diff mayachemtools/lib/MolecularDescriptors/RingsCountDescriptors.pm @ 0:73ae111cf86f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayachemtools/lib/MolecularDescriptors/RingsCountDescriptors.pm	Wed Jan 20 11:55:01 2016 -0500
@@ -0,0 +1,305 @@
+package MolecularDescriptors::RingsCountDescriptors;
+#
+# $RCSfile: RingsCountDescriptors.pm,v $
+# $Date: 2015/02/28 20:49:20 $
+# $Revision: 1.10 $
+#
+# Author: Manish Sud <[e-mail]>
+#
+# 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 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($ClassName, @DescriptorNames);
+_InitializeClass();
+
+# Overload Perl functions...
+use overload '""' => 'StringifyRingsCountDescriptors';
+
+# Class constructor...
+sub new {
+  my($Class, %NamesAndValues) = @_;
+
+  # Initialize object...
+  my $This = $Class->SUPER::new();
+  bless $This, ref($Class) || $Class;
+  $This->_InitializeRingsCountDescriptors();
+
+  $This->_InitializeRingsCountDescriptorsProperties(%NamesAndValues);
+
+  return $This;
+}
+
+# Initialize class ...
+sub _InitializeClass {
+  #Class name...
+  $ClassName = __PACKAGE__;
+
+  # Descriptor names...
+  @DescriptorNames = ('Rings', 'AromaticRings');
+
+}
+
+# Get descriptor names as an array.
+#
+# This functionality can be either invoked as a class function or an
+# object method.
+#
+sub GetDescriptorNames {
+  return @DescriptorNames;
+}
+
+# Initialize object data...
+#
+sub _InitializeRingsCountDescriptors {
+  my($This) = @_;
+
+  # Type of MolecularDescriptor...
+  $This->{Type} = 'RingsCount';
+
+  # Intialize descriptor names and values...
+  $This->_InitializeDescriptorNamesAndValues(@DescriptorNames);
+
+  return $This;
+}
+
+# Initialize object properties...
+#
+sub _InitializeRingsCountDescriptorsProperties {
+  my($This, %NamesAndValues) = @_;
+
+  my($Name, $Value, $MethodName);
+  while (($Name, $Value) = each  %NamesAndValues) {
+    $MethodName = "Set${Name}";
+    $This->$MethodName($Value);
+  }
+
+  return $This;
+}
+
+# Generate molecular weight and exact mass values...
+#
+sub GenerateDescriptors {
+  my($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...";
+    return undef;
+  }
+
+  # Set final descriptor values...
+  $This->_SetFinalDescriptorValues();
+
+  return $This;
+}
+
+# Calculate molecular weight and exact mass values..
+#
+sub _CalculateDescriptorValues {
+  my($This) = @_;
+  my($MolecularWeight, $ExactMass);
+
+  $This->{Rings} = $This->{Molecule}->GetNumOfRings();
+  $This->{AromaticRings} = $This->{Molecule}->GetNumOfAromaticRings();
+
+  return $This;
+}
+
+# Setup final descriptor values...
+#
+sub _SetFinalDescriptorValues {
+  my($This) = @_;
+
+  $This->{DescriptorsGenerated} = 1;
+
+  $This->SetDescriptorValues($This->{Rings}, $This->{AromaticRings});
+
+  return $This;
+}
+
+# Return a string containg data for RingsCountDescriptors object...
+#
+sub StringifyRingsCountDescriptors {
+  my($This) = @_;
+  my($TheString);
+
+  $TheString = "MolecularDescriptorType: $This->{Type}; " . $This->_StringifyDescriptorNamesAndValues();
+
+  return $TheString;
+}
+
+# Is it a RingsCountDescriptors object?
+sub _IsRingsCountDescriptors {
+  my($Object) = @_;
+
+  return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+RingsCountDescriptors
+
+=head1 SYNOPSIS
+
+use MolecularDescriptors::RingsCountDescriptors;
+
+use MolecularDescriptors::RingsCountDescriptors qw(:all);
+
+=head1 DESCRIPTION
+
+B<RingsCountDescriptors> class provides the following methods:
+
+new, GenerateDescriptors, GetDescriptorNames, StringifyRingsCountDescriptors
+
+B<RingsCountDescriptors> is derived from B<MolecularDescriptors> class which in turn
+is  derived from B<ObjectProperty> base class that provides methods not explicitly defined
+in B<RingsCountDescriptors>, 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>();
+
+B<RingsCountDescriptors> class doesn't perform any ring or aromaticity detection before
+counting their number in a molecule. Instead, it assumes ring and aromaticity detection have
+been performed by caller using B<DetectRings> [Ref 31] and B<DetectAromaticity> methods
+available in B<Molecule>.
+
+B<DetectAromaticity> method available in B<Molecule> class assigns aromaticity to rings
+using Huckel rule as explained below:
+
+o Ring aromaticity is determined using Huckel's rule: a ring containing 4n + 2 pi electrons is
+considered aromatic.
+
+o Hetrocyclic rings containing N, O and S atoms fall into two classes: Basic aromatic and
+Non-basic aromatic. In Basic aromatic hetrocyclic rings, heteroatom itself is involved in a
+double bond. (e.g. Pyridine) However, in non-basic hetrocyclic rings, heteroatom might have
+an attached hydrogen atom and the remaining lone pair contribute to electron delocalization
+and contributes to 4n + 2 electrons. (e.g. Pyrrole, Furan)
+
+o For molecules containing fused rings, each fused ring set is considered as one aromatic
+system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in
+fused set are treated individually for aromaticity detection. Additionally, non-fused
+rings are handled on their own during aromaticity detection.
+
+=head2 METHODS
+
+=over 4
+
+=item B<new>
+
+    $NewRingsCountDescriptors = new MolecularDescriptors::
+                                RingsCountDescriptors(
+                                %NamesAndValues);
+
+Using specified I<RingsCountDescriptors> property names and values hash, B<new>
+method creates a new object and returns a reference to newly created B<RingsCountDescriptors>
+object. By default, the following properties are initialized:
+
+    Molecule = ''
+    Type = 'RingsCount'
+
+    @DescriptorNames = ('Rings', 'AromaticRings')
+    @DescriptorValues = ('None', 'None')
+
+Examples:
+
+    $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors(
+                              'Molecule' => $Molecule);
+
+    $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors();
+
+    $RingsCountDescriptors->SetMolecule($Molecule);
+    $RingsCountDescriptors->GenerateDescriptors();
+    print "RingsCountDescriptors: $RingsCountDescriptors\n";
+
+=item B<GenerateDescriptors>
+
+    $RingsCountDescriptors->GenerateDescriptors();
+
+Calculate number of rings and aromatic rings in a molecule and returns
+I<RingsCountDescriptors>.
+
+=item B<GetDescriptorNames>
+
+    @DescriptorNames = $RingsCountDescriptors->GetDescriptorNames();
+    @DescriptorNames = MolecularDescriptors::RingsCountDescriptors::
+                       GetDescriptorNames();
+
+Returns all available descriptor names as an array.
+
+=item B<StringifyRingsCountDescriptors>
+
+    $String = $RingsCountDescriptors->
+                              StringifyRingsCountDescriptors();
+
+Returns a string containing information about I<RingsCountDescriptors> object.
+
+=back
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=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