Mercurial > repos > deepakjadmin > mayatool3_test2
diff lib/Fingerprints/TopologicalAtomTripletsFingerprints.pm @ 0:4816e4a8ae95 draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/Fingerprints/TopologicalAtomTripletsFingerprints.pm Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1174 @@ +package Fingerprints::TopologicalAtomTripletsFingerprints; +# +# $RCSfile: TopologicalAtomTripletsFingerprints.pm,v $ +# $Date: 2015/02/28 20:48:54 $ +# $Revision: 1.15 $ +# +# Author: Manish Sud <msud@san.rr.com> +# +# 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. +# +# MayaChemTools is distributed in the hope that it will be useful, but without +# any warranty; without even the implied warranty of merchantability of fitness +# for a particular purpose. See the GNU Lesser General Public License for more +# details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or +# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, +# Boston, MA, 02111-1307, USA. +# + +use strict; +use Carp; +use Exporter; +use Fingerprints::Fingerprints; +use TextUtil (); +use Molecule; +use AtomTypes::AtomicInvariantsAtomTypes; +use AtomTypes::DREIDINGAtomTypes; +use AtomTypes::EStateAtomTypes; +use AtomTypes::FunctionalClassAtomTypes; +use AtomTypes::MMFF94AtomTypes; +use AtomTypes::SLogPAtomTypes; +use AtomTypes::SYBYLAtomTypes; +use AtomTypes::TPSAAtomTypes; +use AtomTypes::UFFAtomTypes; + +use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS); + +@ISA = qw(Fingerprints::Fingerprints Exporter); +@EXPORT = qw(); +@EXPORT_OK = qw(); + +%EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]); + +# Setup class variables... +my($ClassName); +_InitializeClass(); + +# Overload Perl functions... +use overload '""' => 'StringifyTopologicalAtomTripletsFingerprints'; + +# Class constructor... +sub new { + my($Class, %NamesAndValues) = @_; + + # Initialize object... + my $This = $Class->SUPER::new(); + bless $This, ref($Class) || $Class; + $This->_InitializeTopologicalAtomTripletsFingerprints(); + + $This->_InitializeTopologicalAtomTripletsFingerprintsProperties(%NamesAndValues); + + return $This; +} + +# Initialize object data... +# +sub _InitializeTopologicalAtomTripletsFingerprints { + my($This) = @_; + + # Type of fingerprint... + $This->{Type} = 'TopologicalAtomTriplets'; + + # Type of vector... + $This->{VectorType} = 'FingerprintsVector'; + + # Type of FingerprintsVector... + $This->{FingerprintsVectorType} = 'NumericalValues'; + + # Minimum and maximum bond distance between atom paris... + $This->{MinDistance} = 1; + $This->{MaxDistance} = 10; + + # Determines whether to apply triangle inequality to distance triplets... + # + $This->{UseTriangleInequality} = 0; + + # Atom identifier type to use for atom IDs in atom triplets... + # + # Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, + # EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + # SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes + # + $This->{AtomIdentifierType} = ''; + + # Atom types assigned to each heavy atom... + # + %{$This->{AssignedAtomTypes}} = (); + + # All atom triplets between minimum and maximum distance... + # + @{$This->{AtomTripletsIDs}} = (); + %{$This->{AtomTripletsCount}} = (); +} + +# Initialize class ... +sub _InitializeClass { + #Class name... + $ClassName = __PACKAGE__; +} + +# Initialize object properties.... +sub _InitializeTopologicalAtomTripletsFingerprintsProperties { + my($This, %NamesAndValues) = @_; + + my($Name, $Value, $MethodName); + while (($Name, $Value) = each %NamesAndValues) { + $MethodName = "Set${Name}"; + $This->$MethodName($Value); + } + + # Make sure molecule object was specified... + if (!exists $NamesAndValues{Molecule}) { + croak "Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."; + } + if (!exists $NamesAndValues{AtomIdentifierType}) { + croak "Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."; + } + + $This->_InitializeFingerprintsVector(); + + return $This; +} + +# Set minimum distance for atom triplets... +# +sub SetMinDistance { + my($This, $Value) = @_; + + if (!TextUtil::IsPositiveInteger($Value)) { + croak "Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."; + } + $This->{MinDistance} = $Value; + + return $This; +} + +# Set maximum distance for atom triplets... +# +sub SetMaxDistance { + my($This, $Value) = @_; + + if (!TextUtil::IsPositiveInteger($Value)) { + croak "Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."; + } + $This->{MaxDistance} = $Value; + + return $This; +} + +# Set atom identifier type.. +# +sub SetAtomIdentifierType { + my($This, $IdentifierType) = @_; + + if ($IdentifierType !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { + croak "Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes."; + } + + if ($This->{AtomIdentifierType}) { + croak "Error: ${ClassName}->SeAtomIdentifierType: Can't change intial atom identifier type: It's already set..."; + } + + $This->{AtomIdentifierType} = $IdentifierType; + + # Initialize atom identifier type information... + $This->_InitializeAtomIdentifierTypeInformation(); + + return $This; +} + +# Generate fingerprints description... +# +sub GetDescription { + my($This) = @_; + + # Is description explicity set? + if (exists $This->{Description}) { + return $This->{Description}; + } + + # Generate fingerprints description... + + return "$This->{Type}:$This->{AtomIdentifierType}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"; +} + +# Generate topological atom triplets fingerprints... +# +# Let: +# +# AT = Any of the supported atom types +# +# ATx = Atom type for atom x +# ATy = Atom type for atom y +# ATz = Atom type for atom z +# +# Dxy = Distance between Px and Py +# Dxz = Distance between Px and Pz +# Dyz = Distance between Py and Pz +# +# Then: +# +# ATx-Dyz-ATy-Dxz-ATz-Dxy = Atom triplet ID for atom types ATx, ATy and Atz +# +# Methodology: +# . Generate a distance matrix. +# . Assign atom types to all the atoms. +# . Using distance matrix and atom types, count occurrence of unique atom triplets +# within specified distance range along with optional trinagle inequality +# +# Notes: +# . Hydrogen atoms are ignored during the fingerprint generation. +# . For a molecule containing N atoms with all different atom type, the total number of +# possible unique atom triplets without applying triangle inquality check corresponds to: +# +# Factorial( N ) / ( Factorial( N - 3 ) * Factorial (3) ) +# +# However, due to similar atom types assigned to atoms in a molecule for a specific atom +# typing methodology and specified distance range used during fingerprints generation, the +# actual number of unique triplets is usually smaller than the theoretical limit. +# +sub GenerateFingerprints { + my($This) = @_; + + if ($This->{MinDistance} > $This->{MaxDistance}) { + croak "Error: ${ClassName}->GenerateTopologicalAtomTripletsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."; + } + + # Cache appropriate molecule data... + $This->_SetupMoleculeDataCache(); + + # Generate distance matrix... + if (!$This->_SetupDistanceMatrix()) { + carp "Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't generate distance matrix..."; + return $This; + } + + # Assign atom types to all heavy atoms... + if (!$This->_AssignAtomTypes()) { + carp "Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."; + return $This; + } + + # Intialize values of toplogical atom triplets... + $This->_InitializeToplogicalAtomTriplets(); + + # Count atom triplets... + $This->_GenerateAndCountAtomTriplets(); + + # Set final fingerprints... + $This->_SetFinalFingerprints(); + + # Clear cached molecule data... + $This->_ClearMoleculeDataCache(); + + return $This; +} + +# Setup distance matrix... +# +sub _SetupDistanceMatrix { + my($This) = @_; + + $This->{DistanceMatrix} = $This->GetMolecule()->GetDistanceMatrix(); + + if (!$This->{DistanceMatrix}) { + return undef; + } + + return $This; +} + +# Assign appropriate atom types to all heavy atoms... +# +sub _AssignAtomTypes { + my($This) = @_; + my($SpecifiedAtomTypes, $Atom, $AtomID, $IgnoreHydrogens); + + %{$This->{AssignedAtomTypes}} = (); + $IgnoreHydrogens = 1; + + $SpecifiedAtomTypes = undef; + + IDENTIFIERTYPE: { + if ($This->{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) { + $SpecifiedAtomTypes = new AtomTypes::AtomicInvariantsAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens, 'AtomicInvariantsToUse' => $This->{AtomicInvariantsToUse}); + last IDENTIFIERTYPE; + } + + if ($This->{AtomIdentifierType} =~ /^DREIDINGAtomTypes$/i) { + $SpecifiedAtomTypes = new AtomTypes::DREIDINGAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens); + last IDENTIFIERTYPE; + } + + if ($This->{AtomIdentifierType} =~ /^EStateAtomTypes$/i) { + $SpecifiedAtomTypes = new AtomTypes::EStateAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens); + last IDENTIFIERTYPE; + } + + if ($This->{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) { + $SpecifiedAtomTypes = new AtomTypes::FunctionalClassAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens, 'FunctionalClassesToUse' => $This->{FunctionalClassesToUse}); + last IDENTIFIERTYPE; + } + + if ($This->{AtomIdentifierType} =~ /^MMFF94AtomTypes$/i) { + $SpecifiedAtomTypes = new AtomTypes::MMFF94AtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens); + last IDENTIFIERTYPE; + } + + if ($This->{AtomIdentifierType} =~ /^SLogPAtomTypes$/i) { + $SpecifiedAtomTypes = new AtomTypes::SLogPAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens); + last IDENTIFIERTYPE; + } + if ($This->{AtomIdentifierType} =~ /^SYBYLAtomTypes$/i) { + $SpecifiedAtomTypes = new AtomTypes::SYBYLAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens); + last IDENTIFIERTYPE; + } + + if ($This->{AtomIdentifierType} =~ /^TPSAAtomTypes$/i) { + $SpecifiedAtomTypes = new AtomTypes::TPSAAtomTypes('Molecule' => $This->{Molecule}, 'IgnorePhosphorus' => 0, 'IgnoreSulfur' => 0); + last IDENTIFIERTYPE; + } + + if ($This->{AtomIdentifierType} =~ /^UFFAtomTypes$/i) { + $SpecifiedAtomTypes = new AtomTypes::UFFAtomTypes('Molecule' => $This->{Molecule}, 'IgnoreHydrogens' => $IgnoreHydrogens); + last IDENTIFIERTYPE; + } + + croak "Error: ${ClassName}->_AssignAtomTypes: Unknown atom indentifier type $This->{AtomIdentifierType}..."; + } + + # Assign atom types... + $SpecifiedAtomTypes->AssignAtomTypes(); + + # Make sure atom types assignment is successful... + if (!$SpecifiedAtomTypes->IsAtomTypesAssignmentSuccessful()) { + return undef; + } + + # Collect assigned atom types... + ATOM: for $Atom (@{$This->{Atoms}}) { + if ($Atom->IsHydrogen()) { + next ATOM; + } + $AtomID = $Atom->GetID(); + $This->{AssignedAtomTypes}{$AtomID} = $SpecifiedAtomTypes->GetAtomType($Atom); + } + + return $This; +} + +# Initialize topological atom triplets between specified distance range... +# +sub _InitializeToplogicalAtomTriplets { + my($This) = @_; + my($Distance); + + @{$This->{AtomTripletsIDs}} = (); + %{$This->{AtomTripletsCount}} = (); + + return $This; +} + +# Count atom triplets between mininum and maximum distance at each +# distance using distance matrix and atom types assiged to each heavy +# atom. +# +sub _GenerateAndCountAtomTriplets { + my($This) = @_; + my($NumOfAtoms, $AtomIndex1, $AtomIndex2, $AtomIndex3, $AtomID1, $AtomID2, $AtomID3, $AtomType1, $AtomType2, $AtomType3, $Distance12, $Distance13, $Distance23, $SkipIndexCheck, $DistanceMatrix, $AtomTripletID); + + $NumOfAtoms = @{$This->{Atoms}}; + $DistanceMatrix = $This->{DistanceMatrix}; + $SkipIndexCheck = 0; + + ATOMINDEX1: for $AtomIndex1 (0 .. ($NumOfAtoms - 1)) { + $AtomID1 = $This->{AtomIndexToID}{$AtomIndex1}; + if (!exists($This->{AssignedAtomTypes}{$AtomID1})) { + next ATOMINDEX1; + } + $AtomType1 = $This->{AssignedAtomTypes}{$AtomID1}; + + ATOMINDEX2: for $AtomIndex2 (($AtomIndex1 + 1) .. ($NumOfAtoms - 1)) { + $AtomID2 = $This->{AtomIndexToID}{$AtomIndex2}; + if (!exists($This->{AssignedAtomTypes}{$AtomID2})) { + next ATOMINDEX2; + } + $AtomType2 = $This->{AssignedAtomTypes}{$AtomID2}; + + $Distance12 = $DistanceMatrix->GetValue($AtomIndex1, $AtomIndex2, $SkipIndexCheck); + if ($Distance12 < $This->{MinDistance} || $Distance12 > $This->{MaxDistance}) { + next ATOMINDEX2; + } + + ATOMINDEX3: for $AtomIndex3 (($AtomIndex2 + 1) .. ($NumOfAtoms - 1)) { + $AtomID3 = $This->{AtomIndexToID}{$AtomIndex3}; + if (!exists($This->{AssignedAtomTypes}{$AtomID3})) { + next ATOMINDEX3; + } + $AtomType3 = $This->{AssignedAtomTypes}{$AtomID3}; + + $Distance13 = $DistanceMatrix->GetValue($AtomIndex1, $AtomIndex3, $SkipIndexCheck); + $Distance23 = $DistanceMatrix->GetValue($AtomIndex2, $AtomIndex3, $SkipIndexCheck); + + if ($Distance13 < $This->{MinDistance} || $Distance13 > $This->{MaxDistance}) { + next ATOMINDEX3; + } + if ($Distance23 < $This->{MinDistance} || $Distance23 > $This->{MaxDistance}) { + next ATOMINDEX3; + } + if ($This->{UseTriangleInequality} && !$This->_DoDistancesSatisfyTriangleInequality($Distance12, $Distance13, $Distance23)) { + next ATOMINDEX3; + } + + $AtomTripletID = $This->_GetAtomTripletID($AtomType1, $Distance23, $AtomType2, $Distance13, $AtomType3, $Distance12); + if (!exists $This->{AtomTripletsCount}{$AtomTripletID}) { + $This->{AtomTripletsCount}{$AtomTripletID} = 0; + } + $This->{AtomTripletsCount}{$AtomTripletID} += 1; + } + } + } + return $This; +} + +# Check triangle inequality... +# +sub _DoDistancesSatisfyTriangleInequality { + my($This, $Distance1, $Distance2, $Distance3) = @_; + + if ( !($Distance1 > abs($Distance2 - $Distance3) && $Distance1 < ($Distance2 + $Distance3)) ) { + return 0; + } + if ( !($Distance2 > abs($Distance1 - $Distance3) && $Distance2 < ($Distance1 + $Distance3)) ) { + return 0; + } + if ( !($Distance3 > abs($Distance1 - $Distance2) && $Distance3 < ($Distance1 + $Distance2)) ) { + return 0; + } + return 1; +} + +# Get atom triplet ID corresponding to atom types and distances corresponding to atom triplet... +# +sub _GetAtomTripletID { + my($This, $ATx, $Dyz, $ATy, $Dxz, $ATz, $Dxy) = @_; + my($AtomTripletID, @AtomIDs); + + @AtomIDs = (); + + @AtomIDs = sort("${ATx}-D${Dyz}", "${ATy}-D${Dxz}", "${ATz}-D${Dxy}"); + $AtomTripletID = join "-", @AtomIDs; + + return $AtomTripletID; +} + +# Set final fingerpritns vector... +# +sub _SetFinalFingerprints { + my($This) = @_; + my($AtomTripletID, $Value, @Values); + + # Mark successful generation of fingerprints... + $This->{FingerprintsGenerated} = 1; + + @Values = (); + @{$This->{AtomTripletsIDs}} = (); + + for $AtomTripletID (sort keys %{$This->{AtomTripletsCount}}) { + push @{$This->{AtomTripletsIDs}}, $AtomTripletID; + $Value = $This->{AtomTripletsCount}{$AtomTripletID}; + push @Values, $Value; + } + + # Add AtomTripletsIDs and values to fingerprint vector... + $This->{FingerprintsVector}->AddValueIDs(\@{$This->{AtomTripletsIDs}}); + $This->{FingerprintsVector}->AddValues(\@Values); + + return $This; +} + +# Get atom triplet IDs corresponding to atom triplets count values in fingerprint +# vector as an array or reference to an array... +# +# AtomTripletIDs list differes in molecules and is generated during finalization +# of fingerprints to make sure the fingerprint vector containing count values +# matches the atom triplets array. +# +sub GetAtomTripletIDs { + my($This) = @_; + + return wantarray ? @{$This->{AtomTripletsIDs}} : \@{$This->{AtomTripletsIDs}}; +} + +# Cache appropriate molecule data... +# +sub _SetupMoleculeDataCache { + my($This) = @_; + + # Get all atoms including hydrogens to correctly map atom indices to atom IDs for + # usage of distance matrix. The hydrogen atoms are ignored during processing... + # + @{$This->{Atoms}} = $This->GetMolecule()->GetAtoms(); + + # Get all atom IDs... + my(@AtomIDs); + @AtomIDs = (); + @AtomIDs = map { $_->GetID() } @{$This->{Atoms}}; + + # Set AtomIndex to AtomID hash... + %{$This->{AtomIndexToID}} = (); + @{$This->{AtomIndexToID}}{ (0 .. $#AtomIDs) } = @AtomIDs; + + return $This; +} + +# Set atomic invariants to use for atom identifiers... +# +sub SetAtomicInvariantsToUse { + my($This, @Values) = @_; + my($FirstValue, $TypeOfFirstValue, $AtomicInvariant, $SpecifiedAtomicInvariant, $AtomicInvariantValue, @SpecifiedAtomicInvariants, @AtomicInvariantsToUse); + + if (!@Values) { + carp "Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."; + return; + } + + $FirstValue = $Values[0]; + $TypeOfFirstValue = ref $FirstValue; + + @SpecifiedAtomicInvariants = (); + @AtomicInvariantsToUse = (); + + if ($TypeOfFirstValue =~ /^ARRAY/) { + push @SpecifiedAtomicInvariants, @{$FirstValue}; + } + else { + push @SpecifiedAtomicInvariants, @Values; + } + + # Make sure specified AtomicInvariants are valid... + for $SpecifiedAtomicInvariant (@SpecifiedAtomicInvariants) { + if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($SpecifiedAtomicInvariant)) { + croak "Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "; + } + $AtomicInvariant = $SpecifiedAtomicInvariant; + push @AtomicInvariantsToUse, $AtomicInvariant; + } + + # Set atomic invariants to use... + @{$This->{AtomicInvariantsToUse}} = (); + push @{$This->{AtomicInvariantsToUse}}, @AtomicInvariantsToUse; + + return $This; +} + +# Set functional classes to use for atom identifiers... +# +sub SetFunctionalClassesToUse { + my($This, @Values) = @_; + my($FirstValue, $TypeOfFirstValue, $FunctionalClass, $SpecifiedFunctionalClass, @SpecifiedFunctionalClasses, @FunctionalClassesToUse); + + if (!@Values) { + carp "Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."; + return; + } + + if ($This->{AtomIdentifierType} !~ /^FunctionalClassAtomTypes$/i) { + carp "Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."; + return; + } + + $FirstValue = $Values[0]; + $TypeOfFirstValue = ref $FirstValue; + + @SpecifiedFunctionalClasses = (); + @FunctionalClassesToUse = (); + + if ($TypeOfFirstValue =~ /^ARRAY/) { + push @SpecifiedFunctionalClasses, @{$FirstValue}; + } + else { + push @SpecifiedFunctionalClasses, @Values; + } + + # Make sure specified FunctionalClasses are valid... + for $SpecifiedFunctionalClass (@SpecifiedFunctionalClasses) { + if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($SpecifiedFunctionalClass)) { + croak "Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "; + } + push @FunctionalClassesToUse, $SpecifiedFunctionalClass; + } + + # Set functional classes to use... + @{$This->{FunctionalClassesToUse}} = (); + push @{$This->{FunctionalClassesToUse}}, @FunctionalClassesToUse; + + return $This; +} + +# Initialize atom indentifier type information... +# +# Current supported values: +# +# AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, +# MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes +# +sub _InitializeAtomIdentifierTypeInformation { + my($This) = @_; + + if ($This->{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) { + $This->_InitializeAtomicInvariantsAtomTypesInformation(); + } + elsif ($This->{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) { + $This->_InitializeFunctionalClassAtomTypesInformation(); + } + elsif ($This->{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { + # Nothing to do for now... + } + else { + croak "Error: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."; + } + + return $This; +} + +# Initialize atomic invariants atom types to use for generating atom IDs in atom triplets... +# +# Let: +# AS = Atom symbol corresponding to element symbol +# +# X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom +# BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom +# LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom +# SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom +# DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom +# TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom +# 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) +# +# ATx = Atomic invariants atom type for atom x +# ATy = Atomic invariants atom type for atom y +# ATz = Atomic invariants atom type for atom z +# +# Dxy = Distance between Px and Py +# Dxz = Distance between Px and Pz +# Dyz = Distance between Py and Pz +# +# Then: +# +# Atom triplet AtomID generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to: +# +# AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n> +# +# Toplogical atom triplet ID between atom IDs ATx, ATy and ATz corresponds to: +# +# ATx-Dyz-ATy-Dxz-ATz-Dxy +# +# Except for AS which is a required atomic invariant in atom triplet AtomIDs, all other atomic invariants are +# optional. Default atomic invariants used for AtomID are: AS, X<n>, BO<n>, H<n>, FC<+n/-n>. +# AtomID specification doesn't include atomic invariants with zero or undefined values. +# +# Examples of atom triplet AtomIDs: +# +# O.X1.BO1.H1 - Hydroxyl oxygen in carboxylate with attached hydrogen and no explicit charge +# O.X1.BO1.FC-1 - Hydroxyl ozygen in carboxylate with explicit negative charge +# O.X1.BO2 - Carbonyl oxygen in carboxylate with double bond to carbon +# O.X2.BO2 - Hydroxyl ozygen in carboxylate attached to carbonyl carbon and another heavy atom +# +# C.X2.BO3.H1.Ar - Aromatic carbon +# +sub _InitializeAtomicInvariantsAtomTypesInformation { + my($This) = @_; + + # Default atomic invariants to use for generating atom triplet atom IDs: AS, X, BO, H, FC + # + @{$This->{AtomicInvariantsToUse}} = (); + @{$This->{AtomicInvariantsToUse}} = ('AS', 'X', 'BO', 'H', 'FC'); + + return $This; +} + +# Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes +# class, to use for generating atom identifiers... +# +# Let: +# HBD: HydrogenBondDonor +# HBA: HydrogenBondAcceptor +# PI : PositivelyIonizable +# NI : NegativelyIonizable +# Ar : Aromatic +# Hal : Halogen +# H : Hydrophobic +# RA : RingAtom +# CA : ChainAtom +# +# Then: +# +# Functiononal class atom type specification for an atom corresponds to: +# +# Ar.CA.H.HBA.HBD.Hal.NI.PI.RA +# +# Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal +# +# FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]: +# +# HydrogenBondDonor: NH, NH2, OH +# HydrogenBondAcceptor: N[!H], O +# PositivelyIonizable: +, NH2 +# NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH +# +sub _InitializeFunctionalClassAtomTypesInformation { + my($This) = @_; + + # Default functional class atom typess to use for generating atom identifiers + # are: HBD, HBA, PI, NI, Ar, Hal + # + @{$This->{FunctionalClassesToUse}} = (); + @{$This->{FunctionalClassesToUse}} = ('HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'); + + return $This; +} + +# Clear cached molecule data... +# +sub _ClearMoleculeDataCache { + my($This) = @_; + + @{$This->{Atoms}} = (); + + return $This; +} + +# Return a string containg data for TopologicalAtomTripletsFingerprints object... +# +sub StringifyTopologicalAtomTripletsFingerprints { + my($This) = @_; + my($FingerprintsString); + + # Type of fingerprint... + $FingerprintsString = "Fingerprint type: $This->{Type}; AtomIdentifierType: $This->{AtomIdentifierType}"; + + # Min and max distance... + $FingerprintsString .= "; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}; UseTriangleInequality: " . ($This->{UseTriangleInequality} ? "Yes" : "No"); + + if ($This->{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) { + my($AtomicInvariant, @AtomicInvariants, @AtomicInvariantsOrder, %AvailableAtomicInvariants); + + @AtomicInvariantsOrder = AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder(); + %AvailableAtomicInvariants = AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants(); + + for $AtomicInvariant (@AtomicInvariantsOrder) { + push @AtomicInvariants, "$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"; + } + + $FingerprintsString .= "; AtomicInvariantsToUse: <" . TextUtil::JoinWords(\@{$This->{AtomicInvariantsToUse}}, ", ", 0) . ">"; + $FingerprintsString .= "; AtomicInvariantsOrder: <" . TextUtil::JoinWords(\@AtomicInvariantsOrder, ", ", 0) . ">"; + $FingerprintsString .= "; AvailableAtomicInvariants: <" . TextUtil::JoinWords(\@AtomicInvariants, ", ", 0) . ">"; + } + elsif ($This->{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) { + my($FunctionalClass, @FunctionalClasses, @FunctionalClassesOrder, %AvailableFunctionalClasses); + + @FunctionalClassesOrder = AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder(); + %AvailableFunctionalClasses = AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses(); + + for $FunctionalClass (@FunctionalClassesOrder) { + push @FunctionalClasses, "$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}"; + } + + $FingerprintsString .= "; FunctionalClassesToUse: <" . TextUtil::JoinWords(\@{$This->{FunctionalClassesToUse}}, ", ", 0) . ">"; + $FingerprintsString .= "; FunctionalClassesOrder: <" . TextUtil::JoinWords(\@FunctionalClassesOrder, ", ", 0) . ">"; + $FingerprintsString .= "; AvailableFunctionalClasses: <" . TextUtil::JoinWords(\@FunctionalClasses, ", ", 0) . ">"; + } + + # Total number of atom triplets... + $FingerprintsString .= "; NumOfAtomTriplets: " . $This->{FingerprintsVector}->GetNumOfValues(); + + # FingerprintsVector... + $FingerprintsString .= "; FingerprintsVector: < $This->{FingerprintsVector} >"; + + return $FingerprintsString; +} + +1; + +__END__ + +=head1 NAME + +TopologicalAtomTripletsFingerprints + +=head1 SYNOPSIS + +use Fingerprints::TopologicalAtomTripletsFingerprints; + +use Fingerprints::TopologicalAtomTripletsFingerprints qw(:all); + +=head1 DESCRIPTION + +B<TopologicalAtomTripletsFingerprints> [ Ref 57, Ref 59, Ref 72 ] class provides the following methods: + +new, GenerateFingerprints, GetAtomTripletIDs, GetDescription, +SetAtomIdentifierType, SetAtomicInvariantsToUse, SetFunctionalClassesToUse, +SetMaxDistance, SetMinDistance, StringifyTopologicalAtomTripletsFingerprints + +B<TopologicalAtomTripletsFingerprints> is derived from B<Fingerprints> class which in turn +is derived from B<ObjectProperty> base class that provides methods not explicitly defined +in B<TopologicalAtomTripletsFingerprints>, B<Fingerprints> or B<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>(); + +The current release of MayaChemTools supports generation of B<TopologicalAtomTripletsFingerprints> +corresponding to following B<AtomtomIdentifierTypes>: + + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes + +Based on the values specified for B<AtomIdentifierType> along with other specified +parameters such as B<AtomicInvariantsToUse> and B<FunctionalClassesToUse>, initial +atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance +matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom +triplets within B<MinDistance> and B<MaxDistance> are identified and counted. An atom triplet +identifier is generated for each unique atom triplet; the format of atom triplet identifier is: + + <ATx>-Dyz-<ATy>-Dxz-<ATz>-Dxy + + ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z + Dxy: Distance between atom x and atom y + Dxz: Distance between atom x and atom z + Dyz: Distance between atom y and atom z + + where <AT1>-D23 <= <AT2>-D13 <= <AT3>-D12 + +The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute +topological atom triplets fingerprints of the molecule. + +The current release of MayaChemTools generates the following types of topological atom triplets +fingerprints vector strings: + + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M + inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 + .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 + 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1 + -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; + 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 + 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8... + + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M + inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString + ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO + 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X + 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2 + -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2... + + FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan + ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D + 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_ + 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_ + 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...; + 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2 + 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1... + + FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance + 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D + 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC + H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1- + aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...; + 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2 + 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1 + 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ... + + FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi + nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1 + -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal + -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar + -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...; + 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5 + 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3 + 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2... + + FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance + 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1- + N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A + -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B + -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3- + O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-... + + FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1 + :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11 + -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D + 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C + 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1 + -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS... + + FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 + :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C + .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3- + D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2 + -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C. + 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7... + + FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1: + MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non + e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D + 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5 + N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21- + D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-... + + FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M + axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3 + -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9 + C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1- + C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5- + C_3-D6 C_2-D1-C_3-D5-O_3-D4 C_2-D1-C_3-D6-C_3-D7 C_2-D1-C_3-D7-C_3-... + +=head2 METHODS + +=over 4 + +=item B<new> + + $NewTopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + %NamesAndValues); + +Using specified I<TopologicalAtomTripletsFingerprints> property names and values hash, B<new> +method creates a new object and returns a reference to newly created B<TopologicalAtomTripletsFingerprints> +object. By default, the following properties are initialized: + + Molecule = '' + Type = 'TopologicalAtomTriplets' + MinDistance = 1 + MaxDistance = 10 + UseTriangleInequality = 1 + AtomIdentifierType = '' + AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC'] + FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] + +Examples: + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes'); + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => + ['AS', 'X', 'BO', 'H', 'FC'] ); + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'DREIDINGAtomTypes'); + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'MMFF94AtomTypes'); + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'TPSAAtomTypes'); + + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'AtomIdentifierType' => + 'FunctionalClassAtomTypes', + 'FunctionalClassesToUse' => + ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']); + + $TopologicalAtomTripletsFingerprints->GenerateFingerprints(); + print "$TopologicalAtomTripletsFingerprints\n"; + +=item B<GetDescription> + + $Return = $TopologicalAtomTripletsFingerprints->GetDescription(); + +Returns a string containing description of topological atom triplets fingerprints. + +=item B<GenerateFingerprints> + + $TopologicalAtomTripletsFingerprints->GenerateFingerprints(); + +Generates topological atom triplets fingerprints and returns I<TopologicalAtomTripletsFingerprints>. + +=item B<GetAtomTripletIDs> + + $AtomTripletIDsRef = $TopologicalAtomTripletsFingerprints->GetAtomTripletIDs(); + @AtomTripletIDs = $TopologicalAtomTripletsFingerprints->GetAtomTripletIDs(); + +Returns atom triplet IDs corresponding to atom triplets count values in topological atom triplets +fingerprints vector as an array or reference to an array. + +=item B<SetAtomIdentifierType> + + $TopologicalAtomTripletsFingerprints->SetAtomIdentifierType($IdentifierType); + +Sets atom I<IdentifierType> to use during atom triplets fingerprints generation and +returns I<TopologicalAtomTripletsFingerprints>. + +Possible values: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes>. + +=item B<SetAtomicInvariantsToUse> + + $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse($ValuesRef); + $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse(@Values); + +Sets atomic invariants to use during I<AtomicInvariantsAtomTypes> value of I<AtomIdentifierType> +for topological atom triplets fingerprints generation and returns I<TopologicalAtomTripletsFingerprints>. + +Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB, +H, Ar, RA, FC, MN, SM>. Default value: I<AS,X,BO,H,FC>. + +The atomic invariants abbreviations correspond to: + + 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) + +Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to: + + AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n> + +Except for AS 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. + +In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words +are also allowed: + + 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 + +I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant +atom types. + +=item B<SetFunctionalClassesToUse> + + $TopologicalTripletsFingerprints->SetFunctionalClassesToUse($ValuesRef); + $TopologicalTripletsFingerprints->SetFunctionalClassesToUse(@Values); + +Sets functional classes invariants to use during I<FunctionalClassAtomTypes> value of I<AtomIdentifierType> +for topological atom triplets fingerprints generation and returns I<TopologicalAtomTripletsFingerprints>. + +Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>. +Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>. + +The functional class abbreviations correspond to: + + 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 + +I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class 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 + +=item B<SetMaxDistance> + + $TopologicalAtomTripletsFingerprints->SetMaxDistance($Distance); + +Sets maximum distance to use during topological atom triplets fingerprints generation and +returns I<TopologicalAtomTripletsFingerprints>. + +=item B<SetMinDistance> + + $TopologicalAtomTripletsFingerprints->SetMinDistance($Distance); + +Sets minimum distance to use during topological atom triplets fingerprints generation and +returns I<TopologicalAtomTripletsFingerprints>. + +=item B<StringifyTopologicalAtomTripletsFingerprints> + + $String = $TopologicalAtomTripletsFingerprints-> + StringifyTopologicalAtomTripletsFingerprints(); + +Returns a string containing information about I<TopologicalAtomTripletsFingerprints> object. + +=back + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm, +AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm, +MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm, +TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm, +TopologicalPharmacophoreAtomTripletsFingerprints.pm + +=head1 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. + +=cut