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.\" ========================================================================
.\"
.IX Title "MOLECULARCOMPLEXITYDESCRIPTORS 1"
.TH MOLECULARCOMPLEXITYDESCRIPTORS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
MolecularComplexityDescriptors
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use MolecularDescriptors::MolecularComplexityDescriptors;
.PP
use MolecularDescriptors::MolecularComplexityDescriptors qw(:all);
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBMolecularComplexityDescriptors\fR class provides the following methods:
.PP
new, GenerateDescriptors, GetDescriptorNames,
GetMolecularComplexityTypeAbbreviation, MACCSKeysSize, SetAtomIdentifierType,
SetAtomicInvariantsToUse, SetDistanceBinSize, SetFunctionalClassesToUse,
SetMaxDistance, SetMaxPathLength, SetMinDistance, SetMinPathLength,
SetMolecularComplexityType, SetNeighborhoodRadius, SetNormalizationMethodology,
StringifyMolecularComplexityDescriptors
.PP
\&\fBMolecularComplexityDescriptors\fR is derived from \fBMolecularDescriptors\fR class which in turn
is  derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
in \fBMolecularComplexityDescriptors\fR, \fBMolecularDescriptors\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
The current release of MayaChemTools supports calculation of molecular complexity using
\&\fIMolecularComplexityType\fR parameter corresponding to number of bits-set or unique
keys [ Ref 117\-119 ] in molecular  fingerprints. The valid values for \fIMolecularComplexityType\fR
are:
.PP
.Vb 9
\&    AtomTypesFingerprints
\&    ExtendedConnectivityFingerprints
\&    MACCSKeys
\&    PathLengthFingerprints
\&    TopologicalAtomPairsFingerprints
\&    TopologicalAtomTripletsFingerprints
\&    TopologicalAtomTorsionsFingerprints
\&    TopologicalPharmacophoreAtomPairsFingerprints
\&    TopologicalPharmacophoreAtomTripletsFingerprints
.Ve
.PP
Default value for \fIMolecularComplexityType\fR: \fIMACCSKeys\fR.
.PP
\&\fIAtomIdentifierType\fR parameter name corresponds to atom types used during generation of
fingerprints. The valid values for \fIAtomIdentifierType\fR are: \fIAtomicInvariantsAtomTypes,
DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\fR. \fIAtomicInvariantsAtomTypes\fR
is not supported for following values of \fIMolecularComplexityType\fR: \fIMACCSKeys,
TopologicalPharmacophoreAtomPairsFingerprints, TopologicalPharmacophoreAtomTripletsFingerprints\fR.
\&\fIFunctionalClassAtomTypes\fR is the only valid value of \fIAtomIdentifierType\fR for topological
pharmacophore fingerprints.
.PP
Default value for \fIAtomIdentifierType\fR: \fIAtomicInvariantsAtomTypes\fR for all fingerprints;
\&\fIFunctionalClassAtomTypes\fR for topological pharmacophore fingerprints.
.PP
\&\fIAtomicInvariantsToUse\fR parameter name and values are used during \fIAtomicInvariantsAtomTypes\fR
value of parameter \fIAtomIdentifierType\fR. It's a list of space separated valid atomic invariant atom types.
.PP
Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0,  \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0, H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR.
Default value for \fIAtomicInvariantsToUse\fR parameter are set differently for different fingerprints
using \fIMolecularComplexityType\fR parameter as shown below:
.PP
.Vb 1
\&    MolecularComplexityType              AtomicInvariantsToUse
\&
\&    AtomTypesFingerprints                AS X BO H FC
\&    TopologicalAtomPairsFingerprints     AS X BO H FC
\&    TopologicalAtomTripletsFingerprints  AS X BO H FC
\&    TopologicalAtomTorsionsFingerprints  AS X BO H FC
\&
\&    ExtendedConnectivityFingerprints     AS X  BO H FC MN
\&    PathLengthFingerprints               AS
.Ve
.PP
\&\fIFunctionalClassesToUse\fR parameter name and values are used during \fIFunctionalClassAtomTypes\fR
value of parameter \fIAtomIdentifierType\fR. It's a list of space separated valid atomic invariant atom types.
.PP
Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR.
.PP
Default value for \fIFunctionalClassesToUse\fR parameter is set to:
.PP
.Vb 1
\&    HBD HBA PI NI Ar Hal
.Ve
.PP
for all fingerprints except for the following two \fIMolecularComplexityType\fR fingerints:
.PP
.Vb 1
\&    MolecularComplexityType                           FunctionalClassesToUse
\&
\&    TopologicalPharmacophoreAtomPairsFingerprints     HBD HBA P, NI H
\&    TopologicalPharmacophoreAtomTripletsFingerprints  HBD HBA PI NI H Ar
.Ve
.PP
\&\fIMACCSKeysSize\fR parameter name is only used during \fIMACCSKeys\fR value of
\&\fIMolecularComplexityType\fR and corresponds to size of \s-1MACCS\s0 key set. Possible
values: \fI166 or 322\fR. Default value: \fI166\fR.
.PP
\&\fINeighborhoodRadius\fR parameter name is only used during \fIExtendedConnectivityFingerprints\fR
value of \fIMolecularComplexityType\fR and corresponds to atomic neighborhoods radius for
generating extended connectivity fingerprints. Possible values: positive integer. Default value:
\&\fI2\fR.
.PP
\&\fIMinPathLength\fR and \fIMaxPathLength\fR parameters are only used during \fIPathLengthFingerprints\fR
value of \fIMolecularComplexityType\fR and correspond to minimum and maximum path lengths to use
for generating path length fingerprints. Possible values: positive integers. Default value: \fIMinPathLength \- 1\fR;
\&\fIMaxPathLength \- 8\fR.
.PP
\&\fIUseBondSymbols\fR parameter is only used during \fIPathLengthFingerprints\fR value of
\&\fIMolecularComplexityType\fR and indicates whether bond symbols are included in atom path
strings used to generate path length fingerprints. Possible value: \fIYes or No\fR. Default value:
\&\fIYes\fR.
.PP
\&\fIMinDistance\fR and \fIMaxDistance\fR parameters are only used during \fITopologicalAtomPairsFingerprints\fR
and \fITopologicalAtomTripletsFingerprints\fR values of \fIMolecularComplexityType\fR and correspond to
minimum and maximum bond distance between atom pairs during topological pharmacophore fingerprints.
Possible values: positive integers. Default value: \fIMinDistance \- 1\fR; \fIMaxDistance \- 10\fR.
.PP
\&\fIUseTriangleInequality\fR parameter is used during these values for \fIMolecularComplexityType\fR:
\&\fITopologicalAtomTripletsFingerprints\fR and \fITopologicalPharmacophoreAtomTripletsFingerprints\fR.
Possible values: \fIYes or No\fR. It determines wheter to apply triangle inequality to distance triplets.
Default value: \fITopologicalAtomTripletsFingerprints \- No\fR;
\&\fITopologicalPharmacophoreAtomTripletsFingerprints \- Yes\fR.
.PP
\&\fIDistanceBinSize\fR parameter is used during \fITopologicalPharmacophoreAtomTripletsFingerprints\fR
value of \fIMolecularComplexityType\fR and corresponds to distance bin size used for binning
distances during generation of topological pharmacophore atom triplets fingerprints. Possible
value: positive integer. Default value: \fI2\fR.
.PP
\&\fINormalizationMethodology\fR is only used for these values for \fIMolecularComplexityType\fR:
\&\fIExtendedConnectivityFingerprints\fR, \fITopologicalPharmacophoreAtomPairsFingerprints\fR
and \fITopologicalPharmacophoreAtomTripletsFingerprints\fR. It corresponds to normalization
methodology to use for scaling the number of bits-set or unique keys during generation of
fingerprints. Possible values during \fIExtendedConnectivityFingerprints\fR: \fINone or
ByHeavyAtomsCount\fR; Default value: \fINone\fR. Possible values during topological
pharmacophore atom pairs and triplets fingerprints: \fINone or ByPossibleKeysCount\fR;
Default value: \fINone\fR. \fIByPossibleKeysCount\fR corresponds to total number of
possible topological pharmacophore atom pairs or triplets in a molecule.
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.IP "\fBnew\fR" 4
.IX Item "new"
.Vb 3
\&    $NewMolecularComplexityDescriptors = new MolecularDescriptors::
\&                                         MolecularComplexityDescriptors(
\&                                             %NamesAndValues);
.Ve
.Sp
Using specified \fIMolecularComplexityDescriptors\fR property names and values hash, \fBnew\fR
method creates a new object and returns a reference to newly created \fBMolecularComplexityDescriptors\fR
object. By default, the following properties are initialized:
.Sp
.Vb 10
\&    Molecule = \*(Aq\*(Aq
\&    Type = \*(AqMolecularComplexity\*(Aq
\&    MolecularComplexityType = \*(AqMACCSKeys\*(Aq
\&    AtomIdentifierType = \*(Aq\*(Aq
\&    MACCSKeysSize = 166
\&    NeighborhoodRadius = 2
\&    MinPathLength = 1
\&    MaxPathLength = 8
\&    UseBondSymbols = 1
\&    MinDistance = 1
\&    MaxDistance = 10
\&    UseTriangleInequality = \*(Aq\*(Aq
\&    DistanceBinSize = 2
\&    NormalizationMethodology = \*(AqNone\*(Aq
\&    @DescriptorNames = (\*(AqMolecularComplexity\*(Aq)
\&    @DescriptorValues = (\*(AqNone\*(Aq)
.Ve
.Sp
Examples:
.Sp
.Vb 3
\&    $MolecularComplexityDescriptors = new MolecularDescriptors::
\&                                      MolecularComplexityDescriptors(
\&                                      \*(AqMolecule\*(Aq => $Molecule);
\&
\&    $MolecularComplexityDescriptors = new MolecularDescriptors::
\&                                      MolecularComplexityDescriptors();
\&
\&    $MolecularComplexityDescriptors\->SetMolecule($Molecule);
\&    $MolecularComplexityDescriptors\->GenerateDescriptors();
\&    print "MolecularComplexityDescriptors: $MolecularComplexityDescriptors\en";
.Ve
.IP "\fBGenerateDescriptors\fR" 4
.IX Item "GenerateDescriptors"
.Vb 1
\&    $MolecularComplexityDescriptors\->GenerateDescriptors();
.Ve
.Sp
Calculates MolecularComplexity value for a molecule and returns \fIMolecularComplexityDescriptors\fR.
.IP "\fBGetDescriptorNames\fR" 4
.IX Item "GetDescriptorNames"
.Vb 3
\&    @DescriptorNames = $MolecularComplexityDescriptors\->GetDescriptorNames();
\&    @DescriptorNames = MolecularDescriptors::MolecularComplexityDescriptors::
\&                       GetDescriptorNames();
.Ve
.Sp
Returns all available descriptor names as an array.
.IP "\fBGetMolecularComplexityTypeAbbreviation\fR" 4
.IX Item "GetMolecularComplexityTypeAbbreviation"
.Vb 4
\&    $Abbrev = $MolecularComplexityDescriptors\->
\&                  GetMolecularComplexityTypeAbbreviation();
\&    $Abbrev = MolecularDescriptors::MolecularComplexityDescriptors::
\&                  GetMolecularComplexityTypeAbbreviation($ComplexityType);
.Ve
.Sp
Returns abbreviation for a specified molecular complexity type or corresponding to
\&\fIMolecularComplexityDescriptors\fR object.
.IP "\fBSetMACCSKeysSize\fR" 4
.IX Item "SetMACCSKeysSize"
.Vb 1
\&    $MolecularComplexityDescriptors\->MACCSKeysSize($Size);
.Ve
.Sp
Sets \s-1MACCS\s0 keys size and returns \fIMolecularComplexityDescriptors\fR.
.IP "\fBSetAtomIdentifierType\fR" 4
.IX Item "SetAtomIdentifierType"
.Vb 1
\&    $MolecularComplexityDescriptors\->SetAtomIdentifierType($IdentifierType);
.Ve
.Sp
Sets atom \fIIdentifierType\fR to use during fingerprints generation corresponding to
\&\fIMolecularComplexityType\fR and returns \fIMolecularComplexityDescriptors\fR.
.Sp
Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
TPSAAtomTypes, UFFAtomTypes\fR.
.IP "\fBSetAtomicInvariantsToUse\fR" 4
.IX Item "SetAtomicInvariantsToUse"
.Vb 2
\&    $MolecularComplexityDescriptors\->SetAtomicInvariantsToUse($ValuesRef);
\&    $MolecularComplexityDescriptors\->SetAtomicInvariantsToUse(@Values);
.Ve
.Sp
Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
for fingerprints generation and returns \fIMolecularComplexityDescriptors\fR.
.Sp
Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0,  \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0,
H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value [ Ref 24 ]: \fI\s-1AS\s0,X,BO,H,FC,MN\fR.
.Sp
The atomic invariants abbreviations correspond to:
.Sp
.Vb 1
\&    AS = Atom symbol corresponding to element symbol
\&
\&    X<n>   = Number of non\-hydrogen atom neighbors or heavy atoms
\&    BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
\&    LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
\&    SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
\&    DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
\&    TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
\&    H<n>   = Number of implicit and explicit hydrogens for atom
\&    Ar     = Aromatic annotation indicating whether atom is aromatic
\&    RA     = Ring atom annotation indicating whether atom is a ring
\&    FC<+n/\-n> = Formal charge assigned to atom
\&    MN<n> = Mass number indicating isotope other than most abundant isotope
\&    SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
\&            3 (triplet)
.Ve
.Sp
Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
.Sp
.Vb 1
\&    AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
.Ve
.Sp
Except for \s-1AS\s0 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.
.Sp
In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
are also allowed:
.Sp
.Vb 12
\&    X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
\&    BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
\&    LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
\&    SB :  NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
\&    DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
\&    TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
\&    H :  NumOfImplicitAndExplicitHydrogens
\&    Ar : Aromatic
\&    RA : RingAtom
\&    FC : FormalCharge
\&    MN : MassNumber
\&    SM : SpinMultiplicity
.Ve
.Sp
\&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
atom types.
.IP "\fBSetDistanceBinSize\fR" 4
.IX Item "SetDistanceBinSize"
.Vb 1
\&    $MolecularComplexityDescriptors\->SetDistanceBinSize($BinSize);
.Ve
.Sp
Sets distance bin size used to bin distances between atom pairs in atom triplets for
topological pharmacophore atom triplets fingerprints generation and returns
\&\fIMolecularComplexityDescriptors\fR.
.IP "\fBSetFunctionalClassesToUse\fR" 4
.IX Item "SetFunctionalClassesToUse"
.Vb 2
\&    $MolecularComplexityDescriptors\->SetFunctionalClassesToUse($ValuesRef);
\&    $MolecularComplexityDescriptors\->SetFunctionalClassesToUse(@Values);
.Ve
.Sp
Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
for fingerprints generation and returns \fIMolecularComplexityDescriptors\fR.
.Sp
Possible values for atom functional classes 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 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
.Sp
The functional class abbreviations correspond to:
.Sp
.Vb 9
\&    HBD: HydrogenBondDonor
\&    HBA: HydrogenBondAcceptor
\&    PI :  PositivelyIonizable
\&    NI : NegativelyIonizable
\&    Ar : Aromatic
\&    Hal : Halogen
\&    H : Hydrophobic
\&    RA : RingAtom
\&    CA : ChainAtom
\&
\& Functional class atom type specification for an atom corresponds to:
\&
\&    Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
.Ve
.Sp
\&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class 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 "\fBSetMaxDistance\fR" 4
.IX Item "SetMaxDistance"
.Vb 1
\&    $MolecularComplexityDescriptors\->SetMaxDistance($MaxDistance);
.Ve
.Sp
Sets maximum distance to use during topological atom pairs and triplets fingerprints
generation and returns \fIMolecularComplexityDescriptors\fR.
.IP "\fBSetMaxPathLength\fR" 4
.IX Item "SetMaxPathLength"
.Vb 1
\&    $MolecularComplexityDescriptors\->SetMaxPathLength($Length);
.Ve
.Sp
Sets maximum path length to use during path length fingerprints generation and returns
\&\fIMolecularComplexityDescriptors\fR.
.IP "\fBSetMinDistance\fR" 4
.IX Item "SetMinDistance"
.Vb 1
\&    $MolecularComplexityDescriptors\->SetMinDistance($MinDistance);
.Ve
.Sp
Sets minimum distance to use during topological atom pairs and triplets fingerprints
generation and returns \fIMolecularComplexityDescriptors\fR.
.IP "\fBSetMinPathLength\fR" 4
.IX Item "SetMinPathLength"
.Vb 1
\&    $MolecularComplexityDescriptors\->SetMinPathLength($MinPathLength);
.Ve
.Sp
Sets minimum path length to use during path length fingerprints generation and returns
\&\fIMolecularComplexityDescriptors\fR.
.IP "\fBSetMolecularComplexityType\fR" 4
.IX Item "SetMolecularComplexityType"
.Vb 1
\&    $MolecularComplexityDescriptors\->SetMolecularComplexityType($ComplexityType);
.Ve
.Sp
Sets molecular complexity type to use for calculating its value and returns
\&\fIMolecularComplexityDescriptors\fR.
.IP "\fBSetNeighborhoodRadius\fR" 4
.IX Item "SetNeighborhoodRadius"
.Vb 1
\&    $MolecularComplexityDescriptors\->SetNeighborhoodRadius($Radius);
.Ve
.Sp
Sets neighborhood radius to use during extended connectivity fingerprints generation and
returns \fIMolecularComplexityDescriptors\fR.
.IP "\fBSetNormalizationMethodology\fR" 4
.IX Item "SetNormalizationMethodology"
.Vb 1
\&    $MolecularComplexityDescriptors\->SetNormalizationMethodology($Methodology);
.Ve
.Sp
Sets normalization methodology to use during calculation of molecular complexity
corresponding to extended connectivity, topological pharmacophore atom pairs and
tripletes fingerprints returns \fIMolecularComplexityDescriptors\fR.
.IP "\fBStringifyMolecularComplexityDescriptors\fR" 4
.IX Item "StringifyMolecularComplexityDescriptors"
.Vb 2
\&    $String = $MolecularComplexityDescriptors\->
\&                  StringifyMolecularComplexityDescriptors();
.Ve
.Sp
Returns a string containing information about \fIMolecularComplexityDescriptors\fR object.
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
MolecularDescriptors.pm, MolecularDescriptorsGenerator.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.