Mercurial > repos > deepakjadmin > mayatool3_test2

comparison docs/scripts/html/TopologicalAtomTripletsFingerprints.html @ 0:4816e4a8ae95 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 09:23:18 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:4816e4a8ae95
1 <html>
2 <head>
3 <title>MayaChemTools:Documentation:TopologicalAtomTripletsFingerprints.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="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalAtomTripletsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomTripletsFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/TopologicalAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/TopologicalAtomTripletsFingerprints.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>TopologicalAtomTripletsFingerprints.pl - Generate topological atom triplets fingerprints for SD files</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>TopologicalAtomTripletsFingerprints.pl SDFile(s)...</p>
26 <p>TopologicalAtomTripletsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
27 [<strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes</em>]
28 [<strong>--AtomicInvariantsToUse</strong> <em>&quot;AtomicInvariant,AtomicInvariant...&quot;</em>]
29 [<strong>--FunctionalClassesToUse</strong> <em>&quot;FunctionalClass1,FunctionalClass2...&quot;</em>]
30 [<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>] [<strong>--CompoundIDLabel</strong> <em>text</em>]
31 [<strong>--CompoundIDMode</strong>] [<strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</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>--MinDistance</strong> <em>number</em>] [<strong>--MaxDistance</strong> <em>number</em>]
35 [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>]
36 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-u, --UseTriangleInequality</strong> <em>Yes | No</em>]
37 [<strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>]
38 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
39 <p>
40 </p>
41 <h2>DESCRIPTION</h2>
42 <p>Generate topological atom triplets fingerprints for <em>SDFile(s)</em> and create
43 appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to
44 molecular fingerprints.</p>
45 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
46 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
47 can be specified either by <em>*.sdf</em> or the current directory name.</p>
48 <p>The current release of MayaChemTools supports generation of topological atom triplets
49 fingerprints corresponding to following <strong>-a, --AtomIdentifierTypes</strong>:</p>
50 <div class="OptionsBox">
51 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
52 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
53 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
54 <p>Based on the values specified for <strong>-a, --AtomIdentifierType</strong> and <strong>--AtomicInvariantsToUse</strong>,
55 initial atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance
56 matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom
57 pairs within <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> are identified and counted. An atom triplet
58 identifier is generated for each unique atom triplet; the format of the atom triplet identifier is:</p>
59 <div class="OptionsBox">
60 &lt;ATx&gt;-Dyz-&lt;ATy&gt;-Dxz-&lt;ATz&gt;-Dxy</div>
61 <div class="OptionsBox">
62 ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z
63 <br/> Dxy: Distance between atom x and atom y
64 <br/> Dxz: Distance between atom x and atom z
65 <br/> Dyz: Distance between atom y and atom z</div>
66 <div class="OptionsBox">
67 where &lt;AT1&gt;-D23 &lt;= &lt;AT2&gt;-D13 &lt;= &lt;AT3&gt;-D12</div>
68 <p>The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute
69 topological atom triplets fingerprints of the molecule.</p>
70 <p>Example of <em>SD</em> file containing topological atom triplets fingerprints string data:</p>
71 <div class="OptionsBox">
72 ... ...
73 <br/> ... ...
74 <br/> $$$$
75 <br/> ... ...
76 <br/> ... ...
77 <br/> ... ...
78 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
79 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
80 <br/> ... ...
81 <br/> 2 3 1 0 0 0 0
82 <br/> ... ...
83 <br/> M END
84 <br/> &gt; &lt;CmpdID&gt;
85 <br/> Cmpd1</div>
86 <div class="OptionsBox">
87 &gt; &lt;TopologicalAtomTripletsFingerprints&gt;
88 <br/> FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi
89 <br/> nDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1.B
90 <br/> O1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D10-C
91 <br/> .X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1...;
92 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2
93 <br/> 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...</div>
94 <div class="OptionsBox">
95 $$$$
96 <br/> ... ...
97 <br/> ... ...</div>
98 <p>Example of <em>FP</em> file containing topological atom triplets fingerprints string data:</p>
99 <div class="OptionsBox">
100 #
101 <br/> # Package = MayaChemTools 7.4
102 <br/> # Release Date = Oct 21, 2010
103 <br/> #
104 <br/> # TimeStamp = Fri Mar 11 15:24:01 2011
105 <br/> #
106 <br/> # FingerprintsStringType = FingerprintsVector
107 <br/> #
108 <br/> # Description = TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi...
109 <br/> # VectorStringFormat = IDsAndValuesString
110 <br/> # VectorValuesType = NumericalValues
111 <br/> #
112 <br/> Cmpd1 3096;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2...;1 2 2 2 2...
113 <br/> Cmpd2 1093;C.X1.BO1.H3-D1-C.X1.BO1.H3-D3-C.X2.BO2.H2-D4...;2 2 2 2 2...
114 <br/> ... ...
115 <br/> ... ..</div>
116 <p>Example of CSV <em>Text</em> file containing topological atom triplets fingerprints string data:</p>
117 <div class="OptionsBox">
118 &quot;CompoundID&quot;,&quot;TopologicalAtomTripletsFingerprints&quot;
119 <br/> &quot;Cmpd1&quot;,&quot;FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAto
120 <br/> mTypes:MinDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesStri
121 <br/> ng;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2
122 <br/> .H2-D10-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1....;
123 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2
124 <br/> 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...
125 <br/> ... ...
126 <br/> ... ...</div>
127 <p>The current release of MayaChemTools generates the following types of topological atom triplets
128 fingerprints vector strings:</p>
129 <div class="OptionsBox">
130 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
131 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
132 <br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
133 <br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
134 <br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
135 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
136 <br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div>
137 <div class="OptionsBox">
138 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
139 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
140 <br/> ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO
141 <br/> 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X
142 <br/> 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2
143 <br/> -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...</div>
144 <div class="OptionsBox">
145 FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan
146 <br/> ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D
147 <br/> 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_
148 <br/> 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_
149 <br/> 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...;
150 <br/> 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2
151 <br/> 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...</div>
152 <div class="OptionsBox">
153 FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance
154 <br/> 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D
155 <br/> 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC
156 <br/> H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1-
157 <br/> aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...;
158 <br/> 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2
159 <br/> 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1
160 <br/> 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...</div>
161 <div class="OptionsBox">
162 FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi
163 <br/> nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1
164 <br/> -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal
165 <br/> -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar
166 <br/> -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...;
167 <br/> 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5
168 <br/> 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3
169 <br/> 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...</div>
170 <div class="OptionsBox">
171 FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance
172 <br/> 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1-
173 <br/> N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A
174 <br/> -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B
175 <br/> -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3-
176 <br/> O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-...</div>
177 <div class="OptionsBox">
178 FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1
179 <br/> :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11
180 <br/> -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D
181 <br/> 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C
182 <br/> 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1
183 <br/> -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS...</div>
184 <div class="OptionsBox">
185 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
186 <br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
187 <br/> .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
188 <br/> D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
189 <br/> -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
190 <br/> 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...</div>
191 <div class="OptionsBox">
192 FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1:
193 <br/> MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non
194 <br/> e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D
195 <br/> 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5
196 N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21-
197 <br/> D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-...</div>
198 <div class="OptionsBox">
199 FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M
200 <br/> axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3
201 <br/> -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9
202 <br/> C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1-
203 <br/> C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5-
204 <br/> C_3-D6 C_2-D1-C_3-D5-O_3-D4 C_2-D1-C_3-D6-C_3-D7 C_2-D1-C_3-D7-C_3-...</div>
205 <p>
206 </p>
207 <h2>OPTIONS</h2>
208 <dl>
209 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
210 <dd>
211 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
212 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
213 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
214 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
215 <p>The supported aromaticity model names along with model specific control parameters
216 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
217 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
218 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
219 for detecting aromaticity corresponding to a specific model.</p>
220 </dd>
221 <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt>
222 <dd>
223 <p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
224 atoms during calculation of topological atom triplets fingerprints. Possible values in the current
225 release are: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
226 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
227 TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p>
228 </dd>
229 <dt><strong><strong>--AtomicInvariantsToUse</strong> <em>&quot;AtomicInvariant,AtomicInvariant...&quot;</em></strong></dt>
230 <dd>
231 <p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
232 option. It's a list of comma separated valid atomic invariant atom types.</p>
233 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
234 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
235 <p>The atomic invariants abbreviations correspond to:</p>
236 <div class="OptionsBox">
237 AS = Atom symbol corresponding to element symbol</div>
238 <div class="OptionsBox">
239 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
240 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
241 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
242 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
243 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
244 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
245 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
246 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
247 <br/> RA = Ring atom annotation indicating whether atom is a ring
248 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
249 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
250 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
251 3 (triplet)</div>
252 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
253 <div class="OptionsBox">
254 AS.X&lt;n&gt;.BO&lt;n&gt;.LBO&lt;n&gt;.&lt;SB&gt;&lt;n&gt;.&lt;DB&gt;&lt;n&gt;.&lt;TB&gt;&lt;n&gt;.H&lt;n&gt;.Ar.RA.FC&lt;+n/-n&gt;.MN&lt;n&gt;.SM&lt;n&gt;</div>
255 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
256 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
257 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
258 are also allowed:</p>
259 <div class="OptionsBox">
260 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
261 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
262 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
263 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
264 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
265 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
266 <br/> H : NumOfImplicitAndExplicitHydrogens
267 <br/> Ar : Aromatic
268 <br/> RA : RingAtom
269 <br/> FC : FormalCharge
270 <br/> MN : MassNumber
271 <br/> SM : SpinMultiplicity</div>
272 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
273 atom types.</p>
274 </dd>
275 <dt><strong><strong>--FunctionalClassesToUse</strong> <em>&quot;FunctionalClass1,FunctionalClass2...&quot;</em></strong></dt>
276 <dd>
277 <p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
278 option. It's a list of comma separated valid functional classes.</p>
279 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
280 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
281 <p>The functional class abbreviations correspond to:</p>
282 <div class="OptionsBox">
283 HBD: HydrogenBondDonor
284 <br/> HBA: HydrogenBondAcceptor
285 <br/> PI : PositivelyIonizable
286 <br/> NI : NegativelyIonizable
287 <br/> Ar : Aromatic
288 <br/> Hal : Halogen
289 <br/> H : Hydrophobic
290 <br/> RA : RingAtom
291 <br/> CA : ChainAtom</div>
292 <div class="OptionsBox">
293 Functional class atom type specification for an atom corresponds to:</div>
294 <div class="OptionsBox">
295 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div>
296 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
297 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
298 <div class="OptionsBox">
299 HydrogenBondDonor: NH, NH2, OH
300 <br/> HydrogenBondAcceptor: N[!H], O
301 <br/> PositivelyIonizable: +, NH2
302 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
303 </dd>
304 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
305 <dd>
306 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
307 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
308 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
309 IDs like LabelPrefixString&lt;Number&gt;. Default value, <em>Cmpd</em>, generates compound IDs which
310 look like Cmpd&lt;Number&gt;.</p>
311 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
312 <div class="OptionsBox">
313 MolID
314 <br/> ExtReg</div>
315 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
316 <div class="OptionsBox">
317 Compound</div>
318 <p>The value specified above generates compound IDs which correspond to Compound&lt;Number&gt;
319 instead of default value of Cmpd&lt;Number&gt;.</p>
320 </dd>
321 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
322 <dd>
323 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
324 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
325 </dd>
326 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
327 <dd>
328 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
329 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
330 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
331 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
332 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
333 Default value: <em>LabelPrefix</em>.</p>
334 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
335 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
336 values are replaced with sequential compound IDs.</p>
337 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
338 </dd>
339 <dt><strong><strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em></strong></dt>
340 <dd>
341 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
342 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
343 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
344 <p>Examples:</p>
345 <div class="OptionsBox">
346 Extreg
347 <br/> MolID,CompoundName</div>
348 </dd>
349 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
350 <dd>
351 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
352 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
353 data field; transfer SD data files common to all compounds; extract specified data fields;
354 generate a compound ID using molname line, a compound prefix, or a combination of both.
355 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
356 </dd>
357 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
358 <dd>
359 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
360 Default value: <em>Yes</em>.</p>
361 <p>By default, compound data is checked before calculating fingerprints and compounds containing
362 atom data corresponding to non-element symbols or no atom data are ignored.</p>
363 </dd>
364 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
365 <dd>
366 <p>SD data label or text file column label to use for fingerprints string in output SD or
367 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>TopologicalAtomTripletsFingerprints</em>.</p>
368 </dd>
369 <dt><strong><strong>-h, --help</strong></strong></dt>
370 <dd>
371 <p>Print this help message.</p>
372 </dd>
373 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
374 <dd>
375 <p>Generate fingerprints for only the largest component in molecule. Possible values:
376 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
377 <p>For molecules containing multiple connected components, fingerprints can be generated
378 in two different ways: use all connected components or just the largest connected
379 component. By default, all atoms except for the largest connected component are
380 deleted before generation of fingerprints.</p>
381 </dd>
382 <dt><strong><strong>--MinDistance</strong> <em>number</em></strong></dt>
383 <dd>
384 <p>Minimum bond distance between atom triplets for generating topological atom triplets. Default value:
385 <em>1</em>. Valid values: positive integers and less than <strong>--MaxDistance</strong>.</p>
386 </dd>
387 <dt><strong><strong>--MaxDistance</strong> <em>number</em></strong></dt>
388 <dd>
389 <p>Maximum bond distance between atom triplets for generating topological atom triplets. Default value:
390 <em>10</em>. Valid values: positive integers and greater than <strong>--MinDistance</strong>.</p>
391 </dd>
392 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
393 <dd>
394 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
395 Default value: <em>comma</em></p>
396 </dd>
397 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
398 <dd>
399 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
400 </dd>
401 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
402 <dd>
403 <p>Overwrite existing files.</p>
404 </dd>
405 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
406 <dd>
407 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
408 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
409 </dd>
410 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
411 <dd>
412 <p>New file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. Default for new file names:
413 &lt;SDFileName&gt;&lt;TopologicalAtomTripletsFP&gt;.&lt;Ext&gt;. The file type determines &lt;Ext&gt; value.
414 The sdf, fpf, csv, and tsv &lt;Ext&gt; values are used for SD, FP, comma/semicolon, and tab
415 delimited text files, respectively.This option is ignored for multiple input files.</p>
416 </dd>
417 <dt><strong><strong>-u, --UseTriangleInequality</strong> <em>Yes | No</em></strong></dt>
418 <dd>
419 <p>Specify whether to imply triangle distance inequality test to distances between atom pairs in
420 atom triplets during generation of atom triplets generation. Possible values: <em>Yes or No</em>.
421 Default value: <em>No</em>.</p>
422 <p>Triangle distance inequality test implies that distance or binned distance between any two atom
423 pairs in an atom triplet must be less than the sum of distances or binned distances between other
424 two atoms pairs and greater than the difference of their distances.</p>
425 <div class="OptionsBox">
426 For atom triplet ATx-Dyz-ATy-Dxz-ATz-Dxy to satisfy triangle inequality:</div>
427 <div class="OptionsBox">
428 Dyz &gt; |Dxz - Dxy| and Dyz &lt; Dxz + Dxy
429 <br/> Dxz &gt; |Dyz - Dxy| and Dyz &lt; Dyz + Dxy
430 <br/> Dxy &gt; |Dyz - Dxz| and Dxy &lt; Dyz + Dxz</div>
431 </dd>
432 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
433 <dd>
434 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
435 <strong>--output</strong> option. Possible values: <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
436 ValuesAndIDsPairsString</em>. Default value: <em>IDsAndValuesString</em>.</p>
437 <p>Examples:</p>
438 <div class="OptionsBox">
439 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
440 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
441 <br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
442 <br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
443 <br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
444 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
445 <br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div>
446 <div class="OptionsBox">
447 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
448 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
449 <br/> ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO
450 <br/> 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X
451 <br/> 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2
452 <br/> -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...</div>
453 </dd>
454 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
455 <dd>
456 <p>Location of working directory. Default value: current directory.</p>
457 </dd>
458 </dl>
459 <p>
460 </p>
461 <h2>EXAMPLES</h2>
462 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
463 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
464 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
465 <div class="ExampleBox">
466 % TopologicalAtomTripletsFingerprints.pl -r SampleTATFP -o Sample.sdf</div>
467 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
468 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf,
469 SampleTATFP.fpf and SampleTATFP.csv files containing sequential compound IDs in CSV file along
470 with fingerprints vector strings data, type:</p>
471 <div class="ExampleBox">
472 % TopologicalAtomTripletsFingerprints.pl --output all -r SampleTATFP
473 -o Sample.sdf</div>
474 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
475 10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTATFP.csv
476 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
477 <div class="ExampleBox">
478 % TopologicalAtomTripletsFingerprints.pl --VectorStringFormat
479 IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf</div>
480 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
481 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTATFP.csv
482 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
483 <div class="ExampleBox">
484 % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes
485 -r SampleTATFP -o Sample.sdf</div>
486 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
487 10 using E-state atom types in IDsAndValuesString format and create a SampleTATFP.csv
488 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
489 <div class="ExampleBox">
490 % TopologicalAtomTripletsFingerprints.pl -a EStateAtomTypes
491 -r SampleTATFP -o Sample.sdf</div>
492 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
493 10 using functional class atom types in IDsAndValuesString format and create a SampleTATFP.csv
494 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
495 <div class="ExampleBox">
496 % TopologicalAtomTripletsFingerprints.pl -a FunctionalClassAtomTypes
497 -r SampleTATFP -o Sample.sdf</div>
498 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
499 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTATFP.csv
500 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
501 <div class="ExampleBox">
502 % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes
503 -r SampleTATFP -o Sample.sdf</div>
504 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
505 10 using MM94 atom types in IDsAndValuesString format and create a SampleTATFP.csv
506 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
507 <div class="ExampleBox">
508 % TopologicalAtomTripletsFingerprints.pl -a MMFF94AtomTypes
509 -r SampleTATFP -o Sample.sdf</div>
510 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
511 10 using SLogP atom types in IDsAndValuesString format and create a SampleTATFP.csv
512 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
513 <div class="ExampleBox">
514 % TopologicalAtomTripletsFingerprints.pl -a SLogPAtomTypes
515 -r SampleTATFP -o Sample.sdf</div>
516 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
517 10 using SYBYL atom types in IDsAndValuesString format and create a SampleTATFP.csv
518 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
519 <div class="ExampleBox">
520 % TopologicalAtomTripletsFingerprints.pl -a SYBYLAtomTypes
521 -r SampleTATFP -o Sample.sdf</div>
522 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
523 10 using TPSA atom types in IDsAndValuesString format and create a SampleTATFP.csv
524 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
525 <div class="ExampleBox">
526 % TopologicalAtomTripletsFingerprints.pl -a TPSAAtomTypes
527 -r SampleTATFP -o Sample.sdf</div>
528 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
529 10 using UFF atom types in IDsAndValuesString format and create a SampleTATFP.csv
530 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
531 <div class="ExampleBox">
532 % TopologicalAtomTripletsFingerprints.pl -a UFFAtomTypes
533 -r SampleTATFP -o Sample.sdf</div>
534 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
535 6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
536 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
537 <div class="ExampleBox">
538 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
539 --MinDistance 1 --MaxDistance 6 -r SampleTATFP -o Sample.sdf</div>
540 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
541 10 using only AS,X atomic invariants atom types in IDsAndValuesString format and create a
542 SampleTATFP.csv file containing sequential compound IDs along with fingerprints vector strings
543 data, type:</p>
544 <div class="ExampleBox">
545 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
546 --AtomicInvariantsToUse &quot;AS,X&quot; --MinDistance 1 --MaxDistance 6
547 -r SampleTATFP -o Sample.sdf</div>
548 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
549 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
550 file containing compound ID from molecule name line along with fingerprints vector strings
551 data, type:</p>
552 <div class="ExampleBox">
553 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
554 --DataFieldsMode CompoundID -CompoundIDMode MolName
555 -r SampleTATFP -o Sample.sdf</div>
556 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
557 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
558 file containing compound IDs using specified data field along with fingerprints vector strings
559 data, type:</p>
560 <div class="ExampleBox">
561 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
562 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
563 Mol_ID -r SampleTATFP -o Sample.sdf</div>
564 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
565 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
566 file containing compound ID using combination of molecule name line and an explicit compound
567 prefix along with fingerprints vector strings data, type:</p>
568 <div class="ExampleBox">
569 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
570 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
571 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf</div>
572 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
573 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
574 file containing specific data fields columns along with fingerprints vector strings
575 data, type:</p>
576 <div class="ExampleBox">
577 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
578 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP
579 -o Sample.sdf</div>
580 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
581 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
582 file containing common data fields columns along with fingerprints vector strings
583 data, type:</p>
584 <div class="ExampleBox">
585 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
586 --DataFieldsMode Common -r SampleTATFP -o Sample.sdf</div>
587 <p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
588 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf,
589 SampleTATFP.fpf and SampleTATFP.csv files containing all data fields columns in CSV file along with
590 fingerprints data, type:</p>
591 <div class="ExampleBox">
592 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes
593 --DataFieldsMode All --output all -r SampleTATFP
594 -o Sample.sdf</div>
595 <p>
596 </p>
597 <h2>AUTHOR</h2>
598 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
599 <p>
600 </p>
601 <h2>SEE ALSO</h2>
602 <p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>,&nbsp<a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>,&nbsp<a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>,&nbsp
603 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>,&nbsp<a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>,&nbsp
604 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,&nbsp
605 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
606 </p>
607 <p>
608 </p>
609 <h2>COPYRIGHT</h2>
610 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
611 <p>This file is part of MayaChemTools.</p>
612 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
613 the terms of the GNU Lesser General Public License as published by the Free
614 Software Foundation; either version 3 of the License, or (at your option)
615 any later version.</p>
616 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
617 <table width="100%" border=0 cellpadding=0 cellspacing=2>
618 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalAtomTripletsFingerprints.pl</strong></td></tr>
619 </table>
620 </div>
621 <br />
622 <center>
623 <img src="../../images/h2o2.png">
624 </center>
625 </body>
626 </html>