|
|
446 % AtomNeighborhoodsFingerprints.pl -a MMFF94AtomTypes -r SampleANFP
|
|
|
447 -o Sample.sdf</div>
|
|
|
448 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
449 2 using SLogP atom types in vector string format and create a SampleANFP.csv
|
|
|
450 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
451 <div class="ExampleBox">
|
|
|
452 % AtomNeighborhoodsFingerprints.pl -a SLogPAtomTypes -r SampleANFP
|
|
|
453 -o Sample.sdf</div>
|
|
|
454 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
455 2 using SYBYL atom types in vector string format and create a SampleANFP.csv
|
|
|
456 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
457 <div class="ExampleBox">
|
|
|
458 % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP
|
|
|
459 -o Sample.sdf</div>
|
|
|
460 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
461 2 using TPSA atom types in vector string format and create a SampleANFP.csv
|
|
|
462 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
463 <div class="ExampleBox">
|
|
|
464 % AtomNeighborhoodsFingerprints.pl -a TPSAAtomTypes -r SampleANFP
|
|
|
465 -o Sample.sdf</div>
|
|
|
466 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
467 2 using UFF atom types in vector string format and create a SampleANFP.csv
|
|
|
468 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
469 <div class="ExampleBox">
|
|
|
470 % AtomNeighborhoodsFingerprints.pl -a UFFAtomTypes -r SampleANFP
|
|
|
471 -o Sample.sdf</div>
|
|
|
472 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
473 2 using atomic invariants atom types in vector string format and create SampleANFP.sdf,
|
|
|
474 SampleANFP.fpf and SampleANFP.csv files containing sequential compound IDs in CSV file along
|
|
|
475 with fingerprints vector strings data, type:</p>
|
|
|
476 <div class="ExampleBox">
|
|
|
477 % AtomNeighborhoodsFingerprints.pl --output all -r SampleANFP
|
|
|
478 -o Sample.sdf</div>
|
|
|
479 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 1 to
|
|
|
480 3 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
481 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
482 <div class="ExampleBox">
|
|
|
483 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
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|
484 --MinNeighborhoodRadius 1 --MaxNeighborhoodRadius 3 -r SampleANFP
|
|
|
485 -o Sample.sdf</div>
|
|
|
486 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
487 2 using only AS,X atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
488 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
489 <div class="ExampleBox">
|
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490 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
491 --AtomicInvariantsToUse "AS,X" --MinNeighborhoodRadius 0
|
|
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492 --MaxNeighborhoodRadius 3 -r SampleANFP -o Sample.sdf</div>
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493 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
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494 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
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495 file containing compound ID from molecule name line along with fingerprints vector strings data, type:</p>
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496 <div class="ExampleBox">
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497 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
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498 --DataFieldsMode CompoundID --CompoundIDMode MolName
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499 -r SampleANFP -o Sample.sdf</div>
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500 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
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501 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
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502 file containing compound IDs using specified data field along with fingerprints vector strings
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503 data, type:</p>
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504 <div class="ExampleBox">
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505 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
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506 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
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507 Mol_ID -r SampleANFP -o Sample.sdf</div>
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508 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
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509 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
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510 file containing compound ID using combination of molecule name line and an explicit compound
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511 prefix along with fingerprints vector strings data, type:</p>
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512 <div class="ExampleBox">
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513 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
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514 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
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515 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleANFP -o Sample.sdf</div>
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516 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
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517 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
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518 file containing specific data fields columns along with fingerprints vector strings
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519 data, type:</p>
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520 <div class="ExampleBox">
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521 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
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522 --DataFieldsMode Specify --DataFields Mol_ID -r SampleANFP
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523 -o Sample.sdf</div>
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524 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
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525 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
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526 file containing common data fields columns along with fingerprints vector strings
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527 data, type:</p>
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528 <div class="ExampleBox">
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529 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
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530 --DataFieldsMode Common -r SampleANFP -o Sample.sdf</div>
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531 <p>To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
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532 2 using atomic invariants atom types in vector string format and create SampleANFP.sdf,
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533 SampleANFP.fpf and SampleANFP.csv files containing all data fields columns in CSV file along with
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534 fingerprints data, type:</p>
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535 <div class="ExampleBox">
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536 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
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537 --DataFieldsMode All --output all -r SampleANFP
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538 -o Sample.sdf</div>
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539 <p>
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540 </p>
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541 <h2>AUTHOR</h2>
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542 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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543 <p>
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544 </p>
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545 <h2>SEE ALSO</h2>
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546 <p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>, <a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>, <a href="./SimilaritySearchingFingerprints.html">SimilaritySearchingFingerprints.pl</a>, 
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547 <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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548 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>, 
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549 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
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550 </p>
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551 <p>
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552 </p>
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553 <h2>COPYRIGHT</h2>
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554 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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555 <p>This file is part of MayaChemTools.</p>
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556 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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557 the terms of the GNU Lesser General Public License as published by the Free
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558 Software Foundation; either version 3 of the License, or (at your option)
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559 any later version.</p>
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560 <p> </p><p> </p><div class="DocNav">
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561 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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562 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AnalyzeTextFilesData.html" title="AnalyzeTextFilesData.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>AtomNeighborhoodsFingerprints.pl</strong></td></tr>
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563 </table>
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564 </div>
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565 <br />
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566 <center>
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567 <img src="../../images/h2o2.png">
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568 </center>
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569 </body>
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570 </html>
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