diff docs/modules/txt/TopologicalPharmacophoreAtomTripletsFingerprints.txt @ 0:4816e4a8ae95 draft default tip

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+++ b/docs/modules/txt/TopologicalPharmacophoreAtomTripletsFingerprints.txt	Wed Jan 20 09:23:18 2016 -0500
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+NAME
+    TopologicalPharmacophoreAtomTripletsFingerprints
+
+SYNOPSIS
+    use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints;
+
+    use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints
+    qw(:all);
+
+DESCRIPTION
+    TopologicalPharmacophoreAtomTripletsFingerprints [ Ref 66, Ref 68-71 ]
+    class provides the following methods:
+
+    new, GenerateFingerprints, , GetDescription, GetAtomTripletIDs,
+    SetAtomTypesToUse, SetDistanceBinSize, SetMaxDistance, SetMinDistance,
+    StringifyTopologicalPharmacophoreAtomTripletsFingerprints
+
+    TopologicalPharmacophoreAtomTripletsFingerprints is derived from
+    Fingerprints class which in turn is derived from ObjectProperty base
+    class that provides methods not explicitly defined in
+    TopologicalPharmacophoreAtomTripletsFingerprints, Fingerprints or
+    ObjectProperty classes using Perl's AUTOLOAD functionality. These
+    methods are generated on-the-fly for a specified object property:
+
+        Set<PropertyName>(<PropertyValue>);
+        $PropertyValue = Get<PropertyName>();
+        Delete<PropertyName>();
+
+    Based on the values specified for AtomTypesToUse, pharmacophore atom
+    types are assigned to all non-hydrogen atoms in a molecule and a
+    distance matrix is generated. Using MinDistance, MaxDistance, and
+    DistanceBinSize 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.
+
+    A pharmacophore atom triplets basis set is generated for all unique atom
+    triplets constituting atom pairs binned distances between --MinDistance
+    and --MaxDistance. The value of --UseTriangleInequality 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.
+
+        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
+
+    Using binned distance matrix and pharmacohore atom types, occurrence of
+    unique pharmacohore atom triplets is counted.
+
+    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.
+
+    For *ArbitrarySize* value of AtomTripletsSetSizeToUse, the fingerprint
+    vector correspond to only those topological pharmacophore atom triplets
+    which are present and have non-zero count. However, for *FixedSize*
+    value of AtomTripletsSetSizeToUse, the fingerprint vector contains all
+    possible valid topological pharmacophore atom triplets with both zero
+    and non-zero count values.
+
+    The current release of MayaChemTools generates the following types of
+    topological pharmacophore atom triplets fingerprints vector strings:
+
+        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 ...
+
+  METHODS
+    new
+            $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
+                                                           %NamesAndValues);
+
+        Using specified *TopologicalPharmacophoreAtomTripletsFingerprints*
+        property names and values hash, new method creates a new object and
+        returns a reference to newly created
+        TopologicalPharmacophoreAtomTripletsFingerprints object. By default,
+        the following properties are initialized:
+
+            Molecule = ''
+            Type = 'TopologicalPharmacophoreAtomTriplets'
+            MinDistance = 1
+            MaxDistance = 10
+            DistanceBinSize = 2
+            UseTriangleInequality = 1
+            AtomTypesToUse = ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar']
+
+        Examples:
+
+            $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
+                                      'Molecule' => $Molecule);
+
+            $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
+                                      'Molecule' => $Molecule,
+                                      'AtomTripletsSetSizeToUse' => 'ArbitrarySize';
+                                      'MinDistance' => 1,
+                                      'MaxDistance' => 10,
+                                      'DistanceBinSize' => 2,
+                                      'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar'],
+                                      'UseTriangleInequality' => 1);
+
+            $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
+                                      'Molecule' => $Molecule,
+                                      'AtomTripletsSetSizeToUse' => 'FixedSize';
+                                      'MinDistance' => 1,
+                                      'MaxDistance' => 10,
+                                      'DistanceBinSize' => 2,
+                                      'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar'],
+                                      'UseTriangleInequality' => 1);
+
+            $TPATFP->GenerateFingerprints();
+            print "$TPATFP\n";
+
+    GetDescription
+            $Description = $TopologicalPharmacophoreAtomTripletsFP->GetDescription();
+
+        Returns a string containing description of topological pharmacophore
+        atom triplets fingerprints.
+
+    GenerateFingerprints
+            $TopologicalPharmacophoreAtomTripletsFP->GenerateFingerprints();
+
+        Generates topological pharmacophore atom triplets fingerprints and
+        returns *TopologicalPharmacophoreAtomTripletsFP*.
+
+    GetAtomTripletIDs
+            $AtomTripletsIDsRef = $TopologicalPharmacophoreATFP->GetAtomTripletIDs();
+            @AtomTripletIDs = $TopologicalPharmacophoreATFP->GetAtomTripletIDs();
+
+        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.
+
+    AtomTripletsSetSizeToUse
+            $TPAFP->AtomTripletsSetSizeToUse($Values);
+
+        Sets pharmacophore atom triplets set size to use for topological
+        pharmacophore fingerprints generation and returns
+        *TopologicalPharmacophoreAtomTripletsFingerprints*.
+
+        Possible values for pharmacophore atom triplets set size are:
+        *ArbitrarySize, FizedSize*. Default value: *ArbitrarySize*.
+
+        For *ArbitrarySize* value of AtomTripletsSetSizeToUse, the
+        fingerprint vector correspond to only those topological
+        pharmacophore atom triplets which are present and have non-zero
+        count. However, for *FixedSize* value of AtomTripletsSetSizeToUse,
+        the fingerprint vector contains all possible valid topological
+        pharmacophore atom triplets with both zero and non-zero count
+        values.
+
+    SetAtomTypesToUse
+            $TopologicalPharmacophoreAtomTripletsFP->SetAtomTypesToUse($ValuesRef);
+            $TopologicalPharmacophoreAtomTripletsFP->SetAtomTypesToUse(@Values);
+
+        Sets pharmacophore atom types to use for topological pharmacophore
+        fingerprints generation and returns
+        *TopologicalPharmacophoreAtomTripletsFingerprints*.
+
+        Possible values for pharmacophore atom types are: *Ar, CA, H, HBA,
+        HBD, Hal, NI, PI, RA*. Default value [ Ref 71 ] :
+        *HBD,HBA,PI,NI,H,Ar*.
+
+        The pharmacophore atom types abbreviations correspond to:
+
+            HBD: HydrogenBondDonor
+            HBA: HydrogenBondAcceptor
+            PI :  PositivelyIonizable
+            NI : NegativelyIonizable
+            Ar : Aromatic
+            Hal : Halogen
+            H : Hydrophobic
+            RA : RingAtom
+            CA : ChainAtom
+
+        *AtomTypes::FunctionalClassAtomTypes* module is used to assign
+        pharmacophore atom types. It uses following definitions [ Ref 60-61,
+        Ref 65-66 ]:
+
+            HydrogenBondDonor: NH, NH2, OH
+            HydrogenBondAcceptor: N[!H], O
+            PositivelyIonizable: +, NH2
+            NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
+
+    SetDistanceBinSize
+            $TopologicalPharmacophoreAtomTripletsFP->SetDistanceBinSize($Value);
+
+        Sets distance bin size used to bin distances between atom pairs in
+        atom triplets and returns *TopologicalPharmacophoreAtomTriplesFP*.
+
+        For default MinDistance and MaxDistance values of 1 and 10 with
+        DistanceBinSize of 2 [ Ref 70 ], the following 5 distance bins are
+        generated:
+
+            [1, 2] [3, 4] [5, 6] [7, 8] [9 10]
+
+        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.
+
+        In order to distribute distance bins of equal size, the last bin is
+        allowed to go past MaxDistance by up to distance bin size. For
+        example, MinDistance and MaxDistance values of 2 and 10 with
+        DistanceBinSize of 2 generates the following 6 distance bins:
+
+            [2, 3] [4, 5] [6, 7] [8, 9] [10 11]
+
+    SetMaxDistance
+            $TopologicalPharmacophoreAtomTriplesFP->SetMaxDistance($Value);
+
+        Sets maximum bond distance between atom pairs corresponding to atom
+        triplets for generating topological pharmacophore atom triplets
+        fingerprints and returns *TopologicalPharmacophoreAtomTriplesFP*.
+
+    SetMinDistance
+            $TopologicalPharmacophoreAtomTriplesFP->SetMinDistance($Value);
+
+        Sets minimum bond distance between atom pairs corresponding to atom
+        triplets for generating topological pharmacophore atom triplets
+        fingerprints and returns *TopologicalPharmacophoreAtomTriplesFP*.
+
+    StringifyTopologicalPharmacophoreAtomTripletsFingerprints
+            $String = $TopologicalPharmacophoreAtomTripletsFingerprints->
+                           StringifyTopologicalPharmacophoreAtomTripletsFingerprints();
+
+        Returns a string containing information about
+        *TopologicalPharmacophoreAtomTripletsFingerprints* object.
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+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,
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    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.
+