1 package MolecularDescriptors::Fsp3CarbonsDescriptors;
   2 #
   3 # File: Fsp3CarbonsDescriptors.pm
   4 # Author: Manish Sud <msud@san.rr.com>
   5 #
   6 # Copyright (C) 2024 Manish Sud. All rights reserved.
   7 #
   8 # This file is part of MayaChemTools.
   9 #
  10 # MayaChemTools is free software; you can redistribute it and/or modify it under
  11 # the terms of the GNU Lesser General Public License as published by the Free
  12 # Software Foundation; either version 3 of the License, or (at your option) any
  13 # later version.
  14 #
  15 # MayaChemTools is distributed in the hope that it will be useful, but without
  16 # any warranty; without even the implied warranty of merchantability of fitness
  17 # for a particular purpose.  See the GNU Lesser General Public License for more
  18 # details.
  19 #
  20 # You should have received a copy of the GNU Lesser General Public License
  21 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
  22 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
  23 # Boston, MA, 02111-1307, USA.
  24 #
  25 
  26 use strict;
  27 use Carp;
  28 use Exporter;
  29 use Scalar::Util ();
  30 use TextUtil ();
  31 use MathUtil ();
  32 use Atom;
  33 use Molecule;
  34 use MolecularDescriptors::MolecularDescriptors;
  35 
  36 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
  37 
  38 @ISA = qw(MolecularDescriptors::MolecularDescriptors Exporter);
  39 @EXPORT = qw();
  40 @EXPORT_OK = qw(GetDescriptorNames);
  41 
  42 %EXPORT_TAGS = (all  => [@EXPORT, @EXPORT_OK]);
  43 
  44 # Setup class variables...
  45 my($ClassName, @DescriptorNames);
  46 _InitializeClass();
  47 
  48 # Overload Perl functions...
  49 use overload '""' => 'StringifyFsp3CarbonsDescriptors';
  50 
  51 # Class constructor...
  52 sub new {
  53   my($Class, %NamesAndValues) = @_;
  54 
  55   # Initialize object...
  56   my $This = $Class->SUPER::new();
  57   bless $This, ref($Class) || $Class;
  58   $This->_InitializeFsp3CarbonsDescriptors();
  59 
  60   $This->_InitializeFsp3CarbonsDescriptorsProperties(%NamesAndValues);
  61 
  62   return $This;
  63 }
  64 
  65 # Initialize class ...
  66 sub _InitializeClass {
  67   #Class name...
  68   $ClassName = __PACKAGE__;
  69 
  70   # Descriptor names...
  71   @DescriptorNames = ('Fsp3Carbons', 'Sp3Carbons');
  72 
  73 }
  74 
  75 # Get descriptor names as an array.
  76 #
  77 # This functionality can be either invoked as a class function or an
  78 # object method.
  79 #
  80 sub GetDescriptorNames {
  81   return @DescriptorNames;
  82 }
  83 
  84 # Initialize object data...
  85 #
  86 sub _InitializeFsp3CarbonsDescriptors {
  87   my($This) = @_;
  88 
  89   # Type of MolecularDescriptor...
  90   $This->{Type} = 'Fsp3Carbons';
  91 
  92   # Intialize descriptor names and values...
  93   $This->_InitializeDescriptorNamesAndValues(@DescriptorNames);
  94 
  95   return $This;
  96 }
  97 
  98 # Initialize object properties...
  99 #
 100 sub _InitializeFsp3CarbonsDescriptorsProperties {
 101   my($This, %NamesAndValues) = @_;
 102 
 103   my($Name, $Value, $MethodName);
 104   while (($Name, $Value) = each  %NamesAndValues) {
 105     $MethodName = "Set${Name}";
 106     $This->$MethodName($Value);
 107   }
 108 
 109   return $This;
 110 }
 111 
 112 # Calculate fraction of SP3 carbons (Fsp3Carbons)  [ Ref 115-116, Ref 119 ] in a molecule...
 113 #
 114 # It is defined as follows:
 115 #
 116 # Fsp3 = Number of SP3 carbons/Total number of carbons
 117 #
 118 sub GenerateDescriptors {
 119   my($This) = @_;
 120 
 121   # Initialize descriptor values...
 122   $This->_InitializeDescriptorValues();
 123 
 124   # Check availability of molecule...
 125   if (!$This->{Molecule}) {
 126     carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set...";
 127     return undef;
 128   }
 129 
 130   # Calculate descriptor values...
 131   if (!$This->_CalculateDescriptorValues()) {
 132     carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate Fsp3Carbons values corresponding to assigned Fsp3Carbons atom types...";
 133     return undef;
 134   }
 135 
 136   # Set final descriptor values...
 137   $This->_SetFinalDescriptorValues();
 138 
 139   return $This;
 140 }
 141 
 142 # Calculate Fsp3Carbons value...
 143 #
 144 sub _CalculateDescriptorValues {
 145   my($This) = @_;
 146   my($Atom, $AtomID, $TotalCarbons, $NumOfSp3Carbons, $Fsp3Carbons);
 147 
 148   $TotalCarbons = 0;
 149   $NumOfSp3Carbons = 0;
 150 
 151   ATOM: for $Atom ($This->{Molecule}->GetAtoms()) {
 152     if (!$Atom->IsCarbon()) {
 153       next ATOM;
 154     }
 155     $TotalCarbons += 1;
 156 
 157     if ($Atom->DoesAtomNeighborhoodMatch('C.T4.TSB4')) {
 158       $NumOfSp3Carbons += 1;
 159     }
 160   }
 161 
 162   $Fsp3Carbons = $NumOfSp3Carbons ? $NumOfSp3Carbons/$TotalCarbons : 0;
 163 
 164   # Track values...
 165   $This->{Fsp3Carbons} = MathUtil::round($Fsp3Carbons, 2);
 166   $This->{Sp3Carbons} = $NumOfSp3Carbons;
 167 
 168   return $This;
 169 }
 170 
 171 # Setup final descriptor values...
 172 #
 173 sub _SetFinalDescriptorValues {
 174   my($This) = @_;
 175 
 176   $This->{DescriptorsGenerated} = 1;
 177 
 178   $This->SetDescriptorValues($This->{Fsp3Carbons}, $This->{Sp3Carbons});
 179 
 180   return $This;
 181 }
 182 
 183 # Return a string containg data for Fsp3CarbonsDescriptors object...
 184 #
 185 sub StringifyFsp3CarbonsDescriptors {
 186   my($This) = @_;
 187   my($Fsp3CarbonsDescriptorsString);
 188 
 189   $Fsp3CarbonsDescriptorsString = "MolecularDescriptorType: $This->{Type}; " . $This->_StringifyDescriptorNamesAndValues();
 190 
 191   return $Fsp3CarbonsDescriptorsString;
 192 }
 193 
 194 # Is it a Fsp3CarbonsDescriptors object?
 195 sub _IsFsp3CarbonsDescriptors {
 196   my($Object) = @_;
 197 
 198   return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
 199 }
 200