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3 <title>MayaChemTools:Documentation:TopologicalAtomPairsFingerprints.pl</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TextFilesToSDFiles.html" title="TextFilesToSDFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalAtomPairsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomPairsFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/TopologicalAtomPairsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/TopologicalAtomPairsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/TopologicalAtomPairsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/TopologicalAtomPairsFingerprints.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>TopologicalAtomPairsFingerprints.pl - Generate topological atom pairs fingerprints for SD files</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>TopologicalAtomPairsFingerprints.pl SDFile(s)...</p>
26 <p>TopologicalAtomPairsFingerprints.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>]
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 pairs fingerprints [ Ref 57, Ref 59, Ref 72 ] 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 pairs
49 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 pair
58 identifier is generated for each unique atom pair; the format of the atom pair identifier is:</p>
59 <div class="OptionsBox">
60 &lt;AtomType1&gt;-D&lt;n&gt;-&lt;AtomType2&gt;</div>
61 <div class="OptionsBox">
62 AtomType1, AtomType2: Atom types assigned to atom1 and atom2
63 <br/> D: Distance between atom1 and atom2</div>
64 <div class="OptionsBox">
65 where AtomType1 &lt;= AtomType2</div>
66 <p>The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute
67 topological atom pairs fingerprints of the molecule.</p>
68 <p>Example of <em>SD</em> file containing topological atom pairs fingerprints string data:</p>
69 <div class="OptionsBox">
70 ... ...
71 <br/> ... ...
72 <br/> $$$$
73 <br/> ... ...
74 <br/> ... ...
75 <br/> ... ...
76 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
77 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
78 <br/> ... ...
79 <br/> 2 3 1 0 0 0 0
80 <br/> ... ...
81 <br/> M END
82 <br/> &gt; &lt;CmpdID&gt;
83 <br/> Cmpd1</div>
84 <div class="OptionsBox">
85 &gt; &lt;TopologicalAtomPairsFingerprints&gt;
86 <br/> FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi
87 <br/> stance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1.H
88 <br/> 3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.H1
89 <br/> C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-C.X2...;
90 <br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
91 <br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...</div>
92 <div class="OptionsBox">
93 $$$$
94 <br/> ... ...
95 <br/> ... ...</div>
96 <p>Example of <em>FP</em> file containing topological atom pairs fingerprints string data:</p>
97 <div class="OptionsBox">
98 #
99 <br/> # Package = MayaChemTools 7.4
100 <br/> # Release Date = Oct 21, 2010
101 <br/> #
102 <br/> # TimeStamp = Fri Mar 11 15:04:36 2011
103 <br/> #
104 <br/> # FingerprintsStringType = FingerprintsVector
105 <br/> #
106 <br/> # Description = TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi...
107 <br/> # VectorStringFormat = IDsAndValuesString
108 <br/> # VectorValuesType = NumericalValues
109 <br/> #
110 <br/> Cmpd1 223;C.X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2...;1 1...
111 <br/> Cmpd2 128;C.X1.BO1.H3-D1-C.X2.BO2.H2 C.X1.BO1.H3-D1-C.X3.BO4...;1 1...
112 <br/> ... ...
113 <br/> ... ..</div>
114 <p>Example of CSV <em>Text</em> file containing topological atom pairs fingerprints string data:</p>
115 <div class="OptionsBox">
116 &quot;CompoundID&quot;,&quot;TopologicalAtomPairsFingerprints&quot;
117 <br/> &quot;Cmpd1&quot;,&quot;FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTy
118 <br/> pes:MinDistance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C
119 <br/> .X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X
120 <br/> 3.BO3.H1C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1...;
121 <br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
122 <br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...
123 <br/> ... ...
124 <br/> ... ...</div>
125 <p>The current release of MayaChemTools generates the following types of topological atom pairs
126 fingerprints vector strings:</p>
127 <div class="OptionsBox">
128 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
129 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
130 <br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
131 <br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
132 <br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
133 <br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...</div>
134 <div class="OptionsBox">
135 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
136 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
137 <br/> 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
138 <br/> C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2
139 <br/> .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
140 <br/> 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...</div>
141 <div class="OptionsBox">
142 FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
143 <br/> :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D
144 <br/> 1-C_R C_2-D1-N_3 C_2-D1-O_2 C_2-D1-O_3 C_3-D1-C_3 C_3-D1-C_R C_3-D1-N_
145 <br/> R C_3-D1-O_3 C_R-D1-C_R C_R-D1-F_ C_R-D1-N_3 C_R-D1-N_R C_2-D2-C_3 C_2
146 <br/> 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
147 <br/> 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...</div>
148 <div class="OptionsBox">
149 FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
150 <br/> axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH-
151 <br/> D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH
152 <br/> aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...;
153 <br/> 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
154 <br/> 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...</div>
155 <div class="OptionsBox">
156 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
157 <br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
158 <br/> Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
159 <br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
160 <br/> 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
161 <br/> 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...</div>
162 <div class="OptionsBox">
163 FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
164 <br/> axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2
165 <br/> C5A-D1-CB 1 C5A-D1-CR 1 C5A-D1-N5 2 C5B-D1-C5B 1 C5B-D1-C=ON 1 C5B-D1-
166 <br/> CB 1 C=ON-D1-NC=O 1 C=ON-D1-O=CN 1 CB-D1-CB 18 CB-D1-F 1 CB-D1-NC=O 1
167 <br/> COO-D1-CR 1 COO-D1-O=CO 1 COO-D1-OC=O 1 CR-D1-CR 7 CR-D1-N5 1 CR-D1-OR
168 <br/> 2 C5A-D2-C5A 1 C5A-D2-C5B 2 C5A-D2-C=ON 1 C5A-D2-CB 3 C5A-D2-CR 4 ...</div>
169 <div class="OptionsBox">
170 FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
171 <br/> xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1
172 <br/> -D1-C11 2 C1-D1-C5 1 C1-D1-CS 4 C10-D1-N11 1 C11-D1-C21 1 C14-D1-C18 2
173 <br/> C14-D1-F 1 C18-D1-C18 10 C18-D1-C20 4 C18-D1-C22 2 C20-D1-C20 3 C20-D
174 <br/> 1-C21 1 C20-D1-N11 1 C21-D1-C21 1 C21-D1-C5 1 C21-D1-N11 1 C22-D1-N4 1
175 <br/> C5-D1-N4 1 C5-D1-O10 1 C5-D1-O2 1 C5-D1-O9 1 CS-D1-O2 2 C1-D2-C1 3...</div>
176 <div class="OptionsBox">
177 FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
178 <br/> xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C
179 <br/> .2-D1-C.ar 1 C.2-D1-N.am 1 C.2-D1-O.2 1 C.2-D1-O.co2 2 C.3-D1-C.3 7 C.
180 <br/> 3-D1-C.ar 1 C.3-D1-N.ar 1 C.3-D1-O.3 2 C.ar-D1-C.ar 23 C.ar-D1-F 1 C.a
181 <br/> r-D1-N.am 1 C.ar-D1-N.ar 2 C.2-D2-C.3 1 C.2-D2-C.ar 3 C.3-D2-C.3 5 C.3
182 <br/> -D2-C.ar 5 C.3-D2-N.ar 2 C.3-D2-O.3 4 C.3-D2-O.co2 2 C.ar-D2-C.ar 2...</div>
183 <div class="OptionsBox">
184 FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
185 <br/> Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7
186 <br/> -D1-None 2 None-D1-None 34 None-D1-O3 2 None-D1-O4 3 N21-D2-None 5 N7-
187 <br/> D2-None 3 N7-D2-O3 1 None-D2-None 44 None-D2-O3 2 None-D2-O4 5 O3-D2-O
188 <br/> 4 1 N21-D3-None 7 N7-D3-None 4 None-D3-None 45 None-D3-O3 4 None-D3-O4
189 <br/> 5 N21-D4-N7 1 N21-D4-None 5 N21-D4-O3 1 N21-D4-O4 1 N7-D4-None 4 N...</div>
190 <div class="OptionsBox">
191 FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
192 <br/> istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2
193 <br/> -D1-C_R 1 C_2-D1-N_3 1 C_2-D1-O_2 2 C_2-D1-O_3 1 C_3-D1-C_3 7 C_3-D1-C
194 <br/> _R 1 C_3-D1-N_R 1 C_3-D1-O_3 2 C_R-D1-C_R 23 C_R-D1-F_ 1 C_R-D1-N_3 1
195 <br/> C_R-D1-N_R 2 C_2-D2-C_3 1 C_2-D2-C_R 3 C_3-D2-C_3 5 C_3-D2-C_R 5 C_3-D
196 <br/> 2-N_R 2 C_3-D2-O_2 1 C_3-D2-O_3 5 C_R-D2-C_R 28 C_R-D2-F_ 2 C_R-D2-...</div>
197 <p>
198 </p>
199 <h2>OPTIONS</h2>
200 <dl>
201 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
202 <dd>
203 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
204 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
205 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
206 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
207 <p>The supported aromaticity model names along with model specific control parameters
208 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
209 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
210 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
211 for detecting aromaticity corresponding to a specific model.</p>
212 </dd>
213 <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt>
214 <dd>
215 <p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
216 atoms during calculation of topological atom pairs fingerprints. Possible values in the current
217 release are: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
218 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
219 TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p>
220 </dd>
221 <dt><strong><strong>--AtomicInvariantsToUse</strong> <em>&quot;AtomicInvariant,AtomicInvariant...&quot;</em></strong></dt>
222 <dd>
223 <p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
224 option. It's a list of comma separated valid atomic invariant atom types.</p>
225 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
226 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
227 <p>The atomic invariants abbreviations correspond to:</p>
228 <div class="OptionsBox">
229 AS = Atom symbol corresponding to element symbol</div>
230 <div class="OptionsBox">
231 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
232 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
233 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
234 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
235 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
236 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
237 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
238 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
239 <br/> RA = Ring atom annotation indicating whether atom is a ring
240 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
241 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
242 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
243 3 (triplet)</div>
244 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
245 <div class="OptionsBox">
246 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>
247 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
248 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
249 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
250 are also allowed:</p>
251 <div class="OptionsBox">
252 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
253 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
254 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
255 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
256 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
257 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
258 <br/> H : NumOfImplicitAndExplicitHydrogens
259 <br/> Ar : Aromatic
260 <br/> RA : RingAtom
261 <br/> FC : FormalCharge
262 <br/> MN : MassNumber
263 <br/> SM : SpinMultiplicity</div>
264 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
265 atom types.</p>
266 </dd>
267 <dt><strong><strong>--FunctionalClassesToUse</strong> <em>&quot;FunctionalClass1,FunctionalClass2...&quot;</em></strong></dt>
268 <dd>
269 <p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
270 option. It's a list of comma separated valid functional classes.</p>
271 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
272 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
273 <p>The functional class abbreviations correspond to:</p>
274 <div class="OptionsBox">
275 HBD: HydrogenBondDonor
276 <br/> HBA: HydrogenBondAcceptor
277 <br/> PI : PositivelyIonizable
278 <br/> NI : NegativelyIonizable
279 <br/> Ar : Aromatic
280 <br/> Hal : Halogen
281 <br/> H : Hydrophobic
282 <br/> RA : RingAtom
283 <br/> CA : ChainAtom</div>
284 <div class="OptionsBox">
285 Functional class atom type specification for an atom corresponds to:</div>
286 <div class="OptionsBox">
287 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div>
288 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
289 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
290 <div class="OptionsBox">
291 HydrogenBondDonor: NH, NH2, OH
292 <br/> HydrogenBondAcceptor: N[!H], O
293 <br/> PositivelyIonizable: +, NH2
294 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
295 </dd>
296 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
297 <dd>
298 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
299 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
300 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
301 IDs like LabelPrefixString&lt;Number&gt;. Default value, <em>Cmpd</em>, generates compound IDs which
302 look like Cmpd&lt;Number&gt;.</p>
303 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
304 <div class="OptionsBox">
305 MolID
306 <br/> ExtReg</div>
307 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
308 <div class="OptionsBox">
309 Compound</div>
310 <p>The value specified above generates compound IDs which correspond to Compound&lt;Number&gt;
311 instead of default value of Cmpd&lt;Number&gt;.</p>
312 </dd>
313 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
314 <dd>
315 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
316 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
317 </dd>
318 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
319 <dd>
320 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
321 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
322 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
323 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
324 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
325 Default value: <em>LabelPrefix</em>.</p>
326 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
327 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
328 values are replaced with sequential compound IDs.</p>
329 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
330 </dd>
331 <dt><strong><strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em></strong></dt>
332 <dd>
333 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
334 with generated fingerprints for <em>text | both</em> values of <strong>--output</strong> option.</p>
335 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
336 <p>Examples:</p>
337 <div class="OptionsBox">
338 Extreg
339 <br/> MolID,CompoundName</div>
340 </dd>
341 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
342 <dd>
343 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
344 with generated fingerprints for <em>text | both</em> values of <strong>--output</strong> option: transfer all SD
345 data field; transfer SD data files common to all compounds; extract specified data fields;
346 generate a compound ID using molname line, a compound prefix, or a combination of both.
347 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
348 </dd>
349 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
350 <dd>
351 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
352 Default value: <em>Yes</em>.</p>
353 <p>By default, compound data is checked before calculating fingerprints and compounds containing
354 atom data corresponding to non-element symbols or no atom data are ignored.</p>
355 </dd>
356 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
357 <dd>
358 <p>SD data label or text file column label to use for fingerprints string in output SD or
359 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>TopologicalAtomPairsFingerprints</em>.</p>
360 </dd>
361 <dt><strong><strong>-h, --help</strong></strong></dt>
362 <dd>
363 <p>Print this help message.</p>
364 </dd>
365 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
366 <dd>
367 <p>Generate fingerprints for only the largest component in molecule. Possible values:
368 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
369 <p>For molecules containing multiple connected components, fingerprints can be generated
370 in two different ways: use all connected components or just the largest connected
371 component. By default, all atoms except for the largest connected component are
372 deleted before generation of fingerprints.</p>
373 </dd>
374 <dt><strong><strong>--MinDistance</strong> <em>number</em></strong></dt>
375 <dd>
376 <p>Minimum bond distance between atom pairs for generating topological atom pairs. Default value:
377 <em>1</em>. Valid values: positive integers and less than <strong>--MaxDistance</strong>.</p>
378 </dd>
379 <dt><strong><strong>--MaxDistance</strong> <em>number</em></strong></dt>
380 <dd>
381 <p>Maximum bond distance between atom pairs for generating topological atom pairs. Default value:
382 <em>10</em>. Valid values: positive integers and greater than <strong>--MinDistance</strong>.</p>
383 </dd>
384 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
385 <dd>
386 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
387 Default value: <em>comma</em></p>
388 </dd>
389 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
390 <dd>
391 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
392 </dd>
393 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
394 <dd>
395 <p>Overwrite existing files.</p>
396 </dd>
397 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
398 <dd>
399 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
400 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
401 </dd>
402 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
403 <dd>
404 <p>New file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. Default for new file names:
405 &lt;SDFileName&gt;&lt;TopologicalAtomPairsFP&gt;.&lt;Ext&gt;. The file type determines &lt;Ext&gt; value.
406 The sdf, fpf, csv, and tsv &lt;Ext&gt; values are used for SD, FP, comma/semicolon, and tab
407 delimited text files, respectively.This option is ignored for multiple input files.</p>
408 </dd>
409 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
410 <dd>
411 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
412 <strong>--output</strong> option. Possible values: <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
413 ValuesAndIDsPairsString</em>. Default value: <em>IDsAndValuesString</em>.</p>
414 <p>Examples:</p>
415 <div class="OptionsBox">
416 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
417 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
418 <br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
419 <br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
420 <br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
421 <br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...</div>
422 <div class="OptionsBox">
423 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
424 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
425 <br/> 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
426 <br/> C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2
427 <br/> .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
428 <br/> 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...</div>
429 </dd>
430 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
431 <dd>
432 <p>Location of working directory. Default value: current directory.</p>
433 </dd>
434 </dl>
435 <p>
436 </p>
437 <h2>EXAMPLES</h2>
438 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
439 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
440 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
441 <div class="ExampleBox">
442 % TopologicalAtomPairsFingerprints.pl -r SampleTAPFP -o Sample.sdf</div>
443 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
444 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf,
445 SampleTAPFP.fpf and SampleTAPFP.csv files containing sequential compound IDs in CSV file along
446 with fingerprints vector strings data, type:</p>
447 <div class="ExampleBox">
448 % TopologicalAtomPairsFingerprints.pl --output all -r SampleTAPFP
449 -o Sample.sdf</div>
450 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
451 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTAPFP.csv
452 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
453 <div class="ExampleBox">
454 % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes
455 -r SampleTAPFP -o Sample.sdf</div>
456 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
457 10 using E-state types in IDsAndValuesString format and create a SampleTAPFP.csv
458 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
459 <div class="ExampleBox">
460 % TopologicalAtomPairsFingerprints.pl -a EStateAtomTypes
461 -r SampleTAPFP -o Sample.sdf</div>
462 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
463 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTAPFP.csv
464 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
465 <div class="ExampleBox">
466 % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes
467 -r SampleTAPFP -o Sample.sdf</div>
468 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
469 10 using functional class atom types in IDsAndValuesString format and create a SampleTAPFP.csv
470 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
471 <div class="ExampleBox">
472 % TopologicalAtomPairsFingerprints.pl -a FunctionalClassAtomTypes
473 -r SampleTAPFP -o Sample.sdf</div>
474 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
475 10 using MMFF94 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
476 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
477 <div class="ExampleBox">
478 % TopologicalAtomPairsFingerprints.pl -a MMFF94AtomTypes
479 -r SampleTAPFP -o Sample.sdf</div>
480 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
481 10 using SLogP atom types in IDsAndValuesString format and create a SampleTAPFP.csv
482 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
483 <div class="ExampleBox">
484 % TopologicalAtomPairsFingerprints.pl -a SLogPAtomTypes
485 -r SampleTAPFP -o Sample.sdf</div>
486 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
487 10 using SYBYL atom types in IDsAndValuesString format and create a SampleTAPFP.csv
488 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
489 <div class="ExampleBox">
490 % TopologicalAtomPairsFingerprints.pl -a SYBYLAtomTypes
491 -r SampleTAPFP -o Sample.sdf</div>
492 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
493 10 using TPSA atom types in IDsAndValuesString format and create a SampleTAPFP.csv
494 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
495 <div class="ExampleBox">
496 % TopologicalAtomPairsFingerprints.pl -a TPSAAtomTypes
497 -r SampleTAPFP -o Sample.sdf</div>
498 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
499 10 using UFF atom types in IDsAndValuesString format and create a SampleTAPFP.csv
500 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
501 <div class="ExampleBox">
502 % TopologicalAtomPairsFingerprints.pl -a UFFAtomTypes
503 -r SampleTAPFP -o Sample.sdf</div>
504 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
505 10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTAPFP.csv
506 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
507 <div class="ExampleBox">
508 % TopologicalAtomPairsFingerprints.pl --VectorStringFormat
509 IDsAndValuesPairsString -r SampleTAPFP -o Sample.sdf</div>
510 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
511 6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
512 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
513 <div class="ExampleBox">
514 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
515 --MinDistance 1 --MaxDistance 6 -r SampleTAPFP -o Sample.sdf</div>
516 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
517 10 using only AS,X atomic invariants atom types in IDsAndValuesString format and create a
518 SampleTAPFP.csv file containing sequential compound IDs along with fingerprints vector strings
519 data, type:</p>
520 <div class="ExampleBox">
521 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
522 --AtomicInvariantsToUse &quot;AS,X&quot; --MinDistance 1 --MaxDistance 6
523 -r SampleTAPFP -o Sample.sdf</div>
524 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
525 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
526 file containing compound ID from molecule name line along with fingerprints vector strings
527 data, type:</p>
528 <div class="ExampleBox">
529 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
530 --DataFieldsMode CompoundID -CompoundIDMode MolName
531 -r SampleTAPFP -o Sample.sdf</div>
532 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
533 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
534 file containing compound IDs using specified data field along with fingerprints vector strings
535 data, type:</p>
536 <div class="ExampleBox">
537 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
538 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
539 Mol_ID -r SampleTAPFP -o Sample.sdf</div>
540 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
541 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
542 file containing compound ID using combination of molecule name line and an explicit compound
543 prefix along with fingerprints vector strings data, type:</p>
544 <div class="ExampleBox">
545 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
546 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
547 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTAPFP -o Sample.sdf</div>
548 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
549 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
550 file containing specific data fields columns along with fingerprints vector strings
551 data, type:</p>
552 <div class="ExampleBox">
553 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
554 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTAPFP
555 -o Sample.sdf</div>
556 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
557 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
558 file containing common data fields columns along with fingerprints vector strings
559 data, type:</p>
560 <div class="ExampleBox">
561 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
562 --DataFieldsMode Common -r SampleTAPFP -o Sample.sdf</div>
563 <p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
564 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf,
565 SampleTAPFP.fpf and SampleTAPFP.csv files containing all data fields columns in CSV file along
566 with fingerprints data, type:</p>
567 <div class="ExampleBox">
568 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
569 --DataFieldsMode All --output all -r SampleTAPFP
570 -o Sample.sdf</div>
571 <p>
572 </p>
573 <h2>AUTHOR</h2>
574 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
575 <p>
576 </p>
577 <h2>SEE ALSO</h2>
578 <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
579 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>,&nbsp<a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>,&nbsp
580 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,&nbsp
581 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
582 </p>
583 <p>
584 </p>
585 <h2>COPYRIGHT</h2>
586 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
587 <p>This file is part of MayaChemTools.</p>
588 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
589 the terms of the GNU Lesser General Public License as published by the Free
590 Software Foundation; either version 3 of the License, or (at your option)
591 any later version.</p>
592 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
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594 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TextFilesToSDFiles.html" title="TextFilesToSDFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalAtomPairsFingerprints.pl</strong></td></tr>
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