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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/EStateIndiciesFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,415 @@ +<html> +<head> +<title>MayaChemTools:Documentation:EStateIndiciesFingerprints.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysisTextFiles.html" title="ElementalAnalysisTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/EStateIndiciesFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/EStateIndiciesFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>EStateIndiciesFingerprints.pl - Generate E-state indicies fingerprints for SD files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>EStateIndiciesFingerprints.pl SDFile(s)...</p> +<p>EStateIndiciesFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>] +[<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>] +[<strong>--CompoundIDLabel</strong> <em>text</em>] [<strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>] +[<strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em>] [<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>] +[<strong>-e, --EStateAtomTypesSetToUse</strong> <em>ArbitrarySize or FixedSize</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>] +[<strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>] [<strong>--FingerprintsLabel</strong> <em>text</em>] +[<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>] +[<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>] +[<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>] +[<strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>] +[<strong>-w, --WorkingDir</strong> <em>DirName</em>]</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Generate E-state indicies fingerprints [ Ref 75-78 ] for <em>SDFile(s)</em> and create appropriate SD, +FP, or CSV/TSV text file(s) containing fingerprints bit-vector or vector strings corresponding to +molecular fingerprints.</p> +<p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em> +and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory +can be specified either by <em>*.sdf</em> or the current directory name.</p> +<p>E-state atom types are assigned to all non-hydrogen atoms in a molecule using module +AtomTypes::EStateAtomTypes.pm and E-state values are calculated using module +AtomicDescriptors::EStateValues.pm. Using E-state atom types and E-state values, +<strong>EStateIndiciesFingerprints</strong> constituting sum of E-state values for E-sate atom types +is generated.</p> +<p>Two types of E-state atom types set size are allowed:</p> +<div class="OptionsBox"> + ArbitrarySize - Corresponds to only E-state atom types detected + in molecule +<br/> FixedSize - Corresponds to fixed number of E-state atom types previously + defined</div> +<p>Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types to +non-hydrogen atoms in the molecule, is able to assign atom types to any valid +atom group. However, for <em>FixedSize</em> value of <strong>EStateAtomTypesSetToUse</strong>, only a +fixed set of E-state atom types corresponding to specific atom groups [ Appendix III in +Ref 77 ] are used for fingerprints.</p> +<p>The fixed size E-state atom type set size used during generation of fingerprints contains +87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with +MayaChemTools.</p> +<p>Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of +E-state indicies fingerprints:</p> +<div class="OptionsBox"> + Type EStateAtomTypesSetToUse</div> +<div class="OptionsBox"> + EStateIndicies ArbitrarySize [ default fingerprints ] +<br/> EStateIndicies FixedSize</div> +<p>Example of <em>SD</em> file containing E-state indicies fingerprints string data:</p> +<div class="OptionsBox"> + ... ... +<br/> ... ... +<br/> $$$$ +<br/> ... ... +<br/> ... ... +<br/> ... ... +<br/> 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> ... ... +<br/> 2 3 1 0 0 0 0 +<br/> ... ... +<br/> M END +<br/> > <CmpdID> +<br/> Cmpd1</div> +<div class="OptionsBox"> + > <EStateIndiciesFingerprints> +<br/> FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDsA +<br/> ndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssNH +<br/> SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3.02 +<br/> 4 -2.270</div> +<div class="OptionsBox"> + $$$$ +<br/> ... ... +<br/> ... ...</div> +<p>Example of <em>FP</em> file containing E-state indicies fingerprints string data:</p> +<div class="OptionsBox"> + # +<br/> # Package = MayaChemTools 7.4 +<br/> # Release Date = Oct 21, 2010 +<br/> # +<br/> # TimeStamp = Fri Mar 11 14:35:11 2011 +<br/> # +<br/> # FingerprintsStringType = FingerprintsVector +<br/> # +<br/> # Description = EStateIndicies:ArbitrarySize +<br/> # VectorStringFormat = IDsAndValuesString +<br/> # VectorValuesType = NumericalValues +<br/> # +<br/> Cmpd1 11;SaaCH SaasC SaasN SdO SdssC...;24.778 4.387 1.993 25.023 -1... +<br/> Cmpd2 9;SdNH SdO SdssC SsCH3 SsNH...;7.418 22.984 -1.583 5.387 5.400... +<br/> ... ... +<br/> ... ..</div> +<p>Example of CSV <em>Text</em> file containing E-state indicies fingerprints string data:</p> +<div class="OptionsBox"> + "CompoundID","EStateIndiciesFingerprints" +<br/> "Cmpd1","FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalVa +<br/> lues;IDsAndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssC +<br/> H2 SssNH SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0 +<br/> .073 3.024 -2.270" +<br/> "Cmpd2","FingerprintsVector;EStateIndicies:ArbitrarySize;9;NumericalVal +<br/> ues;IDsAndValuesString;SdNH SdO SdssC SsCH3 SsNH2 SsOH SssCH2 SssNH Sss +<br/> sCH;7.418 22.984 -1.583 5.387 5.400 19.852 1.737 5.624 -3.319" +<br/> ... ... +<br/> ... ...</div> +<p>The current release of MayaChemTools generates the following types of E-state +fingerprints vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs +<br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN +<br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3 +<br/> .024 -2.270</div> +<div class="OptionsBox"> + FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues; +<br/> ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 +<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 +<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 +<br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div> +<div class="OptionsBox"> + FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues; +<br/> IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3 +<br/> SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss +<br/> C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd +<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 +<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 +<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> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt> +<dd> +<p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current +release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, +ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel +or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p> +<p>The supported aromaticity model names along with model specific control parameters +are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release +and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from +this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong> +for detecting aromaticity corresponding to a specific model.</p> +</dd> +<dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt> +<dd> +<p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p> +<p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name +whose value is used as compound ID; otherwise, it's a prefix string used for generating compound +IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which +look like Cmpd<Number>.</p> +<p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p> +<div class="OptionsBox"> + MolID +<br/> ExtReg</div> +<p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p> +<div class="OptionsBox"> + Compound</div> +<p>The value specified above generates compound IDs which correspond to Compound<Number> +instead of default value of Cmpd<Number>.</p> +</dd> +<dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt> +<dd> +<p>Specify compound ID column label for FP or CSV/TSV text file(s) used during <em>CompoundID</em> value +of <strong>--DataFieldsMode</strong> option. Default: <em>CompoundID</em>.</p> +</dd> +<dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt> +<dd> +<p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated +fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value; +use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination +of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p> +<p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>. +Default: <em>LabelPrefix</em>.</p> +<p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes +precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname +values are replaced with sequential compound IDs.</p> +<p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p> +</dd> +<dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt> +<dd> +<p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along +with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p> +<p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p> +<p>Examples:</p> +<div class="OptionsBox"> + Extreg +<br/> MolID,CompoundName</div> +</dd> +<dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt> +<dd> +<p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along +with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD +data field; transfer SD data files common to all compounds; extract specified data fields; +generate a compound ID using molname line, a compound prefix, or a combination of both. +Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p> +</dd> +<dt><strong><strong>-e, --EStateAtomTypesSetToUse</strong> <em>ArbitrarySize | FixedSize</em></strong></dt> +<dd> +<p>E-state atom types set size to use during generation of E-state indicies fingerprints. +Possible values: <em>ArbitrarySize | FixedSize</em>; Default value: <em>ArbitrarySize</em>.</p> +<p><em>ArbitrarySize</em> corrresponds to only E-state atom types detected in molecule; <em>FixedSize</em> +corresponds to fixed number of previously defined E-state atom types.</p> +<p>For <em>EStateIndicies</em>, a fingerprint vector string is generated. The vector string corresponding to +<em>EStateIndicies</em> contains sum of E-state values for E-state atom types.</p> +<p>Module <strong>AtomTypes::EStateAtomTypes.pm</strong> is used to assign E-state atom types to +non-hydrogen atoms in the molecule which is able to assign atom types to any valid +atom group. However, for <em>FixedSize</em> value of <strong>EStateAtomTypesSetToUse</strong>, +only a fixed set of E-state atom types corresponding to specific atom groups [ Appendix +III in Ref 77 ] are used for fingerprints.</p> +<p>The fixed size E-state atom type set size used during generation of fingerprints contains +87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with +MayaChemTools.</p> +</dd> +<dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt> +<dd> +<p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>. +Default value: <em>Yes</em>.</p> +<p>By default, compound data is checked before calculating fingerprints and compounds containing +atom data corresponding to non-element symbols or no atom data are ignored.</p> +</dd> +<dt><strong><strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em></strong></dt> +<dd> +<p>Specify how fingerprints label is generated in conjunction with <strong>--FingerprintsLabel</strong> option value: +use fingerprints label generated only by <strong>--FingerprintsLabel</strong> option value or append E-state +atom type value IDs to <strong>--FingerprintsLabel</strong> option value.</p> +<p>Possible values: <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>. Default value: +<em>FingerprintsLabelOnly</em>.</p> +<p>This option is only used for <em>FixedSize</em> value of <strong>-e, --EStateAtomTypesSetToUse</strong> option during +generation of <em>EStateIndicies</em> E-state fingerprints.</p> +<p>E-state atom type IDs appended to <strong>--FingerprintsLabel</strong> value during <em>FingerprintsLabelWithIDs</em> +values of <strong>--FingerprintsLabelMode</strong> correspond to fixed number of previously defined E-state +atom types.</p> +</dd> +<dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt> +<dd> +<p>SD data label or text file column label to use for fingerprints string in output SD or +CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>EStateIndiciesFingerprints</em>.</p> +</dd> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt> +<dd> +<p>Generate fingerprints for only the largest component in molecule. Possible values: +<em>Yes or No</em>. Default value: <em>Yes</em>.</p> +<p>For molecules containing multiple connected components, fingerprints can be generated +in two different ways: use all connected components or just the largest connected +component. By default, all atoms except for the largest connected component are +deleted before generation of fingerprints.</p> +</dd> +<dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt> +<dd> +<p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em> +Default value: <em>comma</em>.</p> +</dd> +<dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt> +<dd> +<p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p> +</dd> +<dt><strong><strong>-o, --overwrite</strong></strong></dt> +<dd> +<p>Overwrite existing files.</p> +</dd> +<dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt> +<dd> +<p>Put quote around column values in output CSV/TSV text file(s). Possible values: +<em>Yes or No</em>. Default value: <em>Yes</em>.</p> +</dd> +<dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt> +<dd> +<p>New file name is generated using the root: <Root>.<Ext>. Default for new file +names: <SDFileName><EStateIndiciesFP>.<Ext>. The file type determines <Ext> value. +The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab +delimited text files, respectively.This option is ignored for multiple input files.</p> +</dd> +<dt><strong><strong>--ValuesPrecision</strong> <em>number</em></strong></dt> +<dd> +<p>Precision of values for E-state indicies option. Default value: up to <em>3</em> decimal places. +Valid values: positive integers.</p> +</dd> +<dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt> +<dd> +<p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by +<strong>--output</strong> used for <em>EStateIndicies</em>. Possible values: <em>ValuesString, IDsAndValuesString, +IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString</em>.</p> +<p>Default value during <em>ArbitrarySize</em> value of <strong>-e, --EStateAtomTypesSetToUse</strong> +option: <em>IDsAndValuesString</em>. Default value during <em>FixedSize</em> value of +<strong>-e, --EStateAtomTypesSetToUse</strong> option: <em>ValuesString</em>.</p> +<p>Examples:</p> +<div class="OptionsBox"> + FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs +<br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN +<br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3 +<br/> .024 -2.270</div> +</dd> +<dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt> +<dd> +<p>Location of working directory. Default: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>To generate E-state fingerprints of arbitrary size in vector string format and create a +SampleESFP.csv file containing sequential compound IDs along with fingerprints +vector strings data, type:</p> +<div class="ExampleBox"> + % EStateIndiciesFingerprints.pl -r SampleESFP -o Sample.sdf</div> +<p>To generate E-state fingerprints of fixed size in vector string format and create a +SampleESFP.csv file containing sequential compound IDs along with fingerprints +vector strings data, type:</p> +<div class="ExampleBox"> + % EStateIndiciesFingerprints.pl -e FixedSize -r SampleESFP + -o Sample.sdf</div> +<p>To generate E-state fingerprints of fixed size in vector string with IDsAndValues +format and create a SampleESFP.csv file containing sequential compound IDs +along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % EStateIndiciesFingerprints.pl -e FixedSize -v IDsAndValuesString + -r SampleESFP -o Sample.sdf</div> +<p>To generate E-state fingerprints of fixed size in vector string format +and create a SampleESFP.csv file containing compound ID from molecule +name line along with fingerprints vector strings data, type</p> +<div class="ExampleBox"> + % EStateIndiciesFingerprints.pl -e FixedSize + --DataFieldsMode CompoundID --CompoundIDMode MolName + -r SampleESFP -o Sample.sdf</div> +<p>To generate E-state fingerprints of fixed size in vector string format +and create a SampleESFP.csv file containing compound IDs using specified +data field along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % EStateIndiciesFingerprints.pl -e FixedSize + --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID + Mol_ID -r SampleESFP -o Sample.sdf</div> +<p>To generate E-state fingerprints of fixed size in vector string format +and create a SampleESFP.csv file containing compound ID using combination +of molecule name line and an explicit compound prefix along with fingerprints vector +strings data, type:</p> +<div class="ExampleBox"> + % EStateIndiciesFingerprints.pl -e FixedSize + --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleESFP -o Sample.sdf</div> +<p>To generate E-state fingerprints of fixed size in vector string format +and create a SampleESFP.csv file containing specific data fields columns along +with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % EStateIndiciesFingerprints.pl -e FixedSize + --DataFieldsMode Specify --DataFields Mol_ID -r SampleESFP + -o Sample.sdf</div> +<p>To generate E-state fingerprints of fixed size in vector string format +and create a SampleESFP.csv file containing common data fields columns along +with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % EStateIndiciesFingerprints.pl -e FixedSize + --DataFieldsMode Common -r SampleESFP -o Sample.sdf</div> +<p>To generate E-state fingerprints of fixed size in vector string format and create +SampleESFP.sdf, SampleESFP.fpf, and SampleESFP.csv files containing all data +fields columns in CSV file along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % EStateIndiciesFingerprints.pl -e FixedSize + --DataFieldsMode All --output all -r SampleESFP -o Sample.sdf</div> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>, <a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>,  +<a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingeprints.html">MACCSKeysFingeprints.pl</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,  +<a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,  +<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysisTextFiles.html" title="ElementalAnalysisTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>