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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysisTextFiles.html" title="ElementalAnalysisTextFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>EStateIndiciesFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/EStateIndiciesFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/EStateIndiciesFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/EStateIndiciesFingerprints.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>EStateIndiciesFingerprints.pl - Generate E-state indicies fingerprints for SD files</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>EStateIndiciesFingerprints.pl SDFile(s)...</p>
26 <p>EStateIndiciesFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
27 [<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>]
28 [<strong>--CompoundIDLabel</strong> <em>text</em>] [<strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>]
29 [<strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em>] [<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>]
30 [<strong>-e, --EStateAtomTypesSetToUse</strong> <em>ArbitrarySize or FixedSize</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>]
31 [<strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>] [<strong>--FingerprintsLabel</strong> <em>text</em>]
32 [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>]
33 [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>]
34 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-s, --size</strong> <em>number</em>] [<strong>--ValuesPrecision</strong> <em>number</em>]
35 [<strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>]
36 [<strong>-w, --WorkingDir</strong> <em>DirName</em>]</p>
37 <p>
38 </p>
39 <h2>DESCRIPTION</h2>
40 <p>Generate E-state indicies fingerprints [ Ref 75-78 ] for <em>SDFile(s)</em> and create appropriate SD,
41 FP, or CSV/TSV text file(s) containing fingerprints bit-vector or 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>E-state atom types are assigned to all non-hydrogen atoms in a molecule using module
47 AtomTypes::EStateAtomTypes.pm and E-state values are calculated using module
48 AtomicDescriptors::EStateValues.pm. Using E-state atom types and E-state values,
49 <strong>EStateIndiciesFingerprints</strong> constituting sum of E-state values for E-sate atom types
50 is generated.</p>
51 <p>Two types of E-state atom types set size are allowed:</p>
52 <div class="OptionsBox">
53 ArbitrarySize - Corresponds to only E-state atom types detected
54 in molecule
55 <br/> FixedSize - Corresponds to fixed number of E-state atom types previously
56 defined</div>
57 <p>Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types to
58 non-hydrogen atoms in the molecule, is able to assign atom types to any valid
59 atom group. However, for <em>FixedSize</em> value of <strong>EStateAtomTypesSetToUse</strong>, only a
60 fixed set of E-state atom types corresponding to specific atom groups [ Appendix III in
61 Ref 77 ] are used for fingerprints.</p>
62 <p>The fixed size E-state atom type set size used during generation of fingerprints contains
63 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
64 MayaChemTools.</p>
65 <p>Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
66 E-state indicies fingerprints:</p>
67 <div class="OptionsBox">
68 Type EStateAtomTypesSetToUse</div>
69 <div class="OptionsBox">
70 EStateIndicies ArbitrarySize [ default fingerprints ]
71 <br/> EStateIndicies FixedSize</div>
72 <p>Example of <em>SD</em> file containing E-state indicies fingerprints string data:</p>
73 <div class="OptionsBox">
74 ... ...
75 <br/> ... ...
76 <br/> $$$$
77 <br/> ... ...
78 <br/> ... ...
79 <br/> ... ...
80 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
81 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
82 <br/> ... ...
83 <br/> 2 3 1 0 0 0 0
84 <br/> ... ...
85 <br/> M END
86 <br/> &gt; &lt;CmpdID&gt;
87 <br/> Cmpd1</div>
88 <div class="OptionsBox">
89 &gt; &lt;EStateIndiciesFingerprints&gt;
90 <br/> FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDsA
91 <br/> ndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssNH
92 <br/> SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3.02
93 <br/> 4 -2.270</div>
94 <div class="OptionsBox">
95 $$$$
96 <br/> ... ...
97 <br/> ... ...</div>
98 <p>Example of <em>FP</em> file containing E-state indicies 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 14:35:11 2011
105 <br/> #
106 <br/> # FingerprintsStringType = FingerprintsVector
107 <br/> #
108 <br/> # Description = EStateIndicies:ArbitrarySize
109 <br/> # VectorStringFormat = IDsAndValuesString
110 <br/> # VectorValuesType = NumericalValues
111 <br/> #
112 <br/> Cmpd1 11;SaaCH SaasC SaasN SdO SdssC...;24.778 4.387 1.993 25.023 -1...
113 <br/> Cmpd2 9;SdNH SdO SdssC SsCH3 SsNH...;7.418 22.984 -1.583 5.387 5.400...
114 <br/> ... ...
115 <br/> ... ..</div>
116 <p>Example of CSV <em>Text</em> file containing E-state indicies fingerprints string data:</p>
117 <div class="OptionsBox">
118 &quot;CompoundID&quot;,&quot;EStateIndiciesFingerprints&quot;
119 <br/> &quot;Cmpd1&quot;,&quot;FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalVa
120 <br/> lues;IDsAndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssC
121 <br/> H2 SssNH SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0
122 <br/> .073 3.024 -2.270&quot;
123 <br/> &quot;Cmpd2&quot;,&quot;FingerprintsVector;EStateIndicies:ArbitrarySize;9;NumericalVal
124 <br/> ues;IDsAndValuesString;SdNH SdO SdssC SsCH3 SsNH2 SsOH SssCH2 SssNH Sss
125 <br/> sCH;7.418 22.984 -1.583 5.387 5.400 19.852 1.737 5.624 -3.319&quot;
126 <br/> ... ...
127 <br/> ... ...</div>
128 <p>The current release of MayaChemTools generates the following types of E-state
129 fingerprints vector strings:</p>
130 <div class="OptionsBox">
131 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
132 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
133 <br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
134 <br/> .024 -2.270</div>
135 <div class="OptionsBox">
136 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
137 <br/> ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
138 <br/> 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
139 <br/> 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
140 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div>
141 <div class="OptionsBox">
142 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
143 <br/> IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
144 <br/> SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
145 <br/> C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
146 <br/> 0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 4.387 0 0 0
147 <br/> 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0
148 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...</div>
149 <p>
150 </p>
151 <h2>OPTIONS</h2>
152 <dl>
153 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
154 <dd>
155 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
156 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
157 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
158 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
159 <p>The supported aromaticity model names along with model specific control parameters
160 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
161 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
162 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
163 for detecting aromaticity corresponding to a specific model.</p>
164 </dd>
165 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
166 <dd>
167 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
168 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
169 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
170 IDs like LabelPrefixString&lt;Number&gt;. Default value, <em>Cmpd</em>, generates compound IDs which
171 look like Cmpd&lt;Number&gt;.</p>
172 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
173 <div class="OptionsBox">
174 MolID
175 <br/> ExtReg</div>
176 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
177 <div class="OptionsBox">
178 Compound</div>
179 <p>The value specified above generates compound IDs which correspond to Compound&lt;Number&gt;
180 instead of default value of Cmpd&lt;Number&gt;.</p>
181 </dd>
182 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
183 <dd>
184 <p>Specify compound ID column label for FP or CSV/TSV text file(s) used during <em>CompoundID</em> value
185 of <strong>--DataFieldsMode</strong> option. Default: <em>CompoundID</em>.</p>
186 </dd>
187 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
188 <dd>
189 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
190 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
191 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
192 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
193 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
194 Default: <em>LabelPrefix</em>.</p>
195 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
196 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
197 values are replaced with sequential compound IDs.</p>
198 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
199 </dd>
200 <dt><strong><strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em></strong></dt>
201 <dd>
202 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
203 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
204 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
205 <p>Examples:</p>
206 <div class="OptionsBox">
207 Extreg
208 <br/> MolID,CompoundName</div>
209 </dd>
210 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
211 <dd>
212 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
213 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
214 data field; transfer SD data files common to all compounds; extract specified data fields;
215 generate a compound ID using molname line, a compound prefix, or a combination of both.
216 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
217 </dd>
218 <dt><strong><strong>-e, --EStateAtomTypesSetToUse</strong> <em>ArbitrarySize | FixedSize</em></strong></dt>
219 <dd>
220 <p>E-state atom types set size to use during generation of E-state indicies fingerprints.
221 Possible values: <em>ArbitrarySize | FixedSize</em>; Default value: <em>ArbitrarySize</em>.</p>
222 <p><em>ArbitrarySize</em> corrresponds to only E-state atom types detected in molecule; <em>FixedSize</em>
223 corresponds to fixed number of previously defined E-state atom types.</p>
224 <p>For <em>EStateIndicies</em>, a fingerprint vector string is generated. The vector string corresponding to
225 <em>EStateIndicies</em> contains sum of E-state values for E-state atom types.</p>
226 <p>Module <strong>AtomTypes::EStateAtomTypes.pm</strong> is used to assign E-state atom types to
227 non-hydrogen atoms in the molecule which is able to assign atom types to any valid
228 atom group. However, for <em>FixedSize</em> value of <strong>EStateAtomTypesSetToUse</strong>,
229 only a fixed set of E-state atom types corresponding to specific atom groups [ Appendix
230 III in Ref 77 ] are used for fingerprints.</p>
231 <p>The fixed size E-state atom type set size used during generation of fingerprints contains
232 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
233 MayaChemTools.</p>
234 </dd>
235 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
236 <dd>
237 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
238 Default value: <em>Yes</em>.</p>
239 <p>By default, compound data is checked before calculating fingerprints and compounds containing
240 atom data corresponding to non-element symbols or no atom data are ignored.</p>
241 </dd>
242 <dt><strong><strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em></strong></dt>
243 <dd>
244 <p>Specify how fingerprints label is generated in conjunction with <strong>--FingerprintsLabel</strong> option value:
245 use fingerprints label generated only by <strong>--FingerprintsLabel</strong> option value or append E-state
246 atom type value IDs to <strong>--FingerprintsLabel</strong> option value.</p>
247 <p>Possible values: <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>. Default value:
248 <em>FingerprintsLabelOnly</em>.</p>
249 <p>This option is only used for <em>FixedSize</em> value of <strong>-e, --EStateAtomTypesSetToUse</strong> option during
250 generation of <em>EStateIndicies</em> E-state fingerprints.</p>
251 <p>E-state atom type IDs appended to <strong>--FingerprintsLabel</strong> value during <em>FingerprintsLabelWithIDs</em>
252 values of <strong>--FingerprintsLabelMode</strong> correspond to fixed number of previously defined E-state
253 atom types.</p>
254 </dd>
255 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
256 <dd>
257 <p>SD data label or text file column label to use for fingerprints string in output SD or
258 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>EStateIndiciesFingerprints</em>.</p>
259 </dd>
260 <dt><strong><strong>-h, --help</strong></strong></dt>
261 <dd>
262 <p>Print this help message.</p>
263 </dd>
264 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
265 <dd>
266 <p>Generate fingerprints for only the largest component in molecule. Possible values:
267 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
268 <p>For molecules containing multiple connected components, fingerprints can be generated
269 in two different ways: use all connected components or just the largest connected
270 component. By default, all atoms except for the largest connected component are
271 deleted before generation of fingerprints.</p>
272 </dd>
273 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
274 <dd>
275 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
276 Default value: <em>comma</em>.</p>
277 </dd>
278 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
279 <dd>
280 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
281 </dd>
282 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
283 <dd>
284 <p>Overwrite existing files.</p>
285 </dd>
286 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
287 <dd>
288 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
289 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
290 </dd>
291 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
292 <dd>
293 <p>New file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. Default for new file
294 names: &lt;SDFileName&gt;&lt;EStateIndiciesFP&gt;.&lt;Ext&gt;. The file type determines &lt;Ext&gt; value.
295 The sdf, fpf, csv, and tsv &lt;Ext&gt; values are used for SD, FP, comma/semicolon, and tab
296 delimited text files, respectively.This option is ignored for multiple input files.</p>
297 </dd>
298 <dt><strong><strong>--ValuesPrecision</strong> <em>number</em></strong></dt>
299 <dd>
300 <p>Precision of values for E-state indicies option. Default value: up to <em>3</em> decimal places.
301 Valid values: positive integers.</p>
302 </dd>
303 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
304 <dd>
305 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
306 <strong>--output</strong> used for <em>EStateIndicies</em>. Possible values: <em>ValuesString, IDsAndValuesString,
307 IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString</em>.</p>
308 <p>Default value during <em>ArbitrarySize</em> value of <strong>-e, --EStateAtomTypesSetToUse</strong>
309 option: <em>IDsAndValuesString</em>. Default value during <em>FixedSize</em> value of
310 <strong>-e, --EStateAtomTypesSetToUse</strong> option: <em>ValuesString</em>.</p>
311 <p>Examples:</p>
312 <div class="OptionsBox">
313 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
314 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
315 <br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
316 <br/> .024 -2.270</div>
317 </dd>
318 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
319 <dd>
320 <p>Location of working directory. Default: current directory.</p>
321 </dd>
322 </dl>
323 <p>
324 </p>
325 <h2>EXAMPLES</h2>
326 <p>To generate E-state fingerprints of arbitrary size in vector string format and create a
327 SampleESFP.csv file containing sequential compound IDs along with fingerprints
328 vector strings data, type:</p>
329 <div class="ExampleBox">
330 % EStateIndiciesFingerprints.pl -r SampleESFP -o Sample.sdf</div>
331 <p>To generate E-state fingerprints of fixed size in vector string format and create a
332 SampleESFP.csv file containing sequential compound IDs along with fingerprints
333 vector strings data, type:</p>
334 <div class="ExampleBox">
335 % EStateIndiciesFingerprints.pl -e FixedSize -r SampleESFP
336 -o Sample.sdf</div>
337 <p>To generate E-state fingerprints of fixed size in vector string with IDsAndValues
338 format and create a SampleESFP.csv file containing sequential compound IDs
339 along with fingerprints vector strings data, type:</p>
340 <div class="ExampleBox">
341 % EStateIndiciesFingerprints.pl -e FixedSize -v IDsAndValuesString
342 -r SampleESFP -o Sample.sdf</div>
343 <p>To generate E-state fingerprints of fixed size in vector string format
344 and create a SampleESFP.csv file containing compound ID from molecule
345 name line along with fingerprints vector strings data, type</p>
346 <div class="ExampleBox">
347 % EStateIndiciesFingerprints.pl -e FixedSize
348 --DataFieldsMode CompoundID --CompoundIDMode MolName
349 -r SampleESFP -o Sample.sdf</div>
350 <p>To generate E-state fingerprints of fixed size in vector string format
351 and create a SampleESFP.csv file containing compound IDs using specified
352 data field along with fingerprints vector strings data, type:</p>
353 <div class="ExampleBox">
354 % EStateIndiciesFingerprints.pl -e FixedSize
355 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
356 Mol_ID -r SampleESFP -o Sample.sdf</div>
357 <p>To generate E-state fingerprints of fixed size in vector string format
358 and create a SampleESFP.csv file containing compound ID using combination
359 of molecule name line and an explicit compound prefix along with fingerprints vector
360 strings data, type:</p>
361 <div class="ExampleBox">
362 % EStateIndiciesFingerprints.pl -e FixedSize
363 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
364 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleESFP -o Sample.sdf</div>
365 <p>To generate E-state fingerprints of fixed size in vector string format
366 and create a SampleESFP.csv file containing specific data fields columns along
367 with fingerprints vector strings data, type:</p>
368 <div class="ExampleBox">
369 % EStateIndiciesFingerprints.pl -e FixedSize
370 --DataFieldsMode Specify --DataFields Mol_ID -r SampleESFP
371 -o Sample.sdf</div>
372 <p>To generate E-state fingerprints of fixed size in vector string format
373 and create a SampleESFP.csv file containing common data fields columns along
374 with fingerprints vector strings data, type:</p>
375 <div class="ExampleBox">
376 % EStateIndiciesFingerprints.pl -e FixedSize
377 --DataFieldsMode Common -r SampleESFP -o Sample.sdf</div>
378 <p>To generate E-state fingerprints of fixed size in vector string format and create
379 SampleESFP.sdf, SampleESFP.fpf, and SampleESFP.csv files containing all data
380 fields columns in CSV file along with fingerprints vector strings data, type:</p>
381 <div class="ExampleBox">
382 % EStateIndiciesFingerprints.pl -e FixedSize
383 --DataFieldsMode All --output all -r SampleESFP -o Sample.sdf</div>
384 <p>
385 </p>
386 <h2>AUTHOR</h2>
387 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
388 <p>
389 </p>
390 <h2>SEE ALSO</h2>
391 <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
392 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>,&nbsp<a href="./MACCSKeysFingeprints.html">MACCSKeysFingeprints.pl</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,&nbsp
393 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,&nbsp
394 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
395 </p>
396 <p>
397 </p>
398 <h2>COPYRIGHT</h2>
399 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
400 <p>This file is part of MayaChemTools.</p>
401 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
402 the terms of the GNU Lesser General Public License as published by the Free
403 Software Foundation; either version 3 of the License, or (at your option)
404 any later version.</p>
405 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
406 <table width="100%" border=0 cellpadding=0 cellspacing=2>
407 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysisTextFiles.html" title="ElementalAnalysisTextFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>EStateIndiciesFingerprints.pl</strong></td></tr>
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