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view mayachemtools/lib/MolecularDescriptors/Fsp3CarbonsDescriptors.pm @ 2:dfff2614510e draft
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author | deepakjadmin |
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date | Wed, 20 Jan 2016 12:15:15 -0500 |
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package MolecularDescriptors::Fsp3CarbonsDescriptors; # # $RCSfile: Fsp3CarbonsDescriptors.pm,v $ # $Date: 2015/02/28 20:49:19 $ # $Revision: 1.12 $ # # 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 MolecularDescriptors::MolecularDescriptors; use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS); @ISA = qw(MolecularDescriptors::MolecularDescriptors Exporter); @EXPORT = qw(); @EXPORT_OK = qw(GetDescriptorNames); %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]); # Setup class variables... my($ClassName, @DescriptorNames); _InitializeClass(); # Overload Perl functions... use overload '""' => 'StringifyFsp3CarbonsDescriptors'; # Class constructor... sub new { my($Class, %NamesAndValues) = @_; # Initialize object... my $This = $Class->SUPER::new(); bless $This, ref($Class) || $Class; $This->_InitializeFsp3CarbonsDescriptors(); $This->_InitializeFsp3CarbonsDescriptorsProperties(%NamesAndValues); return $This; } # Initialize class ... sub _InitializeClass { #Class name... $ClassName = __PACKAGE__; # Descriptor names... @DescriptorNames = ('Fsp3Carbons', 'Sp3Carbons'); } # Get descriptor names as an array. # # This functionality can be either invoked as a class function or an # object method. # sub GetDescriptorNames { return @DescriptorNames; } # Initialize object data... # sub _InitializeFsp3CarbonsDescriptors { my($This) = @_; # Type of MolecularDescriptor... $This->{Type} = 'Fsp3Carbons'; # Intialize descriptor names and values... $This->_InitializeDescriptorNamesAndValues(@DescriptorNames); return $This; } # Initialize object properties... # sub _InitializeFsp3CarbonsDescriptorsProperties { my($This, %NamesAndValues) = @_; my($Name, $Value, $MethodName); while (($Name, $Value) = each %NamesAndValues) { $MethodName = "Set${Name}"; $This->$MethodName($Value); } return $This; } # Calculate fraction of SP3 carbons (Fsp3Carbons) [ Ref 115-116, Ref 119 ] in a molecule... # # It is defined as follows: # # Fsp3 = Number of SP3 carbons/Total number of carbons # sub GenerateDescriptors { my($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 Fsp3Carbons values corresponding to assigned Fsp3Carbons atom types..."; return undef; } # Set final descriptor values... $This->_SetFinalDescriptorValues(); return $This; } # Calculate Fsp3Carbons value... # sub _CalculateDescriptorValues { my($This) = @_; my($Atom, $AtomID, $TotalCarbons, $NumOfSp3Carbons, $Fsp3Carbons); $TotalCarbons = 0; $NumOfSp3Carbons = 0; ATOM: for $Atom ($This->{Molecule}->GetAtoms()) { if (!$Atom->IsCarbon()) { next ATOM; } $TotalCarbons += 1; if ($Atom->DoesAtomNeighborhoodMatch('C.T4.TSB4')) { $NumOfSp3Carbons += 1; } } $Fsp3Carbons = $NumOfSp3Carbons ? $NumOfSp3Carbons/$TotalCarbons : 0; # Track values... $This->{Fsp3Carbons} = MathUtil::round($Fsp3Carbons, 2); $This->{Sp3Carbons} = $NumOfSp3Carbons; return $This; } # Setup final descriptor values... # sub _SetFinalDescriptorValues { my($This) = @_; $This->{DescriptorsGenerated} = 1; $This->SetDescriptorValues($This->{Fsp3Carbons}, $This->{Sp3Carbons}); return $This; } # Return a string containg data for Fsp3CarbonsDescriptors object... # sub StringifyFsp3CarbonsDescriptors { my($This) = @_; my($Fsp3CarbonsDescriptorsString); $Fsp3CarbonsDescriptorsString = "MolecularDescriptorType: $This->{Type}; " . $This->_StringifyDescriptorNamesAndValues(); return $Fsp3CarbonsDescriptorsString; } # Is it a Fsp3CarbonsDescriptors object? sub _IsFsp3CarbonsDescriptors { my($Object) = @_; return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0; } 1; __END__ =head1 NAME Fsp3CarbonsDescriptors =head1 SYNOPSIS use MolecularDescriptors::Fsp3CarbonsDescriptors; use MolecularDescriptors::Fsp3CarbonsDescriptors qw(:all); =head1 DESCRIPTION B<Fsp3CarbonsDescriptors> class provides the following methods: new, GenerateDescriptors, GetDescriptorNames, StringifyFsp3CarbonsDescriptors B<Fsp3CarbonsDescriptors> is derived from B<MolecularDescriptors> class which in turn is derived from B<ObjectProperty> base class that provides methods not explicitly defined in B<Fsp3CarbonsDescriptors>, 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>(); Fraction sp3 carbons (Fsp3Carbons) [ Ref 115-116, Ref 119 ] value is calculated by dividing the number of sp3 carbons (Sp3Carbons) with the total number of carbons in a molecule. =head2 METHODS =over 4 =item B<new> $NewFsp3CarbonsDescriptors = new MolecularDescriptors:: Fsp3CarbonsDescriptors(%NamesAndValues); Using specified I<Fsp3CarbonsDescriptors> property names and values hash, B<new> method creates a new object and returns a reference to newly created B<Fsp3CarbonsDescriptors> object. By default, the following properties are initialized: Molecule = '' Type = 'Fsp3Carbons' @DescriptorNames = ('Fsp3Carbons', 'Sp3Carbons') @DescriptorValues = ('None', 'None') Examples: $Fsp3CarbonsDescriptors = new MolecularDescriptors::Fsp3CarbonsDescriptors( 'Molecule' => $Molecule); $Fsp3CarbonsDescriptors = new MolecularDescriptors::Fsp3CarbonsDescriptors(); $Fsp3CarbonsDescriptors->SetMolecule($Molecule); $Fsp3CarbonsDescriptors->GenerateDescriptors(); print "Fsp3CarbonsDescriptors: $Fsp3CarbonsDescriptors\n"; =item B<GenerateDescriptors> $Fsp3CarbonsDescriptors->GenerateDescriptors(); Calculates Fsp3Carbons and Sp3Carbons values for a molecule and returns I<Fsp3CarbonsDescriptors>. =item B<GetDescriptorNames> @DescriptorNames = $Fsp3CarbonsDescriptors->GetDescriptorNames(); @DescriptorNames = MolecularDescriptors::Fsp3CarbonsDescriptors:: GetDescriptorNames(); Returns all available descriptor names as an array. =item B<StringifyFsp3CarbonsDescriptors> $String = $Fsp3CarbonsDescriptors->StringifyFsp3CarbonsDescriptors(); Returns a string containing information about I<Fsp3CarbonsDescriptors> 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