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diff lib/MolecularDescriptors/MolecularVolumeDescriptors.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/MolecularDescriptors/MolecularVolumeDescriptors.pm Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,416 @@ +package MolecularDescriptors::MolecularVolumeDescriptors; +# +# $RCSfile: MolecularVolumeDescriptors.pm,v $ +# $Date: 2015/02/28 20:49:20 $ +# $Revision: 1.16 $ +# +# 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 Scalar::Util (); +use TextUtil (); +use MathUtil (); +use Atom; +use Molecule; +use AtomTypes::AtomTypes; +use MolecularDescriptors::MolecularDescriptors; + +use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS); + +@ISA = qw(MolecularDescriptors::MolecularDescriptors Exporter); +@EXPORT = qw(); +@EXPORT_OK = qw(GetDescriptorNames GetVDWAtomRadiiAndVolumesData); + +%EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]); + +# Setup class variables... +my($ClassName, @DescriptorNames, %VDWAtomRadiiAndVolumesDataMap); +_InitializeClass(); + +# Overload Perl functions... +use overload '""' => 'StringifyMolecularVolumeDescriptors'; + +# Class constructor... +sub new { + my($Class, %NamesAndValues) = @_; + + # Initialize object... + my $This = $Class->SUPER::new(); + bless $This, ref($Class) || $Class; + $This->_InitializeMolecularVolumeDescriptors(); + + $This->_InitializeMolecularVolumeDescriptorsProperties(%NamesAndValues); + + return $This; +} + +# Initialize class ... +sub _InitializeClass { + #Class name... + $ClassName = __PACKAGE__; + + # Descriptor names... + @DescriptorNames = ('MolecularVolume'); + + # Initialize the data hash. It'll be loaded on demand later... + %VDWAtomRadiiAndVolumesDataMap = (); + +} + +# Get descriptor names as an array. +# +# This functionality can be either invoked as a class function or an +# object method. +# +sub GetDescriptorNames { + return @DescriptorNames; +} + +# Initialize object data... +# +sub _InitializeMolecularVolumeDescriptors { + my($This) = @_; + + # Type of MolecularDescriptor... + $This->{Type} = 'MolecularVolume'; + + # Intialize descriptor names and values... + $This->_InitializeDescriptorNamesAndValues(@DescriptorNames); + + return $This; +} + +# Initialize object properties... +# +sub _InitializeMolecularVolumeDescriptorsProperties { + my($This, %NamesAndValues) = @_; + + my($Name, $Value, $MethodName); + while (($Name, $Value) = each %NamesAndValues) { + $MethodName = "Set${Name}"; + $This->$MethodName($Value); + } + + return $This; +} + +# Get VDW atom data loaded from VDW atom radii and and volumes data file as +# a reference to hash with the following hash data format: +# +# @{$VDWAtomRadiiAndVolumesDataMap{AtomTypes}} - Array of all possible atom type symbols for all atoms +# @{$VDWAtomRadiiAndVolumesDataMap->{ColLabels}} - Array of column labels +# %{$VDWAtomRadiiAndVolumesDataMap->{DataCol<Num>}} - Hash keys pair: <DataCol<Num>, AtomType> +# +# This functionality can be either invoked as a class function or an +# object method. +# +sub GetVDWAtomRadiiAndVolumesData { + + # Make sure data is loaded... + _CheckAndLoadVDWAtomRadiiAndVolumesData(); + + return \%VDWAtomRadiiAndVolumesDataMap; +} + +# Calculate van der Waals molecular volume [ Ref 93 ] of a molecule using +# atomic and bonds contributions... +# +# van der Waals molecular volume (A**3/molecule) is defined as: +# +# vdwMolecularVolume = SumOfAtomicVDWVolumeContributions - 5.92 * NumOfBonds +# - 14.7 * NumOfAromaticRings - 3.8 * NumOfNonAromaticRings +# +# Methodology: +# . Add up van der Waals atom volumne of all atoms +# . Calculate molecular volume by correcting sum of atom volumes for num of +# bonds and rings +# +# Caveats: +# . All hydrogens must be added to molecule before calling GenerateDescriptors. +# +sub GenerateDescriptors { + my($This) = @_; + + # Initialize descriptor values... + $This->_InitializeDescriptorValues(); + + # Check availability of molecule... + if (!$This->{Molecule}) { + carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."; + return undef; + } + + # Calculate descriptor values... + if (!$This->_CalculateDescriptorValues()) { + carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate MolecularVolume values: van der Waals atom volume data is not available for all atoms..."; + return undef; + } + + # Set final descriptor values... + $This->_SetFinalDescriptorValues(); + + return $This; +} + +# Calculate MolecularVolume value... +# +sub _CalculateDescriptorValues { + my($This) = @_; + my($Atom, $AtomID, $AtomSymbol, $SumOfVDWAtomVolumes, $Molecule, $MolecularVolume, $NumOfBonds, $NumOfAromaticRings, $NumOfNonAromaticRings, $VDWAtomRadiiAndVolumesDataMapRef); + + $MolecularVolume = 0; + + $VDWAtomRadiiAndVolumesDataMapRef = $This->GetVDWAtomRadiiAndVolumesData(); + $Molecule = $This->{Molecule}; + + # Calculate atom volumes contribution to molecular volume... + # + $SumOfVDWAtomVolumes = 0; + + ATOM: for $Atom ($Molecule->GetAtoms()) { + $AtomID = $Atom->GetID(); + $AtomSymbol = $Atom->GetAtomSymbol(); + + # Make sure van der Waals atom volume is available... + if (!exists $VDWAtomRadiiAndVolumesDataMap{DataCol3}{$AtomSymbol}) { + return undef; + } + $SumOfVDWAtomVolumes += $VDWAtomRadiiAndVolumesDataMapRef->{DataCol3}{$AtomSymbol}; + } + + $NumOfBonds = $Molecule->GetNumOfBonds(); + $NumOfAromaticRings = $Molecule->GetNumOfAromaticRings(); + $NumOfNonAromaticRings = $Molecule->GetNumOfRings() - $NumOfAromaticRings; + + # Apply correction for bonds and rings... + $MolecularVolume = $SumOfVDWAtomVolumes - 5.92 * $NumOfBonds - 14.7 * $NumOfAromaticRings - 3.8 * $NumOfNonAromaticRings; + + # Track the calculated values... + $This->{MolecularVolume} = MathUtil::round($MolecularVolume, 2); + + return $This; +} + +# Setup final descriptor values... +# +sub _SetFinalDescriptorValues { + my($This) = @_; + + $This->{DescriptorsGenerated} = 1; + + $This->SetDescriptorValues($This->{MolecularVolume}); + + return $This; +} + +# Return a string containg data for MolecularVolumeDescriptors object... +# +sub StringifyMolecularVolumeDescriptors { + my($This) = @_; + my($MolecularVolumeDescriptorsString); + + $MolecularVolumeDescriptorsString = "MolecularDescriptorType: $This->{Type}; " . $This->_StringifyDescriptorNamesAndValues(); + + return $MolecularVolumeDescriptorsString; +} + +# Is it a MolecularVolumeDescriptors object? +sub _IsMolecularVolumeDescriptors { + my($Object) = @_; + + return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0; +} + +# Check and load van der Waals atom radii and volumes data... +# +sub _CheckAndLoadVDWAtomRadiiAndVolumesData { + + # Is it already loaded? + if (exists $VDWAtomRadiiAndVolumesDataMap{AtomTypes}) { + return; + } + + _LoadVDWAtomRadiiAndVolumesData(); +} + +# Initialize van der Waals atom radii and volumes data from the file... +# +# Format: +# +# "AtomTypeSymbol","VDWAtomRadius(A)","VDWAtomVolume(A**3)/molecule" +# "H","1.20","7.24" +# "He","1.40","11.49" +# +sub _LoadVDWAtomRadiiAndVolumesData { + my($VDWAtomDataFile, $MayaChemToolsLibDir); + + $MayaChemToolsLibDir = FileUtil::GetMayaChemToolsLibDirName(); + + $VDWAtomDataFile = "$MayaChemToolsLibDir" . "/data/VDWAtomRadiiAndVolumes.csv"; + if (! -e "$VDWAtomDataFile") { + croak "Error: MayaChemTools package file, $VDWAtomDataFile, is missing: Possible installation problems..."; + } + + %VDWAtomRadiiAndVolumesDataMap = (); + AtomTypes::AtomTypes::LoadAtomTypesData($VDWAtomDataFile, \%VDWAtomRadiiAndVolumesDataMap); +}; + +1; + +__END__ + +=head1 NAME + +MolecularVolumeDescriptors + +=head1 SYNOPSIS + +use MolecularDescriptors::MolecularVolumeDescriptors; + +use MolecularDescriptors::MolecularVolumeDescriptors qw(:all); + +=head1 DESCRIPTION + +B<MolecularVolumeDescriptors> class provides the following methods: + +new, GenerateDescriptors, GetDescriptorNames, +GetVDWAtomRadiiAndVolumesData, StringifyMolecularVolumeDescriptors + +B<MolecularVolumeDescriptors> is derived from B<MolecularDescriptors> class which in turn +is derived from B<ObjectProperty> base class that provides methods not explicitly defined +in B<MolecularVolumeDescriptors>, B<MolecularDescriptors> 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>(); + +van der Waals molecular volume [ Ref 93 ] (A**3/molecule) of a molecule is +calculated using atomic and bonds contributions along with adjustments for +aromatic and non-aromatic rings using the following equation: + + vdwMolecularVolume = SumOfAtomicVDWVolumeContributions + - 5.92 * NumOfBonds + - 14.7 * NumOfAromaticRings + - 3.8 * NumOfNonAromaticRings + +van der Waals atomic volume for atoms is taken from data file VDWAtomRadiiAndVolumes.csv +distributed with MayaChemTools. It contains van der Waals atom radii and atom and volumes +data for 38 elements; Table 2 [ Ref 93 ] contains data for only 15 elements. After converting +valid van der Waals atom radius data from pm (picometer) to A (Angstrom) available under column +name VanderWaalsRadius in PeriodicTableElementsData.csv data file, van der Waals atom volume +is calculated using: 4/3 * PI * (Radius ** 3). For elements specified in Table 2 [ Ref 93 ] - +H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, Te, I - the van der Waals atom radii and calculated +atom volumes match the values in the table. + +=head2 METHODS + +=over 4 + +=item B<new> + + $NewMolecularVolumeDescriptors = new MolecularDescriptors:: + MolecularVolumeDescriptors( + %NamesAndValues); + +Using specified I<MolecularVolumeDescriptors> property names and values hash, B<new> +method creates a new object and returns a reference to newly created B<MolecularVolumeDescriptors> +object. By default, the following properties are initialized: + + Molecule = '' + Type = 'MolecularVolume' + @DescriptorNames = ('MolecularVolume') + @DescriptorValues = ('None') + +Examples: + + $MolecularVolumeDescriptors = new MolecularDescriptors:: + MolecularVolumeDescriptors(); + + $MolecularVolumeDescriptors->SetMolecule($Molecule); + $MolecularVolumeDescriptors->GenerateDescriptors(); + print "MolecularVolumeDescriptors: $MolecularVolumeDescriptors\n"; + +=item B<GenerateDescriptors> + + $MolecularVolumeDescriptors->GenerateDescriptors(); + +Calculate van der Waals molecular volume descriptor for a molecule and returns +I<MolecularVolumeDescriptors>. + +=item B<GetDescriptorNames> + + @DescriptorNames = $MolecularVolumeDescriptors->GetDescriptorNames(); + @DescriptorNames = MolecularDescriptors::MolecularVolumeDescriptors:: + GetDescriptorNames(); + +Returns all available descriptor names as an array. + +=item B<GetVDWAtomRadiiAndVolumesData> + + $VDWVolumeDataMapRef = $MolecularVolumeDescriptors-> + GetVDWAtomRadiiAndVolumesData(); + $VDWVolumeDataMapRef = MolecularDescriptors::MolecularVolumeDescriptors:: + GetVDWAtomRadiiAndVolumesData(); + +Returns a hash reference to van der Waals atom symbols corresponding to atom types +and associated data loaded from VDWAtomRadiiAndVolumes.csv data file as a reference +to hash with the following hash data format: + + @{$VDWVolumeDataMap{AtomTypes}} - Array of all possible atom + types for all atom symbols + @{$VDWVolumeDataMap->{ColLabels}} - Array of column labels + %{$VDWVolumeDataMap->{DataCol<Num>}} - Hash keys pair: + DataCol<Num>, AtomType + +=item B<StringifyMolecularVolumeDescriptors> + + $String = $MolecularVolumeDescriptors-> + StringifyMolecularVolumeDescriptors(); + +Returns a string containing information about I<MolecularVolumeDescriptors> object. + +=back + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +MolecularDescriptors.pm, MolecularDescriptorsGenerator.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