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| author | deepakjadmin |
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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/modules/man3/TopologicalPharmacophoreAtomTripletsFingerprints.3 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,455 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +TopologicalPharmacophoreAtomTripletsFingerprints +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints; +.PP +use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBTopologicalPharmacophoreAtomTripletsFingerprints\fR [ Ref 66, Ref 68\-71 ] class provides +the following methods: +.PP +new, GenerateFingerprints, , GetDescription, GetAtomTripletIDs, +SetAtomTypesToUse, SetDistanceBinSize, SetMaxDistance, SetMinDistance, +StringifyTopologicalPharmacophoreAtomTripletsFingerprints +.PP +\&\fBTopologicalPharmacophoreAtomTripletsFingerprints\fR is derived from \fBFingerprints\fR class +which in turn is derived from \fBObjectProperty\fR base class that provides methods not explicitly +defined in \fBTopologicalPharmacophoreAtomTripletsFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR +classes using Perl's \s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified +object property: +.PP +.Vb 3 +\& Set<PropertyName>(<PropertyValue>); +\& $PropertyValue = Get<PropertyName>(); +\& Delete<PropertyName>(); +.Ve +.PP +Based on the values specified for \fBAtomTypesToUse\fR, pharmacophore atom types are +assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated. +Using \fBMinDistance\fR, \fBMaxDistance\fR, and \fBDistanceBinSize\fR 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. +.PP +A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting +atom pairs binned distances between \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR. The value +of \fB\-\-UseTriangleInequality\fR 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. +.PP +.Vb 1 +\& Let: +\& +\& P = Valid pharmacophore atom type +\& +\& Px = Pharmacophore atom x +\& Py = Pharmacophore atom y +\& Pz = Pharmacophore atom z +\& +\& Dmin = Minimum distance corresponding to number of bonds between two atoms +\& Dmax = Maximum distance corresponding to number of bonds between two atoms +\& D = Distance corresponding to number of bonds between two atom +\& +\& Bsize = Distance bin size +\& Nbins = Number of distance bins +\& +\& Dxy = Distance or lower bound of binned distance between Px and Py +\& Dxz = Distance or lower bound of binned distance between Px and Pz +\& Dyz = Distance or lower bound of binned distance between Py and Pz +\& +\& Then: +\& +\& PxDyz\-PyDxz\-PzDxy = Pharmacophore atom triplet IDs for atom types Px, +\& Py, and Pz +\& +\& For example: H1\-H1\-H1, H2\-HBA\-H2 and so on. +\& +\& For default values of Dmin = 1 , Dmax = 10 and Bsize = 2, the number of +\& distance bins, Nbins = 5, are: +\& +\& [1, 2] [3, 4] [5, 6] [7, 8] [9 10] +\& +\& and atom triplet basis set size is 2692. +\& +\& Atom triplet basis set size for various values of Dmin, Dmax and Bsize in +\& conjunction with usage of triangle inequality is: +\& +\& Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize +\& 1 10 2 No 4960 +\& 1 10 2 Yes 2692 [ Default ] +\& 2 12 2 No 8436 +\& 2 12 2 Yes 4494 +.Ve +.PP +Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore +atom triplets is counted. +.PP +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. +.PP +For \fIArbitrarySize\fR value of \fBAtomTripletsSetSizeToUse\fR, the fingerprint vector correspond to +only those topological pharmacophore atom triplets which are present and have non-zero count. However, +for \fIFixedSize\fR value of \fBAtomTripletsSetSizeToUse\fR, the fingerprint vector contains all possible +valid topological pharmacophore atom triplets with both zero and non-zero count values. +.PP +The current release of MayaChemTools generates the following types of topological pharmacophore +atom triplets fingerprints vector strings: +.PP +.Vb 8 +\& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: +\& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\- +\& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1 +\& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\- +\& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...; +\& 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 +\& 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 +\& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... +\& +\& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD +\& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;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 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 0 145 132 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 45 10 4 0 +\& 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 ... +\& +\& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD +\& istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString; +\& Ar1\-Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-Ar1\-NI1 Ar1\-Ar1\-P +\& I1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1\-H1\-HBD1 Ar1\-H1\-NI1 Ar1\-H1\-PI1 Ar1\-HBA1\-HB +\& A1 Ar1\-HBA1\-HBD1 Ar1\-HBA1\-NI1 Ar1\-HBA1\-PI1 Ar1\-HBD1\-HBD1 Ar1\-HBD1\-...; +\& 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 +\& 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 +\& 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 ... +.Ve +.SS "\s-1METHODS\s0" +.IX Subsection "METHODS" +.IP "\fBnew\fR" 4 +.IX Item "new" +.Vb 2 +\& $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints( +\& %NamesAndValues); +.Ve +.Sp +Using specified \fITopologicalPharmacophoreAtomTripletsFingerprints\fR property names and values hash, \fBnew\fR +method creates a new object and returns a reference to newly created \fBTopologicalPharmacophoreAtomTripletsFingerprints\fR +object. By default, the following properties are initialized: +.Sp +.Vb 7 +\& Molecule = \*(Aq\*(Aq +\& Type = \*(AqTopologicalPharmacophoreAtomTriplets\*(Aq +\& MinDistance = 1 +\& MaxDistance = 10 +\& DistanceBinSize = 2 +\& UseTriangleInequality = 1 +\& AtomTypesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq, \*(AqAr\*(Aq] +.Ve +.Sp +Examples: +.Sp +.Vb 2 +\& $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule); +\& +\& $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomTripletsSetSizeToUse\*(Aq => \*(AqArbitrarySize\*(Aq; +\& \*(AqMinDistance\*(Aq => 1, +\& \*(AqMaxDistance\*(Aq => 10, +\& \*(AqDistanceBinSize\*(Aq => 2, +\& \*(AqAtomTypesToUse\*(Aq => [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq, \*(AqAr\*(Aq], +\& \*(AqUseTriangleInequality\*(Aq => 1); +\& +\& $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomTripletsSetSizeToUse\*(Aq => \*(AqFixedSize\*(Aq; +\& \*(AqMinDistance\*(Aq => 1, +\& \*(AqMaxDistance\*(Aq => 10, +\& \*(AqDistanceBinSize\*(Aq => 2, +\& \*(AqAtomTypesToUse\*(Aq => [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq, \*(AqAr\*(Aq], +\& \*(AqUseTriangleInequality\*(Aq => 1); +\& +\& $TPATFP\->GenerateFingerprints(); +\& print "$TPATFP\en"; +.Ve +.IP "\fBGetDescription\fR" 4 +.IX Item "GetDescription" +.Vb 1 +\& $Description = $TopologicalPharmacophoreAtomTripletsFP\->GetDescription(); +.Ve +.Sp +Returns a string containing description of topological pharmacophore atom triplets fingerprints. +.IP "\fBGenerateFingerprints\fR" 4 +.IX Item "GenerateFingerprints" +.Vb 1 +\& $TopologicalPharmacophoreAtomTripletsFP\->GenerateFingerprints(); +.Ve +.Sp +Generates topological pharmacophore atom triplets fingerprints and returns +\&\fITopologicalPharmacophoreAtomTripletsFP\fR. +.IP "\fBGetAtomTripletIDs\fR" 4 +.IX Item "GetAtomTripletIDs" +.Vb 2 +\& $AtomTripletsIDsRef = $TopologicalPharmacophoreATFP\->GetAtomTripletIDs(); +\& @AtomTripletIDs = $TopologicalPharmacophoreATFP\->GetAtomTripletIDs(); +.Ve +.Sp +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. +.IP "\fBAtomTripletsSetSizeToUse\fR" 4 +.IX Item "AtomTripletsSetSizeToUse" +.Vb 1 +\& $TPAFP\->AtomTripletsSetSizeToUse($Values); +.Ve +.Sp +Sets pharmacophore atom triplets set size to use for topological pharmacophore fingerprints +generation and returns \fITopologicalPharmacophoreAtomTripletsFingerprints\fR. +.Sp +Possible values for pharmacophore atom triplets set size are: \fIArbitrarySize, FizedSize\fR. +Default value: \fIArbitrarySize\fR. +.Sp +For \fIArbitrarySize\fR value of \fBAtomTripletsSetSizeToUse\fR, the fingerprint vector correspond to +only those topological pharmacophore atom triplets which are present and have non-zero count. However, +for \fIFixedSize\fR value of \fBAtomTripletsSetSizeToUse\fR, the fingerprint vector contains all possible +valid topological pharmacophore atom triplets with both zero and non-zero count values. +.IP "\fBSetAtomTypesToUse\fR" 4 +.IX Item "SetAtomTypesToUse" +.Vb 2 +\& $TopologicalPharmacophoreAtomTripletsFP\->SetAtomTypesToUse($ValuesRef); +\& $TopologicalPharmacophoreAtomTripletsFP\->SetAtomTypesToUse(@Values); +.Ve +.Sp +Sets pharmacophore atom types to use for topological pharmacophore fingerprints +generation and returns \fITopologicalPharmacophoreAtomTripletsFingerprints\fR. +.Sp +Possible values for pharmacophore atom types are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR. +Default value [ Ref 71 ] : \fI\s-1HBD\s0,HBA,PI,NI,H,Ar\fR. +.Sp +The pharmacophore atom types abbreviations correspond to: +.Sp +.Vb 9 +\& HBD: HydrogenBondDonor +\& HBA: HydrogenBondAcceptor +\& PI : PositivelyIonizable +\& NI : NegativelyIonizable +\& Ar : Aromatic +\& Hal : Halogen +\& H : Hydrophobic +\& RA : RingAtom +\& CA : ChainAtom +.Ve +.Sp +\&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign pharmacophore atom +types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]: +.Sp +.Vb 4 +\& HydrogenBondDonor: NH, NH2, OH +\& HydrogenBondAcceptor: N[!H], O +\& PositivelyIonizable: +, NH2 +\& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH +.Ve +.IP "\fBSetDistanceBinSize\fR" 4 +.IX Item "SetDistanceBinSize" +.Vb 1 +\& $TopologicalPharmacophoreAtomTripletsFP\->SetDistanceBinSize($Value); +.Ve +.Sp +Sets distance bin size used to bin distances between atom pairs in atom triplets and returns +\&\fITopologicalPharmacophoreAtomTriplesFP\fR. +.Sp +For default \fBMinDistance\fR and \fBMaxDistance\fR values of 1 and 10 with \fBDistanceBinSize\fR +of 2 [ Ref 70 ], the following 5 distance bins are generated: +.Sp +.Vb 1 +\& [1, 2] [3, 4] [5, 6] [7, 8] [9 10] +.Ve +.Sp +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. +.Sp +In order to distribute distance bins of equal size, the last bin is allowed to go past \fBMaxDistance\fR +by up to distance bin size. For example, \fBMinDistance\fR and \fBMaxDistance\fR values of 2 and 10 +with \fBDistanceBinSize\fR of 2 generates the following 6 distance bins: +.Sp +.Vb 1 +\& [2, 3] [4, 5] [6, 7] [8, 9] [10 11] +.Ve +.IP "\fBSetMaxDistance\fR" 4 +.IX Item "SetMaxDistance" +.Vb 1 +\& $TopologicalPharmacophoreAtomTriplesFP\->SetMaxDistance($Value); +.Ve +.Sp +Sets maximum bond distance between atom pairs corresponding to atom triplets for +generating topological pharmacophore atom triplets fingerprints and returns +\&\fITopologicalPharmacophoreAtomTriplesFP\fR. +.IP "\fBSetMinDistance\fR" 4 +.IX Item "SetMinDistance" +.Vb 1 +\& $TopologicalPharmacophoreAtomTriplesFP\->SetMinDistance($Value); +.Ve +.Sp +Sets minimum bond distance between atom pairs corresponding to atom triplets for +generating topological pharmacophore atom triplets fingerprints and returns +\&\fITopologicalPharmacophoreAtomTriplesFP\fR. +.IP "\fBStringifyTopologicalPharmacophoreAtomTripletsFingerprints\fR" 4 +.IX Item "StringifyTopologicalPharmacophoreAtomTripletsFingerprints" +.Vb 2 +\& $String = $TopologicalPharmacophoreAtomTripletsFingerprints\-> +\& StringifyTopologicalPharmacophoreAtomTripletsFingerprints(); +.Ve +.Sp +Returns a string containing information about \fITopologicalPharmacophoreAtomTripletsFingerprints\fR object. +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm, +AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm, +MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm, +TopologicalAtomTripletsFingerprints.pm, TopologicalAtomTorsionsFingerprints.pm, +TopologicalPharmacophoreAtomPairsFingerprints.pm, +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.