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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/TopologicalAtomTripletsFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,626 @@ +<html> +<head> +<title>MayaChemTools:Documentation:TopologicalAtomTripletsFingerprints.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="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalAtomTripletsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomTripletsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalAtomTripletsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>TopologicalAtomTripletsFingerprints.pl - Generate topological atom triplets fingerprints for SD files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>TopologicalAtomTripletsFingerprints.pl SDFile(s)...</p> +<p>TopologicalAtomTripletsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>] +[<strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes</em>] +[<strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em>] +[<strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em>] +[<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>] [<strong>--CompoundIDLabel</strong> <em>text</em>] +[<strong>--CompoundIDMode</strong>] [<strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em>] +[<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>] +[<strong>--FingerprintsLabel</strong> <em>text</em>] [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>] +[<strong>--MinDistance</strong> <em>number</em>] [<strong>--MaxDistance</strong> <em>number</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>-u, --UseTriangleInequality</strong> <em>Yes | No</em>] +[<strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>] +[<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Generate topological atom triplets fingerprints for <em>SDFile(s)</em> and create +appropriate SD, FP or CSV/TSV text file(s) containing fingerprints 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>The current release of MayaChemTools supports generation of topological atom triplets +fingerprints corresponding to following <strong>-a, --AtomIdentifierTypes</strong>:</p> +<div class="OptionsBox"> + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +<br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, +<br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div> +<p>Based on the values specified for <strong>-a, --AtomIdentifierType</strong> and <strong>--AtomicInvariantsToUse</strong>, +initial atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance +matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom +pairs within <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> are identified and counted. An atom triplet +identifier is generated for each unique atom triplet; the format of the atom triplet identifier is:</p> +<div class="OptionsBox"> + <ATx>-Dyz-<ATy>-Dxz-<ATz>-Dxy</div> +<div class="OptionsBox"> + ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z +<br/> Dxy: Distance between atom x and atom y +<br/> Dxz: Distance between atom x and atom z +<br/> Dyz: Distance between atom y and atom z</div> +<div class="OptionsBox"> + where <AT1>-D23 <= <AT2>-D13 <= <AT3>-D12</div> +<p>The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute +topological atom triplets fingerprints of the molecule.</p> +<p>Example of <em>SD</em> file containing topological atom triplets fingerprints string data:</p> +<div class="OptionsBox"> + ... ... +<br/> ... ... +<br/> $$$$ +<br/> ... ... +<br/> ... ... +<br/> ... ... +<br/> 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> ... ... +<br/> 2 3 1 0 0 0 0 +<br/> ... ... +<br/> M END +<br/> > <CmpdID> +<br/> Cmpd1</div> +<div class="OptionsBox"> + > <TopologicalAtomTripletsFingerprints> +<br/> FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi +<br/> nDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1.B +<br/> O1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D10-C +<br/> .X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1...; +<br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2 +<br/> 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...</div> +<div class="OptionsBox"> + $$$$ +<br/> ... ... +<br/> ... ...</div> +<p>Example of <em>FP</em> file containing topological atom triplets fingerprints string data:</p> +<div class="OptionsBox"> + # +<br/> # Package = MayaChemTools 7.4 +<br/> # Release Date = Oct 21, 2010 +<br/> # +<br/> # TimeStamp = Fri Mar 11 15:24:01 2011 +<br/> # +<br/> # FingerprintsStringType = FingerprintsVector +<br/> # +<br/> # Description = TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi... +<br/> # VectorStringFormat = IDsAndValuesString +<br/> # VectorValuesType = NumericalValues +<br/> # +<br/> Cmpd1 3096;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2...;1 2 2 2 2... +<br/> Cmpd2 1093;C.X1.BO1.H3-D1-C.X1.BO1.H3-D3-C.X2.BO2.H2-D4...;2 2 2 2 2... +<br/> ... ... +<br/> ... ..</div> +<p>Example of CSV <em>Text</em> file containing topological atom triplets fingerprints string data:</p> +<div class="OptionsBox"> + "CompoundID","TopologicalAtomTripletsFingerprints" +<br/> "Cmpd1","FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAto +<br/> mTypes:MinDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesStri +<br/> ng;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2 +<br/> .H2-D10-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1....; +<br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2 +<br/> 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ... +<br/> ... ... +<br/> ... ...</div> +<p>The current release of MayaChemTools generates the following types of topological atom triplets +fingerprints vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M +<br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 +<br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 +<br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1 +<br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; +<br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 +<br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M +<br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString +<br/> ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO +<br/> 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X +<br/> 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2 +<br/> -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan +<br/> ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D +<br/> 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_ +<br/> 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_ +<br/> 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...; +<br/> 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2 +<br/> 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance +<br/> 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D +<br/> 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC +<br/> H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1- +<br/> aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...; +<br/> 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2 +<br/> 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1 +<br/> 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi +<br/> nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1 +<br/> -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal +<br/> -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar +<br/> -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...; +<br/> 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5 +<br/> 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3 +<br/> 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance +<br/> 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1- +<br/> N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A +<br/> -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B +<br/> -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3- +<br/> O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1 +<br/> :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11 +<br/> -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D +<br/> 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C +<br/> 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1 +<br/> -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 +<br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C +<br/> .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3- +<br/> D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2 +<br/> -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C. +<br/> 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1: +<br/> MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non +<br/> e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D +<br/> 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5 + N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21- +<br/> D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M +<br/> axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3 +<br/> -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9 +<br/> C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1- +<br/> C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5- +<br/> C_3-D6 C_2-D1-C_3-D5-O_3-D4 C_2-D1-C_3-D6-C_3-D7 C_2-D1-C_3-D7-C_3-...</div> +<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>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt> +<dd> +<p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen +atoms during calculation of topological atom triplets fingerprints. Possible values in the current +release are: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p> +</dd> +<dt><strong><strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</em></strong></dt> +<dd> +<p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong> +option. It's a list of comma separated valid atomic invariant atom types.</p> +<p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB, +H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p> +<p>The atomic invariants abbreviations correspond to:</p> +<div class="OptionsBox"> + AS = Atom symbol corresponding to element symbol</div> +<div class="OptionsBox"> + X<n> = Number of non-hydrogen atom neighbors or heavy atoms +<br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms +<br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms +<br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms +<br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms +<br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms +<br/> H<n> = Number of implicit and explicit hydrogens for atom +<br/> Ar = Aromatic annotation indicating whether atom is aromatic +<br/> RA = Ring atom annotation indicating whether atom is a ring +<br/> FC<+n/-n> = Formal charge assigned to atom +<br/> MN<n> = Mass number indicating isotope other than most abundant isotope +<br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or + 3 (triplet)</div> +<p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p> +<div class="OptionsBox"> + AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></div> +<p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are +optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p> +<p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words +are also allowed:</p> +<div class="OptionsBox"> + X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors +<br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms +<br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms +<br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms +<br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms +<br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms +<br/> H : NumOfImplicitAndExplicitHydrogens +<br/> Ar : Aromatic +<br/> RA : RingAtom +<br/> FC : FormalCharge +<br/> MN : MassNumber +<br/> SM : SpinMultiplicity</div> +<p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant +atom types.</p> +</dd> +<dt><strong><strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em></strong></dt> +<dd> +<p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong> +option. It's a list of comma separated valid functional classes.</p> +<p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>. +Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p> +<p>The functional class abbreviations correspond to:</p> +<div class="OptionsBox"> + HBD: HydrogenBondDonor +<br/> HBA: HydrogenBondAcceptor +<br/> PI : PositivelyIonizable +<br/> NI : NegativelyIonizable +<br/> Ar : Aromatic +<br/> Hal : Halogen +<br/> H : Hydrophobic +<br/> RA : RingAtom +<br/> CA : ChainAtom</div> +<div class="OptionsBox"> + Functional class atom type specification for an atom corresponds to:</div> +<div class="OptionsBox"> + Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div> +<p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom +types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p> +<div class="OptionsBox"> + HydrogenBondDonor: NH, NH2, OH +<br/> HydrogenBondAcceptor: N[!H], O +<br/> PositivelyIonizable: +, NH2 +<br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div> +</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 CSV/TSV text file(s) used during <em>CompoundID</em> value +of <strong>--DataFieldsMode</strong> option. Default value: <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 value: <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>-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>--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>TopologicalAtomTripletsFingerprints</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>--MinDistance</strong> <em>number</em></strong></dt> +<dd> +<p>Minimum bond distance between atom triplets for generating topological atom triplets. Default value: +<em>1</em>. Valid values: positive integers and less than <strong>--MaxDistance</strong>.</p> +</dd> +<dt><strong><strong>--MaxDistance</strong> <em>number</em></strong></dt> +<dd> +<p>Maximum bond distance between atom triplets for generating topological atom triplets. Default value: +<em>10</em>. Valid values: positive integers and greater than <strong>--MinDistance</strong>.</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><TopologicalAtomTripletsFP>.<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>-u, --UseTriangleInequality</strong> <em>Yes | No</em></strong></dt> +<dd> +<p>Specify whether to imply triangle distance inequality test to distances between atom pairs in +atom triplets during generation of atom triplets generation. Possible values: <em>Yes or No</em>. +Default value: <em>No</em>.</p> +<p>Triangle distance inequality test implies that distance or binned distance between any two atom +pairs in an atom triplet must be less than the sum of distances or binned distances between other +two atoms pairs and greater than the difference of their distances.</p> +<div class="OptionsBox"> + For atom triplet ATx-Dyz-ATy-Dxz-ATz-Dxy to satisfy triangle inequality:</div> +<div class="OptionsBox"> + Dyz > |Dxz - Dxy| and Dyz < Dxz + Dxy +<br/> Dxz > |Dyz - Dxy| and Dyz < Dyz + Dxy +<br/> Dxy > |Dyz - Dxz| and Dxy < Dyz + Dxz</div> +</dd> +<dt><strong><strong>-v, --VectorStringFormat</strong> <em>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> option. Possible values: <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | +ValuesAndIDsPairsString</em>. Default value: <em>IDsAndValuesString</em>.</p> +<p>Examples:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M +<br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 +<br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 +<br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1 +<br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; +<br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 +<br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M +<br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString +<br/> ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO +<br/> 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X +<br/> 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2 +<br/> -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...</div> +</dd> +<dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt> +<dd> +<p>Location of working directory. Default value: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf, +SampleTATFP.fpf and SampleTATFP.csv files containing sequential compound IDs in CSV file along +with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl --output all -r SampleTATFP + -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl --VectorStringFormat + IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using DREIDING atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using E-state atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a EStateAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using functional class atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a FunctionalClassAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using DREIDING atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using MM94 atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a MMFF94AtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using SLogP atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a SLogPAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using SYBYL atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a SYBYLAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using TPSA atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a TPSAAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using UFF atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a UFFAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --MinDistance 1 --MaxDistance 6 -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using only AS,X atomic invariants atom types in IDsAndValuesString format and create a +SampleTATFP.csv file containing sequential compound IDs along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6 + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing compound ID from molecule name line along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolName + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID + Mol_ID -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.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"> + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP + -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing common data fields columns along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Common -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf, +SampleTATFP.fpf and SampleTATFP.csv files containing all data fields columns in CSV file along with +fingerprints data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode All --output all -r SampleTATFP + -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="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>,  +<a href="./PathLengthFingerprints.html">PathLengthFingerprints.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="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalAtomTripletsFingerprints.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>