Mercurial > repos > deepakjadmin > mayatool3_test2
diff lib/Fingerprints/TopologicalAtomTorsionsFingerprints.pm @ 0:4816e4a8ae95 draft default tip
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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/lib/Fingerprints/TopologicalAtomTorsionsFingerprints.pm Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1045 @@ +package Fingerprints::TopologicalAtomTorsionsFingerprints; +# +# $RCSfile: TopologicalAtomTorsionsFingerprints.pm,v $ +# $Date: 2015/02/28 20:48:54 $ +# $Revision: 1.26 $ +# +# 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($ClassName); +_InitializeClass(); + +# Overload Perl functions... +use overload '""' => 'StringifyTopologicalAtomTorsionsFingerprints'; + +# Class constructor... +sub new { + my($Class, %NamesAndValues) = @_; + + # Initialize object... + my $This = $Class->SUPER::new(); + bless $This, ref($Class) || $Class; + $This->_InitializeTopologicalAtomTorsionsFingerprints(); + + $This->_InitializeTopologicalAtomTorsionsFingerprintsProperties(%NamesAndValues); + + return $This; +} + +# Initialize object data... +# +sub _InitializeTopologicalAtomTorsionsFingerprints { + my($This) = @_; + + # Type of fingerprint... + $This->{Type} = 'TopologicalAtomTorsions'; + + # Type of vector... + $This->{VectorType} = 'FingerprintsVector'; + + # Type of FingerprintsVector... + $This->{FingerprintsVectorType} = 'NumericalValues'; + + # Atom identifier type to use for atom IDs in atom torsions... + # + # Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, + # EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + # SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes + # + $This->{AtomIdentifierType} = ''; + + # Atom types assigned to each heavy atom... + # + %{$This->{AssignedAtomTypes}} = (); + + # Final unique atom torsions... + # + @{$This->{AtomTorsionsIDs}} = (); + %{$This->{AtomTorsionsCount}} = (); +} + +# Initialize class ... +sub _InitializeClass { + #Class name... + $ClassName = __PACKAGE__; +} + +# Initialize object properties.... +sub _InitializeTopologicalAtomTorsionsFingerprintsProperties { + my($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 $This; +} + +# Set atom identifier type.. +# +sub SetAtomIdentifierType { + my($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}:$This->{AtomIdentifierType}"; +} + +# Generate topological atom torsions [ Ref 58, Ref 72 ] fingerprints... +# +# Methodology: +# . Assign atom types to all the atoms. +# . Generate and count atom torsions. +# +# Notes: +# . Hydrogen atoms are ignored during the fingerprint generation. +# +sub GenerateFingerprints { + my($This) = @_; + + # Cache appropriate molecule data... + $This->_SetupMoleculeDataCache(); + + # Assign atom types to all heavy atoms... + if (!$This->_AssignAtomTypes()) { + carp "Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."; + return $This; + } + + # Count atom torsions... + $This->_GenerateAndCountAtomTorsions(); + + # Set final fingerprints... + $This->_SetFinalFingerprints(); + + # Clear cached molecule data... + $This->_ClearMoleculeDataCache(); + + 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 $This; +} + +# Count atom torsions involving non-hydrogen atoms by going over the structurally +# unique atom torsions... +# +sub _GenerateAndCountAtomTorsions { + my($This) = @_; + my($Atom1, $Atom2, $Atom3, $Atom4, $AtomID1, $AtomID2, $AtomID3, $AtomID4, $AtomTorsionID, @Atom1Neighbors, @Atom2Neighbors, @Atom3Neighbors); + + # Setup a hash to track structurally unique atom torsions by atom IDs... + %{$This->{StructurallyUniqueAtomTorsions}} = (); + + ATOM1: for $Atom1 (@{$This->{Atoms}}) { + if ($Atom1->IsHydrogen()) { + next ATOM1; + } + $AtomID1 = $Atom1->GetID(); + # Go over Atom1 neighbors other than Atom1... + @Atom1Neighbors = $Atom1->GetNeighbors($Atom1); + ATOM2: for $Atom2 (@Atom1Neighbors) { + if ($Atom2->IsHydrogen()) { + next ATOM2; + } + $AtomID2 = $Atom2->GetID(); + # Go over Atom2 neighbors other than Atom1 and Atom2... + @Atom2Neighbors = $Atom2->GetNeighbors($Atom1, $Atom2); + ATOM3: for $Atom3 (@Atom2Neighbors) { + if ($Atom3->IsHydrogen()) { + next ATOM3; + } + $AtomID3 = $Atom3->GetID(); + @Atom3Neighbors = $Atom3->GetNeighbors($Atom1, $Atom2, $Atom3); + # Go over Atom3 neighbors other than Atom1, Atom2 and Atom3... + ATOM4: for $Atom4 (@Atom3Neighbors) { + if ($Atom4->IsHydrogen()) { + next ATOM4; + } + $AtomID4 = $Atom4->GetID(); + + # Is it a structurally unique torsion? + if (!$This->_IsStructurallyUniqueTorsion($AtomID1, $AtomID2, $AtomID3, $AtomID4)) { + next ATOM4; + } + + # Track structurally unique torsions... + $AtomTorsionID = $This->_GetAtomTorsionID($AtomID1, $AtomID2, $AtomID3, $AtomID4); + if (exists $This->{AtomTorsionsCount}{$AtomTorsionID}) { + $This->{AtomTorsionsCount}{$AtomTorsionID} += 1; + } + else { + $This->{AtomTorsionsCount}{$AtomTorsionID} = 1; + } + } + } + } + } + + return $This; +} + +# Is it a structurally unique torsions? +# +# Notes: +# . For a torsion to be structurally unique which hasn't already been encountered, +# all the four atoms involved in the torsion must be new atoms. And this can be +# simply implemented by tracking the torsions using atom IDs and maintaining a +# hash of already encountered torsions using lexicographically smaller torsion ID +# consisting of four atom IDs. +# +sub _IsStructurallyUniqueTorsion { + my($This, @AtomIDs) = @_; + my($TorsionID, $ReverseTorsionID); + + $TorsionID = join "-", @AtomIDs; + $ReverseTorsionID = join "-", reverse @AtomIDs; + + # Use lexicographically smaller string... + if ($ReverseTorsionID lt $TorsionID) { + $TorsionID = $ReverseTorsionID; + } + + if (exists $This->{StructurallyUniqueAtomTorsions}{$TorsionID}) { + return 0; + } + + # Keep track... + $This->{StructurallyUniqueAtomTorsions}{$TorsionID} = 1; + + return 1; +} + +# Get atom torsion ID corresponding to atom types involved in torsion... +# +# Notes: +# . TorsionID corresponds to assigned atom types of all the four torsion atoms +# concatenated by hyphen. +# . TorsionIDs are generated for both forward and backward sequence of atoms +# in the torsion and keeping the lexicographically smaller TorsionID to keep TorsionID +# independent of atom ordering. +# +sub _GetAtomTorsionID { + my($This, @AtomIDs) = @_; + my($AtomTorsionID, $ReverseAtomTorsionID, @AtomTypes); + + @AtomTypes = (); + @AtomTypes = map { $This->{AssignedAtomTypes}{$_} } @AtomIDs; + + $AtomTorsionID = join "-", @AtomTypes; + $ReverseAtomTorsionID = join "-", reverse @AtomTypes; + + # Use lexicographically smaller string as ID... + return ($ReverseAtomTorsionID lt $AtomTorsionID) ? $ReverseAtomTorsionID : $AtomTorsionID; +} + +# Set final fingerpritns vector... +# +sub _SetFinalFingerprints { + my($This) = @_; + my($AtomTorsionID, $Value, @Values); + + # Mark successful generation of fingerprints... + $This->{FingerprintsGenerated} = 1; + + @Values = (); + @{$This->{AtomTorsionsIDs}} = (); + + for $AtomTorsionID (sort keys %{$This->{AtomTorsionsCount}}) { + $Value = $This->{AtomTorsionsCount}{$AtomTorsionID}; + push @{$This->{AtomTorsionsIDs}}, $AtomTorsionID; + push @Values, $Value; + } + + # Add AtomPairsIDs and values to fingerprint vector... + $This->{FingerprintsVector}->AddValueIDs(\@{$This->{AtomTorsionsIDs}}); + $This->{FingerprintsVector}->AddValues(\@Values); + + return $This; +} + +# Get atom torsions IDs corresponding to atom torsions count values in fingerprint +# vector as an array or reference to an array... +# +# AtomTorsionsIDs list differes in molecules and is generated during finalization +# of fingerprints to make sure the fingerprint vector containing count values +# matches the atom torsions array. +# +sub GetAtomTorsionsIDs { + my($This) = @_; + + return wantarray ? @{$This->{AtomTorsionsIDs}} : \@{$This->{AtomTorsionsIDs}}; +} + +# Cache appropriate molecule data... +# +sub _SetupMoleculeDataCache { + my($This) = @_; + + # Get all atoms including hydrogens. The hydrogen atoms are ignored during processing... + @{$This->{Atoms}} = $This->GetMolecule()->GetAtoms(); + + return $This; +} + +# Clear cached molecule data... +# +sub _ClearMoleculeDataCache { + my($This) = @_; + + @{$This->{Atoms}} = (); + + 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 to use for generating atom IDs in atom torsions... +# +# 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) +# +# AtomTypeIDx = Atomic invariants atom type for atom x +# AtomTypeIDy = Atomic invariants atom type for atom y +# AtomTypeIDz = Atomic invariants atom type for atom z +# AtomTypeIDw = Atomic invariants atom type for atom w +# +# Then: +# +# Atom torsion 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> +# +# AtomTorsion ID corresponds to: +# +# AtomTypeIDx-AtomTypeIDy-AtomTypeIDz-AtomTypeIDw +# +# Except for AS which is a required atomic invariant in atom torsions 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 torsion AtomIDs in Aspirin using default atomic invariants: +# +# C.X1.BO1.H3-C.X3.BO4-O.X2.BO2-C.X3.BO4 +# C.X2.BO3.H1-C.X2.BO3.H1-C.X2.BO3.H1-C.X2.BO3.H1 +# C.X3.BO4-C.X3.BO4-O.X2.BO2-C.X3.BO4 +# C.X3.BO4-O.X2.BO2-C.X3.BO4-O.X1.BO2 +# +# Examples of atom torsion AtomIDs in Aspirin using AS, X and BO atomic invariants: +# +# C.X1.BO1-C.X3.BO4-O.X2.BO2-C.X3.BO4 +# C.X2.BO3-C.X2.BO3-C.X2.BO3-C.X2.BO3 +# C.X3.BO4-C.X3.BO4-O.X2.BO2-C.X3.BO4 +# C.X3.BO4-O.X2.BO2-C.X3.BO4-O.X1.BO2 +# +sub _InitializeAtomicInvariantsAtomTypesInformation { + my($This) = @_; + + # Default atomic invariants to use for generating atom torsions 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 $This; +} + +# Return a string containg data for TopologicalAtomTorsionsFingerprints object... +# +sub StringifyTopologicalAtomTorsionsFingerprints { + my($This) = @_; + my($FingerprintsString); + + # Type of fingerprint... + $FingerprintsString = "Fingerprint type: $This->{Type}; AtomIdentifierType: $This->{AtomIdentifierType}"; + + if ($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 torsions... + $FingerprintsString .= "; NumOfAtomTorsions: " . $This->{FingerprintsVector}->GetNumOfValues(); + + # FingerprintsVector... + $FingerprintsString .= "; FingerprintsVector: < $This->{FingerprintsVector} >"; + + return $FingerprintsString; +} + +1; + +__END__ + +=head1 NAME + +TopologicalAtomTorsionsFingerprints + +=head1 SYNOPSIS + +use Fingerprints::TopologicalAtomTorsionsFingerprints; + +use Fingerprints::TopologicalAtomTorsionsFingerprints qw(:all); + +=head1 DESCRIPTION + +B<TopologicalAtomTorsionsFingerprints> class provides the following methods: + +new, GenerateFingerprints, GetAtomTorsionsIDs, GetDescription, +SetAtomIdentifierType, SetAtomicInvariantsToUse, SetFunctionalClassesToUse, +StringifyTopologicalAtomTorsionsFingerprints + +B<TopologicalAtomTorsionsFingerprints> is derived from B<Fingerprints> class which in turn +is derived from B<ObjectProperty> base class that provides methods not explicitly defined +in B<TopologicalAtomTorsionsFingerprints>, 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<TopologicalAtomTorsionsFingerprints> +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 in a molecule. All unique atom torsions +are identified and an atom torsion identifier is generated; the format of atom torsion identifier is: + + <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4> + + AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types + + where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4 + +The atom torsion identifiers for all unique atom torsions corresponding to non-hydrogen atoms constitute +topological atom torsions fingerprints of the molecule. + +The current release of MayaChemTools generates the following types of topological atom torsions +fingerprints vector strings: + + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 + 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4- + C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO + 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...; + 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1 + + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 + 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3 + .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H + 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B + O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B + O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1... + + FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri + calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C + _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2 + C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...; + 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1 + + FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica + lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC + H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC- + ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...; + 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2 + + FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26 + ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar- + Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar + -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...; + 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3 + + FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica + lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5 + B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5 + A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...; + 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1 + 1 1 2 1 1 3 1 3 + + FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical + Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1 + 1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS + 2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1 + C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20 + 2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C... + + FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical + Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2 + -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C. + ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3 + -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C. + ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ... + + FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa + lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4 + None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None- + None-None 44 None-None-None-O3 3 None-None-None-O4 5 + + FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa + lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C + _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3 + -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C + _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2 + C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-... + +=head2 METHODS + +=over 4 + +=item B<new> + + $NewTopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + %NamesAndValues); + +Using specified I<TopologicalAtomTorsionsFingerprints> property names and values hash, B<new> +method creates a new object and returns a reference to newly created B<TopologicalAtomTorsionsFingerprints> +object. By default, the following properties are initialized: + + Molecule = '' + Type = 'TopologicalAtomTorsions' + AtomIdentifierType = '' + AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC'] + FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] + +Examples: + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes'); + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => + ['AS', 'X', 'BO', 'H', 'FC'] ); + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'DREIDINGAtomTypes'); + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'SYBYLAtomTypes'); + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'SLogPAtomTypes'); + + $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'FunctionalClassAtomTypes', + 'FunctionalClassesToUse' => + ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] ); + + + $TopologicalAtomTorsionsFingerprints->GenerateFingerprints(); + print "$TopologicalAtomTorsionsFingerprints\n"; + +=item B<GetDescription> + + $Description = $TopologicalAtomTorsionsFingerprints->GetDescription(); + +Returns a string containing description of topological atom torsions fingerprints. + +=item B<GenerateFingerprints> + + $TopologicalAtomTorsionsFingerprints->GenerateFingerprints(); + +Generates topological atom torsions fingerprints and returns I<TopologicalAtomTorsionsFingerprints>. + +=item B<GetAtomTorsionsIDs> + + $AtomPairIDsRef = $TopologicalAtomTorsionsFingerprints->GetAtomTorsionsIDs(); + @AtomPairIDs = $TopologicalAtomTorsionsFingerprints->GetAtomTorsionsIDs(); + +Returns atom torsion IDs corresponding to atom torsion count values in topological atom torsions +fingerprints vector as an array or reference to an array. + +=item B<SetAtomIdentifierType> + + $TopologicalAtomTorsionsFingerprints->SetAtomIdentifierType($IdentifierType); + +Sets atom I<IdentifierType> to use during atom torsions fingerprints generation and +returns I<TopologicalAtomTorsionsFingerprints>. + +Possible values: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes>. + +=item B<SetAtomicInvariantsToUse> + + $TopologicalAtomTorsionsFingerprints->SetAtomicInvariantsToUse($ValuesRef); + $TopologicalAtomTorsionsFingerprints->SetAtomicInvariantsToUse(@Values); + +Sets atomic invariants to use during I<AtomicInvariantsAtomTypes> value of I<AtomIdentifierType> +for topological atom torsions fingerprints generation and returns I<TopologicalAtomTorsionsFingerprints>. + +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> + + $TopologicalTorsionsFingerprints->SetFunctionalClassesToUse($ValuesRef); + $TopologicalTorsionsFingerprints->SetFunctionalClassesToUse(@Values); + +Sets functional classes invariants to use during I<FunctionalClassAtomTypes> value of I<AtomIdentifierType> +for topological atom torsions fingerprints generation and returns I<TopologicalAtomTorsionsFingerprints>. + +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<StringifyTopologicalAtomTorsionsFingerprints> + + $String = $TopologicalAtomTorsionsFingerprints-> + StringifyTopologicalAtomTorsionsFingerprints(); + +Returns a string containing information about I<TopologicalAtomTorsionsFingerprints> 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, +TopologicalAtomTripletsFingerprints.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