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lib/Chemistry/Artificial/SQL.pm  view on Meta::CPAN

package Chemistry::Artificial::SQL;
$VERSION = '0.01';
# $Id: Chemistry::Artifical::SQL.pm, v 0.01 2005/05/31 12:14:17 brequesens Exp $

=head1 NAME

ArtificialSQL - Artificial chemistry with database support module

=head1 SYNOPSIS

    use strict;
    use Chemistry::SQL;
    use Chemistry::Artificial::SQL;
    
    # Execution: perl gcha.pl DBNAME CHANAME SIZE_VALUE LEVELS 
    # NUMBER_OF_COMPONENTS_TO_PROCESS
    
    my $dbname = $ARGV[0];
    my $chaname = $ARGV[1];
    my $size = $ARGV[2];
    my $levels = $ARGV[3];
    my $compnumber = $ARGV[4];
    
    if (scalar(@ARGV)!=5)
    { print "Incorrect parameter number  \n";
      print "perl gcha.pl DBNAME CHANAME SIZE_VALUE LEVELS 
      NUMBER_OF_COMPONENTS_TO_PROCESS \n";
      exit;
    }
    
    my $db1 = Chemistry::SQL->new(db_host=>"127.0.0.1",db_user=>"root",db_port=>"3306",db_pwd=>"",
    db_name=>"$dbname",db_driver=>"mysql");
    $db1->connect_db;
    
    my $cha = Chemistry::Artificial::SQL->new(db_name=>$db1);
    $cha->new_ch ("$chaname","TEST DESCRIPTION");
    
    
    #Inserting Reactions 
    #In this example file we're working with the reaction C=CC=C.C=C>>C1=CCCCC1
    my $string_react = $db1->string_react(1);
    my $qr=$cha->create_reaction($string_react,'smiles');
    $cha->art_insert_react($qr,"$chaname");
    my $string_react = $db1->string_react(2);
    my $qr=$cha->create_reaction($string_react,'smiles');
    $cha->art_insert_react($qr,"$chaname");
    
    # Inserting Components
    
    my $list = $db1->recover_comp("","");
    
    my $component;
    my $formula;
    my $smilesform;
    
    for (my $index=0; $index<$compnumber; $index++)
    {	@$list[$index]->print(format => 'smiles', unique => 1);
        $cha->art_insert_comp(@$list[$index],"$chaname");
    }
    print ("GENERATING $chaname IN $dbname DATABASE\n");
    $cha->ch_artificial_table($levels,"$chaname",$size);

=head1 DESCRIPTION

This package provides the necessary functions to work with the generation of 
artificial chemistry. The methods implemented in this package, are all 
oriented to generate artificial chemistry. There is a lot of interaction 
with the package Chemistry::SQL, but Chemistry::Artficial::SQL doesnt 
implement any Chemistry::SQL function.

=cut

=head2 Chemistry::Artificial::SQL Attributes

There is only one attribute necessary to work with this module.

	* db: This attribute describes the SQL object to use in the process.

=cut

use strict;
use Chemistry::Reaction;
use Chemistry::SQL;

=head1 METHODS

Methods of Chemistry::Artificial::SQL object.

=over 4

=item Chemistry::Artificial::SQL->new(SQL_OBJECT)

Creates a new I<Chemistry::Articial::SQL> object with the especified attributes.

Example:

	my $db1 = Chemistry::SQL->new(db_host=>"127.0.0.1",db_user=>"root",
        db_port=>"3306",db_pwd=>"",db_name=>"TESTDB",db_driver=>"mysql");
	$db1->connect_db;
	my $cha = Chemistry::Artificial::SQL->new(db_name => $db1);
	$cha->new_ch ("CHATEST","TEST DESCRIPTION");

=cut

sub new { 	
			
my $class = shift;
my %args = @_;
my $self = 
   bless 
   {    
     db_name=>"",
   }, ref $class || $class;