#!/usr/bin/perl

#Atom.pm
#Contains the methods for Atom, an object that represents an atom within a compound.

package Atom;
use base 'Class::Accessor::Faster';
use strict;
#use warnings;

#The following hashes to allow for conversion of mol file charge code to accepted numerical representations of charge and oxidation.
my %SDF_charge_conversion = (2 => 2, 3 => 1, 4 => "Doublet Radical", 5 => -1, 6 => -2, 7 => -3, 0 => 0); 
my %SDF_oxidation_modification = (2 => 2, 3 => 1, 4 => 1, 5 => 1, 6 => 2, 7=> 3, 0 => 0);

#Create prototypical atom object
my @atom_fields =
  (
  "element"            => 0,  #a string representing the element type of the atom
  "SDF_charge"         => 0,  #an integer representing the SDF_charge code of the atom
  "index"              => 0,  #an integer representing the index of the atom in the Atoms array of the molecule
  "bond_count"         => 0,  #an integer representing the number of bonds that contain the atom
  "bond_order_count"   => 0,  #an integer representing the sum of all bond orders of the bonds that contain the atom
  "oxidation_modifier" => 0,  #an integer representing the oxidation state of the atom (calculated from charge)
  "charge"             => 0,  #an integer representing the charge of the atom (calculated from charge)
  );

Atom->mk_accessors( grep { $_ ne "0"; } (@atom_fields));

#Name: new
#Description: Creates a new 'atom' object
#Options: None
#Input: @_ - @(element, SDF_charge, index, bond_count, bond_order_count, oxidation_modifier, charge)
#Output: $self - Atom Object

sub new
  {
  my $proto = shift @_;
  my $self = { @atom_fields, @_ };
  $self = bless ($self, ref($proto) || $proto);
  $self->oxidation_modifier($SDF_oxidation_modification{$self->SDF_charge});
  $self->charge($SDF_charge_conversion{$self->SDF_charge});
  return $self;
  }

1;