|
0
|
1 <html>
|
|
|
2 <head>
|
|
|
3 <title>MayaChemTools:Documentation:TopologicalAtomTorsionsFingerprints.pl</title>
|
|
|
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
|
|
|
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
|
|
|
6 </head>
|
|
|
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
|
|
|
8 <br/>
|
|
|
9 <center>
|
|
|
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
|
|
|
11 </center>
|
|
|
12 <br/>
|
|
|
13 <div class="DocNav">
|
|
|
14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
|
|
|
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalAtomTorsionsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomTorsionsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalAtomTorsionsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalAtomTorsionsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalAtomTorsionsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalAtomTorsionsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
|
|
|
16 </table>
|
|
|
17 </div>
|
|
|
18 <p>
|
|
|
19 </p>
|
|
|
20 <h2>NAME</h2>
|
|
|
21 <p>TopologicalAtomTorsionsFingerprints.pl - Generate topological atom torsions fingerprints for SD files</p>
|
|
|
22 <p>
|
|
|
23 </p>
|
|
|
24 <h2>SYNOPSIS</h2>
|
|
|
25 <p>TopologicalAtomTorsionsFingerprints.pl SDFile(s)...</p>
|
|
|
26 <p>TopologicalAtomTorsionsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
|
|
|
27 [<strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes</em>]
|
|
|
28 [<strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em>]
|
|
|
29 [<strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em>]
|
|
|
30 [<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>] [<strong>--CompoundIDLabel</strong> <em>text</em>]
|
|
|
31 [<strong>--CompoundIDMode</strong>] [<strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em>]
|
|
|
32 [<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>]
|
|
|
33 [<strong>--FingerprintsLabel</strong> <em>text</em>] [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>]
|
|
|
34 [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>]
|
|
|
35 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-v, --VectorStringFormat</strong>]
|
|
|
36 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
|
|
|
37 <p>
|
|
|
38 </p>
|
|
|
39 <h2>DESCRIPTION</h2>
|
|
|
40 <p>Generate topological atom torsions fingerprints [ Ref 58, Ref 72 ] for <em>SDFile(s)</em> and create
|
|
|
41 appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to
|
|
|
42 molecular fingerprints.</p>
|
|
|
43 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
|
|
|
44 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
|
|
|
45 can be specified either by <em>*.sdf</em> or the current directory name.</p>
|
|
|
46 <p>The current release of MayaChemTools supports generation of topological atom torsions
|
|
|
47 fingerprints corresponding to following <strong>-a, --AtomIdentifierTypes</strong>:</p>
|
|
|
48 <div class="OptionsBox">
|
|
|
49 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
50 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
51 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
|
|
|
52 <p>Based on the values specified for <strong>-a, --AtomIdentifierType</strong> and <strong>--AtomicInvariantsToUse</strong>,
|
|
|
53 initial atom types are assigned to all non-hydrogen atoms in a molecule. All unique atom torsions
|
|
|
54 are identified and an atom torsion identifier is generated; the format of atom torsion identifier is:</p>
|
|
|
55 <div class="OptionsBox">
|
|
|
56 <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4></div>
|
|
|
57 <div class="OptionsBox">
|
|
|
58 AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types</div>
|
|
|
59 <div class="OptionsBox">
|
|
|
60 where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4</div>
|
|
|
61 <p>The atom torsion identifiers for all unique atom torsions corresponding to non-hydrogen atoms constitute
|
|
|
62 topological atom torsions fingerprints of the molecule.</p>
|
|
|
63 <p>Example of <em>SD</em> file containing topological atom torsions fingerprints string data:</p>
|
|
|
64 <div class="OptionsBox">
|
|
|
65 ... ...
|
|
|
66 <br/> ... ...
|
|
|
67 <br/> $$$$
|
|
|
68 <br/> ... ...
|
|
|
69 <br/> ... ...
|
|
|
70 <br/> ... ...
|
|
|
71 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
|
|
|
72 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
73 <br/> ... ...
|
|
|
74 <br/> 2 3 1 0 0 0 0
|
|
|
75 <br/> ... ...
|
|
|
76 <br/> M END
|
|
|
77 <br/> > <CmpdID>
|
|
|
78 <br/> Cmpd1</div>
|
|
|
79 <div class="OptionsBox">
|
|
|
80 > <TopologicalAtomTorsionsFingerprints>
|
|
|
81 <br/> FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;33
|
|
|
82 <br/> ;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.
|
|
|
83 <br/> X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO2.H
|
|
|
84 <br/> 2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O.X1....;
|
|
|
85 <br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div>
|
|
|
86 <div class="OptionsBox">
|
|
|
87 $$$$
|
|
|
88 <br/> ... ...
|
|
|
89 <br/> ... ...</div>
|
|
|
90 <p>Example of <em>FP</em> file containing topological atom torsions fingerprints string data:</p>
|
|
|
91 <div class="OptionsBox">
|
|
|
92 #
|
|
|
93 <br/> # Package = MayaChemTools 7.4
|
|
|
94 <br/> # Release Date = Oct 21, 2010
|
|
|
95 <br/> #
|
|
|
96 <br/> # TimeStamp = Fri Mar 11 15:17:20 2011
|
|
|
97 <br/> #
|
|
|
98 <br/> # FingerprintsStringType = FingerprintsVector
|
|
|
99 <br/> #
|
|
|
100 <br/> # Description = TopologicalAtomTorsions:AtomicInvariantsAtomTypes
|
|
|
101 <br/> # VectorStringFormat = IDsAndValuesString
|
|
|
102 <br/> # VectorValuesType = NumericalValues
|
|
|
103 <br/> #
|
|
|
104 <br/> Cmpd1 33;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.X3.BO4...;2 2 1 1 2 2 ...
|
|
|
105 <br/> Cmpd2 23;C.X1.BO1.H3-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2...;2 2 1 5 ...
|
|
|
106 <br/> ... ...
|
|
|
107 <br/> ... ..</div>
|
|
|
108 <p>Example of CSV <em>Text</em> file containing topological atom torsions fingerprints string data:</p>
|
|
|
109 <div class="OptionsBox">
|
|
|
110 "CompoundID","TopologicalAtomTorsionsFingerprints"
|
|
|
111 <br/> "Cmpd1","FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAto
|
|
|
112 <br/> mTypes;33;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.
|
|
|
113 <br/> X3.BO4-C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C
|
|
|
114 <br/> .X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3....;
|
|
|
115 <br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
|
|
|
116 <br/> ... ...
|
|
|
117 <br/> ... ...</div>
|
|
|
118 <p>The current release of MayaChemTools generates the following types of topological atom torsions
|
|
|
119 fingerprints vector strings:</p>
|
|
|
120 <div class="OptionsBox">
|
|
|
121 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
122 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
|
|
|
123 <br/> C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
|
|
|
124 <br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
|
|
|
125 <br/> ;2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div>
|
|
|
126 <div class="OptionsBox">
|
|
|
127 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
128 <br/> 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
|
|
|
129 <br/> .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
|
|
|
130 <br/> 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
|
|
|
131 <br/> O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
|
|
|
132 <br/> O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...</div>
|
|
|
133 <div class="OptionsBox">
|
|
|
134 FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
|
|
|
135 <br/> calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C
|
|
|
136 <br/> _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2
|
|
|
137 <br/> C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...;
|
|
|
138 <br/> 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1</div>
|
|
|
139 <div class="OptionsBox">
|
|
|
140 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
|
|
|
141 <br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
|
|
|
142 <br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
|
|
|
143 <br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
|
|
|
144 <br/> 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2</div>
|
|
|
145 <div class="OptionsBox">
|
|
|
146 FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
|
|
|
147 <br/> ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar-
|
|
|
148 <br/> Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar
|
|
|
149 <br/> -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...;
|
|
|
150 <br/> 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3</div>
|
|
|
151 <div class="OptionsBox">
|
|
|
152 FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
|
|
|
153 <br/> lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5
|
|
|
154 <br/> B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5
|
|
|
155 <br/> A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...;
|
|
|
156 <br/> 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
|
|
|
157 <br/> 1 1 2 1 1 3 1 3</div>
|
|
|
158 <div class="OptionsBox">
|
|
|
159 FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
|
|
|
160 <br/> Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1
|
|
|
161 <br/> 1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS
|
|
|
162 <br/> 2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1
|
|
|
163 <br/> C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20
|
|
|
164 <br/> 2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C...</div>
|
|
|
165 <div class="OptionsBox">
|
|
|
166 FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
|
|
|
167 <br/> Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2
|
|
|
168 <br/> -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C.
|
|
|
169 <br/> ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3
|
|
|
170 <br/> -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C.
|
|
|
171 <br/> ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ...</div>
|
|
|
172 <div class="OptionsBox">
|
|
|
173 FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
|
|
|
174 <br/> lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4
|
|
|
175 <br/> None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None-
|
|
|
176 <br/> None-None 44 None-None-None-O3 3 None-None-None-O4 5</div>
|
|
|
177 <div class="OptionsBox">
|
|
|
178 FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
|
|
|
179 <br/> lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C
|
|
|
180 <br/> _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3
|
|
|
181 <br/> -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C
|
|
|
182 <br/> _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2
|
|
|
183 C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-...</div>
|
|
|
184 <p>
|
|
|
185 </p>
|
|
|
186 <h2>OPTIONS</h2>
|
|
|
187 <dl>
|
|
|
188 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
|
|
|
189 <dd>
|
|
|
190 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
|
|
|
191 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
192 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
|
|
|
193 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
|
|
|
194 <p>The supported aromaticity model names along with model specific control parameters
|
|
|
195 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
|
|
|
196 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
|
|
|
197 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
|
|
|
198 for detecting aromaticity corresponding to a specific model.</p>
|
|
|
199 </dd>
|
|
|
200 <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt>
|
|
|
201 <dd>
|
|
|
202 <p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
|
|
|
203 atoms during calculation of topological atom torsions fingerprints. Possible values in the current
|
|
|
204 release are: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
205 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
206 TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p>
|
|
|
207 </dd>
|
|
|
208 <dt><strong><strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em></strong></dt>
|
|
|
209 <dd>
|
|
|
210 <p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
|
|
|
211 option. It's a list of comma separated valid atomic invariant atom types.</p>
|
|
|
212 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
|
|
|
213 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
|
|
|
214 <p>The atomic invariants abbreviations correspond to:</p>
|
|
|
215 <div class="OptionsBox">
|
|
|
216 AS = Atom symbol corresponding to element symbol</div>
|
|
|
217 <div class="OptionsBox">
|
|
|
218 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
219 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
220 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
221 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
222 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
223 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
224 <br/> H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
225 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
226 <br/> RA = Ring atom annotation indicating whether atom is a ring
|
|
|
227 <br/> FC<+n/-n> = Formal charge assigned to atom
|
|
|
228 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
229 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
230 3 (triplet)</div>
|
|
|
231 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
|
|
|
232 <div class="OptionsBox">
|
|
|
233 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></div>
|
|
|
234 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
235 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
|
|
|
236 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
237 are also allowed:</p>
|
|
|
238 <div class="OptionsBox">
|
|
|
239 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
240 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
241 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
242 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
243 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
244 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
245 <br/> H : NumOfImplicitAndExplicitHydrogens
|
|
|
246 <br/> Ar : Aromatic
|
|
|
247 <br/> RA : RingAtom
|
|
|
248 <br/> FC : FormalCharge
|
|
|
249 <br/> MN : MassNumber
|
|
|
250 <br/> SM : SpinMultiplicity</div>
|
|
|
251 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
|
|
|
252 atom types.</p>
|
|
|
253 </dd>
|
|
|
254 <dt><strong><strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em></strong></dt>
|
|
|
255 <dd>
|
|
|
256 <p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
|
|
|
257 option. It's a list of comma separated valid functional classes.</p>
|
|
|
258 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
|
|
|
259 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
|
|
|
260 <p>The functional class abbreviations correspond to:</p>
|
|
|
261 <div class="OptionsBox">
|
|
|
262 HBD: HydrogenBondDonor
|
|
|
263 <br/> HBA: HydrogenBondAcceptor
|
|
|
264 <br/> PI : PositivelyIonizable
|
|
|
265 <br/> NI : NegativelyIonizable
|
|
|
266 <br/> Ar : Aromatic
|
|
|
267 <br/> Hal : Halogen
|
|
|
268 <br/> H : Hydrophobic
|
|
|
269 <br/> RA : RingAtom
|
|
|
270 <br/> CA : ChainAtom</div>
|
|
|
271 <div class="OptionsBox">
|
|
|
272 Functional class atom type specification for an atom corresponds to:</div>
|
|
|
273 <div class="OptionsBox">
|
|
|
274 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div>
|
|
|
275 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
|
|
|
276 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
|
|
|
277 <div class="OptionsBox">
|
|
|
278 HydrogenBondDonor: NH, NH2, OH
|
|
|
279 <br/> HydrogenBondAcceptor: N[!H], O
|
|
|
280 <br/> PositivelyIonizable: +, NH2
|
|
|
281 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
|
|
|
282 </dd>
|
|
|
283 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
|
|
|
284 <dd>
|
|
|
285 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
|
|
|
286 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
|
|
|
287 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
|
|
|
288 IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which
|
|
|
289 look like Cmpd<Number>.</p>
|
|
|
290 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
|
|
|
291 <div class="OptionsBox">
|
|
|
292 MolID
|
|
|
293 <br/> ExtReg</div>
|
|
|
294 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
|
|
|
295 <div class="OptionsBox">
|
|
|
296 Compound</div>
|
|
|
297 <p>The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
298 instead of default value of Cmpd<Number>.</p>
|
|
|
299 </dd>
|
|
|
300 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
|
|
|
301 <dd>
|
|
|
302 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
|
|
|
303 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
|
|
|
304 </dd>
|
|
|
305 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
|
|
|
306 <dd>
|
|
|
307 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
|
|
|
308 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
|
|
|
309 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
|
|
|
310 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
|
|
|
311 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
|
|
|
312 Default value: <em>LabelPrefix</em>.</p>
|
|
|
313 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
|
|
|
314 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
|
|
|
315 values are replaced with sequential compound IDs.</p>
|
|
|
316 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
|
|
|
317 </dd>
|
|
|
318 <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt>
|
|
|
319 <dd>
|
|
|
320 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
|
|
|
321 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
|
|
|
322 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
|
|
|
323 <p>Examples:</p>
|
|
|
324 <div class="OptionsBox">
|
|
|
325 Extreg
|
|
|
326 <br/> MolID,CompoundName</div>
|
|
|
327 </dd>
|
|
|
328 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
|
|
|
329 <dd>
|
|
|
330 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
|
|
|
331 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
|
|
|
332 data field; transfer SD data files common to all compounds; extract specified data fields;
|
|
|
333 generate a compound ID using molname line, a compound prefix, or a combination of both.
|
|
|
334 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
|
|
|
335 </dd>
|
|
|
336 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
|
|
|
337 <dd>
|
|
|
338 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
|
|
|
339 Default value: <em>Yes</em>.</p>
|
|
|
340 <p>By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
341 atom data corresponding to non-element symbols or no atom data are ignored.</p>
|
|
|
342 </dd>
|
|
|
343 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
|
|
|
344 <dd>
|
|
|
345 <p>SD data label or text file column label to use for fingerprints string in output SD or
|
|
|
346 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>TopologicalAtomTorsionsFingerprints</em>.</p>
|
|
|
347 </dd>
|
|
|
348 <dt><strong><strong>-h, --help</strong></strong></dt>
|
|
|
349 <dd>
|
|
|
350 <p>Print this help message.</p>
|
|
|
351 </dd>
|
|
|
352 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
|
|
|
353 <dd>
|
|
|
354 <p>Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
355 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
|
|
|
356 <p>For molecules containing multiple connected components, fingerprints can be generated
|
|
|
357 in two different ways: use all connected components or just the largest connected
|
|
|
358 component. By default, all atoms except for the largest connected component are
|
|
|
359 deleted before generation of fingerprints.</p>
|
|
|
360 </dd>
|
|
|
361 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
|
|
|
362 <dd>
|
|
|
363 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
|
|
|
364 Default value: <em>comma</em>.</p>
|
|
|
365 </dd>
|
|
|
366 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
|
|
|
367 <dd>
|
|
|
368 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
|
|
|
369 </dd>
|
|
|
370 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
|
|
|
371 <dd>
|
|
|
372 <p>Overwrite existing files.</p>
|
|
|
373 </dd>
|
|
|
374 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
|
|
|
375 <dd>
|
|
|
376 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
377 <em>Yes or No</em>. Default value: <em>Yes</em></p>
|
|
|
378 </dd>
|
|
|
379 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
|
|
|
380 <dd>
|
|
|
381 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file names:
|
|
|
382 <SDFileName><TopologicalAtomTorsionsFP>.<Ext>. The file type determines <Ext> value.
|
|
|
383 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
|
|
|
384 delimited text files, respectively.This option is ignored for multiple input files.</p>
|
|
|
385 </dd>
|
|
|
386 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
|
|
|
387 <dd>
|
|
|
388 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
389 <strong>--output</strong> option. Possible values: <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
390 ValuesAndIDsPairsString</em>. Defaultvalue: <em>IDsAndValuesString</em>.</p>
|
|
|
391 <p>Examples:</p>
|
|
|
392 <div class="OptionsBox">
|
|
|
393 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
394 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
|
|
|
395 <br/> C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
|
|
|
396 <br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
|
|
|
397 <br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div>
|
|
|
398 <div class="OptionsBox">
|
|
|
399 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
400 <br/> 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
|
|
|
401 <br/> .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
|
|
|
402 <br/> 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
|
|
|
403 <br/> O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
|
|
|
404 <br/> O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...</div>
|
|
|
405 </dd>
|
|
|
406 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
|
|
|
407 <dd>
|
|
|
408 <p>Location of working directory. Default value: current directory.</p>
|
|
|
409 </dd>
|
|
|
410 </dl>
|
|
|
411 <p>
|
|
|
412 </p>
|
|
|
413 <h2>EXAMPLES</h2>
|
|
|
414 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
415 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
416 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
417 <div class="ExampleBox">
|
|
|
418 % TopologicalAtomTorsionsFingerprints.pl -r SampleTATFP -o Sample.sdf</div>
|
|
|
419 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
420 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv
|
|
|
421 files containing sequential compound IDs in CSV file along with fingerprints vector strings
|
|
|
422 data, type:</p>
|
|
|
423 <div class="ExampleBox">
|
|
|
424 % TopologicalAtomTorsionsFingerprints.pl --output all -r SampleTATFP
|
|
|
425 -o Sample.sdf</div>
|
|
|
426 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
427 IDsAndValuesPairsString format and create a SampleTATFP.csv file containing sequential
|
|
|
428 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
429 <div class="ExampleBox">
|
|
|
430 % TopologicalAtomTorsionsFingerprints.pl --VectorStringFormat
|
|
|
431 IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf</div>
|
|
|
432 <p>To generate topological atom torsions fingerprints using DREIDING atom types in
|
|
|
433 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
434 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
435 <div class="ExampleBox">
|
|
|
436 % TopologicalAtomTorsionsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
437 -r SampleTATFP -o Sample.sdf</div>
|
|
|
438 <p>To generate topological atom torsions fingerprints using E-state atom types in
|
|
|
439 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
440 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
441 <div class="ExampleBox">
|
|
|
442 % TopologicalAtomTorsionsFingerprints.pl -a EStateAtomTypes
|
|
|
443 -r SampleTATFP -o Sample.sdf</div>
|
|
|
444 <p>To generate topological atom torsions fingerprints using functional class atom types in
|
|
|
445 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
446 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
447 <div class="ExampleBox">
|
|
|
448 % TopologicalAtomTorsionsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
449 -r SampleTATFP -o Sample.sdf</div>
|
|
|
450 <p>To generate topological atom torsions fingerprints using MMFF94 atom types in
|
|
|
451 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
452 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
453 <div class="ExampleBox">
|
|
|
454 % TopologicalAtomTorsionsFingerprints.pl -a MMFF94AtomTypes
|
|
|
455 -r SampleTATFP -o Sample.sdf</div>
|
|
|
456 <p>To generate topological atom torsions fingerprints using SLogP atom types in
|
|
|
457 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
458 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
459 <div class="ExampleBox">
|
|
|
460 % TopologicalAtomTorsionsFingerprints.pl -a SLogPAtomTypes
|
|
|
461 -r SampleTATFP -o Sample.sdf</div>
|
|
|
462 <p>To generate topological atom torsions fingerprints using SYBYL atom types in
|
|
|
463 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
464 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
465 <div class="ExampleBox">
|
|
|
466 % TopologicalAtomTorsionsFingerprints.pl -a SYBYLAtomTypes
|
|
|
467 -r SampleTATFP -o Sample.sdf</div>
|
|
|
468 <p>To generate topological atom torsions fingerprints using TPSA atom types in
|
|
|
469 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
470 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
471 <div class="ExampleBox">
|
|
|
472 % TopologicalAtomTorsionsFingerprints.pl -a TPSAAtomTypes
|
|
|
473 -r SampleTATFP -o Sample.sdf</div>
|
|
|
474 <p>To generate topological atom torsions fingerprints using UFF atom types in
|
|
|
475 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
476 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
477 <div class="ExampleBox">
|
|
|
478 % TopologicalAtomTorsionsFingerprints.pl -a UFFAtomTypes
|
|
|
479 -r SampleTATFP -o Sample.sdf</div>
|
|
|
480 <p>To generate topological atom torsions fingerprints using only AS,X atomic invariants atom
|
|
|
481 types in IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
|
|
|
482 compound IDs along with fingerprints vector strings data, type:</p>
|
|
|
483 <div class="ExampleBox">
|
|
|
484 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
485 --AtomicInvariantsToUse "AS,X" -r SampleTATFP -o Sample.sdf</div>
|
|
|
486 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
487 IDsAndValuesString format and create a SampleTATFP.csv file containing compoundID
|
|
|
488 from molecule name line along with fingerprints vector strings, type:</p>
|
|
|
489 <div class="ExampleBox">
|
|
|
490 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
491 --DataFieldsMode CompoundID -CompoundIDMode MolName
|
|
|
492 -r SampleTATFP -o Sample.sdf</div>
|
|
|
493 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
494 IDsAndValuesString format and create a SampleTATFP.csv file containing compound IDs
|
|
|
495 using specified data field along with fingerprints vector strings, type:</p>
|
|
|
496 <div class="ExampleBox">
|
|
|
497 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
498 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
|
|
|
499 Mol_ID -r SampleTATFP -o Sample.sdf</div>
|
|
|
500 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
501 IDsAndValuesString format and create a SampleTATFP.csv file containing compound ID
|
|
|
502 using combination of molecule name line and an explicit compound prefix along with
|
|
|
503 fingerprints vector strings data, type:</p>
|
|
|
504 <div class="ExampleBox">
|
|
|
505 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
506 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
|
|
|
507 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf</div>
|
|
|
508 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
509 IDsAndValuesString format and create a SampleTATFP.csv file containing specific data
|
|
|
510 fields columns along with fingerprints vector strings, type:</p>
|
|
|
511 <div class="ExampleBox">
|
|
|
512 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
513 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP
|
|
|
514 -o Sample.sdf</div>
|
|
|
515 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
516 IDsAndValuesString format and create a SampleTATFP.csv file containing common
|
|
|
517 data fields columns along with fingerprints vector strings, type:</p>
|
|
|
518 <div class="ExampleBox">
|
|
|
519 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
520 --DataFieldsMode Common -r SampleTATFP -o Sample.sdf</div>
|
|
|
521 <p>To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
522 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv
|
|
|
523 files containing all data fields columns in CSV file along with fingerprints data, type:</p>
|
|
|
524 <div class="ExampleBox">
|
|
|
525 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
526 --DataFieldsMode All --output all -r SampleTATFP
|
|
|
527 -o Sample.sdf</div>
|
|
|
528 <p>
|
|
|
529 </p>
|
|
|
530 <h2>AUTHOR</h2>
|
|
|
531 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
|
|
|
532 <p>
|
|
|
533 </p>
|
|
|
534 <h2>SEE ALSO</h2>
|
|
|
535 <p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>, <a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>, 
|
|
|
536 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>, 
|
|
|
537 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, 
|
|
|
538 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
|
|
|
539 </p>
|
|
|
540 <p>
|
|
|
541 </p>
|
|
|
542 <h2>COPYRIGHT</h2>
|
|
|
543 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
|
|
|
544 <p>This file is part of MayaChemTools.</p>
|
|
|
545 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
546 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
547 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
548 any later version.</p>
|
|
|
549 <p> </p><p> </p><div class="DocNav">
|
|
|
550 <table width="100%" border=0 cellpadding=0 cellspacing=2>
|
|
|
551 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalAtomTorsionsFingerprints.pl</strong></td></tr>
|
|
|
552 </table>
|
|
|
553 </div>
|
|
|
554 <br />
|
|
|
555 <center>
|
|
|
556 <img src="../../images/h2o2.png">
|
|
|
557 </center>
|
|
|
558 </body>
|
|
|
559 </html>
|
