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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/TopologicalPharmacophoreAtomTripletsFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,315 @@ +<html> +<head> +<title>MayaChemTools:Documentation:Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints.pm</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="./CyclesDetection.html" title="CyclesDetection.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints.pm</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</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints;</p> +<p>use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong> [ Ref 66, Ref 68-71 ] class provides +the following methods:</p> +<p>new, GenerateFingerprints, , GetDescription, GetAtomTripletIDs, +SetAtomTypesToUse, SetDistanceBinSize, SetMaxDistance, SetMinDistance, +StringifyTopologicalPharmacophoreAtomTripletsFingerprints</p> +<p><strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong> is derived from <strong>Fingerprints</strong> class +which in turn is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly +defined in <strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> +classes using Perl's AUTOLOAD functionality. These methods are generated on-the-fly for a specified +object property:</p> +<div class="OptionsBox"> + Set<PropertyName>(<PropertyValue>); +<br/> $PropertyValue = Get<PropertyName>(); +<br/> Delete<PropertyName>();</div> +<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, the number of +<br/> 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>, 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>, the fingerprint vector contains all possible +valid topological pharmacophore atom triplets with both zero and non-zero count values.</p> +<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>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints( + %NamesAndValues);</div> +<p>Using specified <em>TopologicalPharmacophoreAtomTripletsFingerprints</em> property names and values hash, <strong>new</strong> +method creates a new object and returns a reference to newly created <strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong> +object. By default, the following properties are initialized:</p> +<div class="OptionsBox"> + Molecule = '' +<br/> Type = 'TopologicalPharmacophoreAtomTriplets' +<br/> MinDistance = 1 +<br/> MaxDistance = 10 +<br/> DistanceBinSize = 2 +<br/> UseTriangleInequality = 1 +<br/> AtomTypesToUse = ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar']</div> +<p>Examples:</p> +<div class="OptionsBox"> + $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints( + 'Molecule' => $Molecule);</div> +<div class="OptionsBox"> + $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomTripletsSetSizeToUse' => 'ArbitrarySize'; + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'DistanceBinSize' => 2, + 'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar'], + 'UseTriangleInequality' => 1);</div> +<div class="OptionsBox"> + $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomTripletsSetSizeToUse' => 'FixedSize'; + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'DistanceBinSize' => 2, + 'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar'], + 'UseTriangleInequality' => 1);</div> +<div class="OptionsBox"> + $TPATFP->GenerateFingerprints(); +<br/> print "$TPATFP\n";</div> +</dd> +<dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Description = $TopologicalPharmacophoreAtomTripletsFP->GetDescription();</div> +<p>Returns a string containing description of topological pharmacophore atom triplets fingerprints.</p> +</dd> +<dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomTripletsFP->GenerateFingerprints();</div> +<p>Generates topological pharmacophore atom triplets fingerprints and returns +<em>TopologicalPharmacophoreAtomTripletsFP</em>.</p> +</dd> +<dt><strong><a name="getatomtripletids" class="item"><strong>GetAtomTripletIDs</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomTripletsIDsRef = $TopologicalPharmacophoreATFP->GetAtomTripletIDs(); +<br/> @AtomTripletIDs = $TopologicalPharmacophoreATFP->GetAtomTripletIDs();</div> +<p>Returns atom triplet IDs corresponding to atom pairs count values in topological pharmacophore +atom triplet fingerprints vector as an array or reference to an array.</p> +</dd> +<dt><strong><a name="atomtripletssetsizetouse" class="item"><strong>AtomTripletsSetSizeToUse</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TPAFP->AtomTripletsSetSizeToUse($Values);</div> +<p>Sets pharmacophore atom triplets set size to use for topological pharmacophore fingerprints +generation and returns <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.</p> +<p>Possible values for pharmacophore atom triplets set size are: <em>ArbitrarySize, FizedSize</em>. +Default value: <em>ArbitrarySize</em>.</p> +<p>For <em>ArbitrarySize</em> value of <strong>AtomTripletsSetSizeToUse</strong>, 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>, the fingerprint vector contains all possible +valid topological pharmacophore atom triplets with both zero and non-zero count values.</p> +</dd> +<dt><strong><a name="setatomtypestouse" class="item"><strong>SetAtomTypesToUse</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomTripletsFP->SetAtomTypesToUse($ValuesRef); +<br/> $TopologicalPharmacophoreAtomTripletsFP->SetAtomTypesToUse(@Values);</div> +<p>Sets pharmacophore atom types to use for topological pharmacophore fingerprints +generation and returns <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.</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><a name="setdistancebinsize" class="item"><strong>SetDistanceBinSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomTripletsFP->SetDistanceBinSize($Value);</div> +<p>Sets distance bin size used to bin distances between atom pairs in atom triplets and returns +<em>TopologicalPharmacophoreAtomTriplesFP</em>.</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><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomTriplesFP->SetMaxDistance($Value);</div> +<p>Sets maximum bond distance between atom pairs corresponding to atom triplets for +generating topological pharmacophore atom triplets fingerprints and returns +<em>TopologicalPharmacophoreAtomTriplesFP</em>.</p> +</dd> +<dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomTriplesFP->SetMinDistance($Value);</div> +<p>Sets minimum bond distance between atom pairs corresponding to atom triplets for +generating topological pharmacophore atom triplets fingerprints and returns +<em>TopologicalPharmacophoreAtomTriplesFP</em>.</p> +</dd> +<dt><strong><a name="stringifytopologicalpharmacophoreatomtripletsfingerprints" class="item"><strong>StringifyTopologicalPharmacophoreAtomTripletsFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $TopologicalPharmacophoreAtomTripletsFingerprints-> + StringifyTopologicalPharmacophoreAtomTripletsFingerprints();</div> +<p>Returns a string containing information about <em>TopologicalPharmacophoreAtomTripletsFingerprints</em> object.</p> +</dd> +</dl> +<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="./Fingerprints.html">Fingerprints.pm</a>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>,  +<a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,  +<a href="./MACCSKeys.html">MACCSKeys.pm</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,  +<a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>,  +<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</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="./CyclesDetection.html" title="CyclesDetection.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>