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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/TopologicalPharmacophoreAtomTripletsFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,582 @@ +<html> +<head> +<title>MayaChemTools:Documentation:TopologicalPharmacophoreAtomTripletsFingerprints.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="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./EndPage.html" title="EndPage.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalPharmacophoreAtomTripletsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalPharmacophoreAtomTripletsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>TopologicalPharmacophoreAtomTripletsFingerprints.pl - Generate topological pharmacophore atom triplets fingerprints for SD files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>TopologicalPharmacophoreAtomTripletsFingerprints.pl SDFile(s)...</p> +<p>TopologicalPharmacophoreAtomTripletsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>] +[<strong>--AtomTripletsSetSizeToUse</strong> <em>ArbitrarySize | FixedSize</em>] +[<strong>-a, --AtomTypesToUse</strong> <em>"AtomType1, AtomType2..."</em>] +[<strong>--AtomTypesWeight</strong> <em>"AtomType1, Weight1, AtomType2, Weight2..."</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>--DistanceBinSize</strong> <em>number</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>--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 pharmacophore atom triplets fingerprints [ Ref 66, Ref 68-71 ] 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>Based on the values specified for <strong>--AtomTypesToUse</strong>, pharmacophore atom types are +assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated. +Using <strong>--MinDistance</strong>, <strong>--MaxDistance</strong>, and <strong>--DistanceBinSize</strong> values, a +binned distance matrix is generated with lower bound on the distance bin as the distance +in distance matrix; the lower bound on the distance bin is also used as the distance between +atom pairs for generation of atom triplet identifiers.</p> +<p>A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting +atom pairs binned distances between <strong>--MinDistance</strong> and <strong>--MaxDistance</strong>. The value +of <strong>--UseTriangleInequality</strong> determines whether the triangle inequality test is applied during +generation of atom triplets basis set. The lower distance bound, along with specified pharmacophore +types, is used during generation of atom triplet IDs.</p> +<div class="OptionsBox"> + Let:</div> +<div class="OptionsBox"> + P = Valid pharmacophore atom type</div> +<div class="OptionsBox"> + Px = Pharmacophore atom x +<br/> Py = Pharmacophore atom y +<br/> Pz = Pharmacophore atom z</div> +<div class="OptionsBox"> + Dmin = Minimum distance corresponding to number of bonds between two atoms +<br/> Dmax = Maximum distance corresponding to number of bonds between two atoms +<br/> D = Distance corresponding to number of bonds between two atom</div> +<div class="OptionsBox"> + Bsize = Distance bin size +<br/> Nbins = Number of distance bins</div> +<div class="OptionsBox"> + Dxy = Distance or lower bound of binned distance between Px and Py +<br/> Dxz = Distance or lower bound of binned distance between Px and Pz +<br/> Dyz = Distance or lower bound of binned distance between Py and Pz</div> +<div class="OptionsBox"> + Then:</div> +<div class="OptionsBox"> + PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet IDs for atom types Px, + Py, and Pz</div> +<div class="OptionsBox"> + For example: H1-H1-H1, H2-HBA-H2 and so on</div> +<div class="OptionsBox"> + For default values of Dmin = 1 , Dmax = 10 and Bsize = 2:</div> +<div class="OptionsBox"> + the number of distance bins, Nbins = 5, are:</div> +<div class="OptionsBox"> + [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</div> +<div class="OptionsBox"> + and atom triplet basis set size is 2692.</div> +<div class="OptionsBox"> + Atom triplet basis set size for various values of Dmin, Dmax and Bsize in +<br/> conjunction with usage of triangle inequality is:</div> +<div class="OptionsBox"> + Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize +<br/> 1 10 2 No 4960 +<br/> 1 10 2 Yes 2692 [ Default ] +<br/> 2 12 2 No 8436 +<br/> 2 12 2 Yes 4494</div> +<p>Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore +atom triplets is counted.</p> +<p>The final pharmacophore atom triples count along with atom pair identifiers involving all non-hydrogen +atoms constitute pharmacophore topological atom triplets fingerprints of the molecule.</p> +<p>For <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option, the fingerprint vector correspond to +only those topological pharmacophore atom triplets which are present and have non-zero count. However, +for <em>FixedSize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option, the fingerprint vector contains all possible +valid topological pharmacophore atom triplets with both zero and non-zero count values.</p> +<p>Example of <em>SD</em> file containing topological pharmacophore atom triplets fingerprints string data:</p> +<div class="OptionsBox"> + ... ... +<br/> ... ... +<br/> $$$$ +<br/> ... ... +<br/> ... ... +<br/> ... ... +<br/> 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> ... ... +<br/> 2 3 1 0 0 0 0 +<br/> ... ... +<br/> M END +<br/> > <CmpdID> +<br/> Cmpd1</div> +<div class="OptionsBox"> + > <TopologicalPharmacophoreAtomTripletsFingerprints> +<br/> FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: +<br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- +<br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 +<br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- +<br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; +<br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 +<br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 +<br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div> +<div class="OptionsBox"> + $$$$ +<br/> ... ... +<br/> ... ...</div> +<p>Example of <em>FP</em> file containing topological pharmacophore 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 15:38:58 2011 +<br/> # +<br/> # FingerprintsStringType = FingerprintsVector +<br/> # +<br/> # Description = TopologicalPharmacophoreAtomTriplets:ArbitrarySize:M... +<br/> # VectorStringFormat = IDsAndValuesString +<br/> # VectorValuesType = NumericalValues +<br/> # +<br/> Cmpd1 696;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1...;;46 106... +<br/> Cmpd2 251;H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-H1-NI1...;4 1 3 1 1 2 2... +<br/> ... ... +<br/> ... ..</div> +<p>Example of CSV <em>Text</em> file containing topological pharmacophore atom triplets fingerprints string data:</p> +<div class="OptionsBox"> + "CompoundID","TopologicalPharmacophoreAtomTripletsFingerprints" +<br/> "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomTriplets:Arbitr +<br/> arySize:MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesStri +<br/> ng;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HB +<br/> A1 Ar1-H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA +<br/> 1 H1-HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 A...; +<br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 +<br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 +<br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... +<br/> ... ... +<br/> ... ...</div> +<p>The current release of MayaChemTools generates the following types of topological pharmacophore +atom triplets fingerprints vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: +<br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- +<br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 +<br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- +<br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; +<br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 +<br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 +<br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD +<br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106 +<br/> 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0 +<br/> 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26 +<br/> 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0 +<br/> 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD +<br/> istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString; +<br/> Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-Ar1-NI1 Ar1-Ar1-P +<br/> I1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1-H1-HBD1 Ar1-H1-NI1 Ar1-H1-PI1 Ar1-HBA1-HB +<br/> A1 Ar1-HBA1-HBD1 Ar1-HBA1-NI1 Ar1-HBA1-PI1 Ar1-HBD1-HBD1 Ar1-HBD1-...; +<br/> 46 106 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 +<br/> 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 +<br/> 132 26 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 ...</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>--AtomTripletsSetSizeToUse</strong> <em>ArbitrarySize | FixedSize</em></strong></dt> +<dd> +<p>Atom triplets set size to use during generation of topological pharmacophore atom triplets +fingerprints.</p> +<p>Possible values: <em>ArbitrarySize | FixedSize</em>; Default value: <em>ArbitrarySize</em>.</p> +<p>For <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option, the fingerprint vector +correspond to only those topological pharmacophore atom triplets which are present and +have non-zero count. However, for <em>FixedSize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> +option, the fingerprint vector contains all possible valid topological pharmacophore atom +triplets with both zero and non-zero count values.</p> +</dd> +<dt><strong><strong>-a, --AtomTypesToUse</strong> <em>"AtomType1,AtomType2,..."</em></strong></dt> +<dd> +<p>Pharmacophore atom types to use during generation of topological phramacophore +atom triplets. It's a list of comma separated valid pharmacophore atom types.</p> +<p>Possible values for pharmacophore atom types are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>. +Default value [ Ref 71 ] : <em>HBD,HBA,PI,NI,H,Ar</em>.</p> +<p>The pharmacophore atom types 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> +<p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign pharmacophore 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>--DistanceBinSize</strong> <em>number</em></strong></dt> +<dd> +<p>Distance bin size used to bin distances between atom pairs in atom triplets. Default value: <em>2</em>. +Valid values: positive integers.</p> +<p>For default <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> values of 1 and 10 with <strong>--DistanceBinSize</strong> +of 2 [ Ref 70 ], the following 5 distance bins are generated:</p> +<div class="OptionsBox"> + [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</div> +<p>The lower distance bound on the distance bin is uses to bin the distance between atom pairs in +atom triplets. So in the previous example, atom pairs with distances 1 and 2 fall in first distance +bin, atom pairs with distances 3 and 4 fall in second distance bin and so on.</p> +<p>In order to distribute distance bins of equal size, the last bin is allowed to go past <strong>--MaxDistance</strong> +by up to distance bin size. For example, <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> values of 2 and 10 +with <strong>--DistanceBinSize</strong> of 2 generates the following 6 distance bins:</p> +<div class="OptionsBox"> + [2, 3] [4, 5] [6, 7] [8, 9] [10 11]</div> +</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 topological +atom pair count value IDs to <strong>--FingerprintsLabel</strong> option value.</p> +<p>Possible values: <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>. Default value: +<em>FingerprintsLabelOnly</em>.</p> +<p>Topological atom pairs IDs appended to <strong>--FingerprintsLabel</strong> value during <em>FingerprintsLabelWithIDs</em> +values of <strong>--FingerprintsLabelMode</strong> correspond to atom pair count values in fingerprint vector string.</p> +<p><em>FingerprintsLabelWithIDs</em> value of <strong>--FingerprintsLabelMode</strong> is ignored during <em>ArbitrarySize</em> value +of <strong>--AtomTripletsSetSizeToUse</strong> option and topological atom triplets IDs not appended to the label.</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>TopologicalPharmacophoreAtomTripletsFingerprints</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 pairs corresponding to atom triplets for generating +topological pharmacophore 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 pairs corresponding to atom triplets for generating +topological pharmacophore 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><TopologicalPharmacophoreAtomTripletsFP>.<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 basis set generation. Possible values: +<em>Yes or No</em>. Default value: <em>Yes</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 PxDyz-PyDxz-PzDxy 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>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> option. Possible values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | +ValuesAndIDsString | ValuesAndIDsPairsString</em>. Defaultvalue: <em>ValuesString</em>.</p> +<p>Default value during <em>FixedSize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option: <em>ValuesString</em>. Default +value during <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option: <em>IDsAndValuesString</em>.</p> +<p><em>ValuesString</em> option value is not allowed for <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> +option.</p> +<p>Examples:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: +<br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- +<br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 +<br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- +<br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; +<br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 +<br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 +<br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD +<br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106 +<br/> 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0 +<br/> 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26 +<br/> 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0 +<br/> 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD +<br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesAndIDsPairsSt +<br/> ring;46 Ar1-Ar1-Ar1 106 Ar1-Ar1-H1 8 Ar1-Ar1-HBA1 3 Ar1-Ar1-HBD1 0 Ar1 +<br/> -Ar1-NI1 0 Ar1-Ar1-PI1 83 Ar1-H1-H1 11 Ar1-H1-HBA1 4 Ar1-H1-HBD1 0 Ar1 +<br/> -H1-NI1 0 Ar1-H1-PI1 0 Ar1-HBA1-HBA1 1 Ar1-HBA1-HBD1 0 Ar1-HBA1-NI1 0 +<br/> Ar1-HBA1-PI1 0 Ar1-HBD1-HBD1 0 Ar1-HBD1-NI1 0 Ar1-HBD1-PI1 0 Ar1-NI...</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 pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl -r SampleTPATFP + -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of fixed size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --AtomTripletsSetSizeToUse FixedSize -r SampleTPATFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files with CSV file containing +sequential compound IDs along with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --output all + -r SampleTPATFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format and atom triplets IDs in the +fingerprint data column label starting with Fingerprints, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --FingerprintsLabelMode FingerprintsLabelWithIDs --FingerprintsLabel + Fingerprints -r SampleTPATFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances not satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --UseTriangleInequality No -r SampleTPATFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6 +distance bins spanning distances from 1 through 12 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --UseTriangleInequality Yes --MinDistance 1 --MaxDistance 12 + --DistanceBinSIze 2 -r SampleTPATFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6 +distance bins spanning distances from 1 through 12 using "HBD,HBA,PI, NI, H, Ar" atoms with distances +satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound +IDs along with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --AtomTypesToUse "HBD,HBA,PI,NI,H,Ar" --UseTriangleInequality Yes + --MinDistance 1 --MaxDistance 12 --DistanceBinSIze 2 + --VectorStringFormat ValuesString -r SampleTPATFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs from +molecule name line along with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolName -r SampleTPATFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs using +specified data field along with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode DataField --CompoundID Mol_ID + -r SampleTPATFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs using +combination of molecule name line and an explicit compound prefix along with fingerprints vector +strings data, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleSampleTPATFP + -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing specific data fields columns along +with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + Specify --DataFields Mol_ID -r SampleTPATFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing common data fields columns along +with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + Common -r SampleTPATFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files containing all +data fields columns in CSV file along with fingerprints data, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + All --output all -r SampleTPATFP -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="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,  +<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.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="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./EndPage.html" title="EndPage.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalPharmacophoreAtomTripletsFingerprints.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>