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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/TopologicalAtomTorsionsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/TopologicalAtomTorsionsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/TopologicalAtomTorsionsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/TopologicalAtomTorsionsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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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>&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>--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 &lt;AtomType1&gt;-&lt;AtomType2&gt;-&lt;AtomType3&gt;-&lt;AtomType4&gt;</div>
57 <div class="OptionsBox">
58 AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types</div>
59 <div class="OptionsBox">
60 where AtomType1 &lt;= AtomType2 &lt;= AtomType3 &lt;= 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/> $$$$
68 <br/> ... ...
69 <br/> ... ...
70 <br/> ... ...
71 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
72 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
73 <br/> ... ...
74 <br/> 2 3 1 0 0 0 0
75 <br/> ... ...
76 <br/> M END
77 <br/> &gt; &lt;CmpdID&gt;
78 <br/> Cmpd1</div>
79 <div class="OptionsBox">
80 &gt; &lt;TopologicalAtomTorsionsFingerprints&gt;
81 <br/> FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;33
82 <br/> ;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.
83 <br/> X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO2.H
84 <br/> 2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O.X1....;
85 <br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div>
86 <div class="OptionsBox">
87 $$$$
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 &quot;CompoundID&quot;,&quot;TopologicalAtomTorsionsFingerprints&quot;
111 <br/> &quot;Cmpd1&quot;,&quot;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>&quot;AtomicInvariant,AtomicInvariant...&quot;</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&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
219 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
220 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
221 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
222 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
223 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
224 <br/> H&lt;n&gt; = 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&lt;+n/-n&gt; = Formal charge assigned to atom
228 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
229 <br/> SM&lt;n&gt; = 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&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>
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>&quot;FunctionalClass1,FunctionalClass2...&quot;</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&lt;Number&gt;. Default value, <em>Cmpd</em>, generates compound IDs which
289 look like Cmpd&lt;Number&gt;.</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&lt;Number&gt;
298 instead of default value of Cmpd&lt;Number&gt;.</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>&quot;FieldLabel1,FieldLabel2,...&quot;</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: &lt;Root&gt;.&lt;Ext&gt;. Default for new file names:
382 &lt;SDFileName&gt;&lt;TopologicalAtomTorsionsFP&gt;.&lt;Ext&gt;. The file type determines &lt;Ext&gt; value.
383 The sdf, fpf, csv, and tsv &lt;Ext&gt; 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 &quot;AS,X&quot; -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>,&nbsp<a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>,&nbsp<a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>,&nbsp
536 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>,&nbsp<a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>,&nbsp
537 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,&nbsp<a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>,&nbsp
538 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>,&nbsp<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>&nbsp</p><p>&nbsp</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>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>
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