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<?php
//
// +----------------------------------------------------------------------+
// | PHP Version 4 |
// +----------------------------------------------------------------------+
// | Copyright (c) 1997-2003 The PHP Group |
// +----------------------------------------------------------------------+
// | This source file is subject to version 2.0 of the PHP license, |
// | that is bundled with this package in the file LICENSE, and is |
// | available at through the world-wide-web at |
// | http://www.php.net/license/2_02.txt. |
// | If you did not receive a copy of the PHP license and are unable to |
// | obtain it through the world-wide-web, please send a note to |
// | license@php.net so we can mail you a copy immediately. |
// +----------------------------------------------------------------------+
// | Authors: Jesus M. Castagnetto <jmcastagnetto@php.net> |
// +----------------------------------------------------------------------+
//
// $Id$
//
require_once "Science/Chemistry/Macromolecule.php";
require_once "Science/Chemistry/Residue_PDB.php";
/**
* Represents a PDB macromolecule, composed of several
* Science_Chemistry_Residue_PDB objects
*
* @author Jesus M. Castagnetto <jmcastagnetto@php.net>
* @version 1.0
* @access public
* @package Science_Chemistry
*/
class Science_Chemistry_Macromolecule_PDB extends Science_Chemistry_Macromolecule {
/**
* Constructor for the class
*
* @param string $pdb PDB ID of the containing file
* @param array $records Array of lines comprising the macromolecule
* @param object PDBFile $pdbfile reference to the PDB file object
* @return object Science_Chemistry_Macromolecule_PDB
* @access public
* @see $pdb
* @see parseResidues()
*/
function Science_Chemistry_Macromolecule_PDB($pdb, $records, $pdbfile="") {
$this->pdb = $pdb;
$this->pdbfile = $pdbfile;
$this->parseResidues($records);
}
/**
* Makes the array of residues in the macromolecule
*
* @param array $records
* @access private
* @see Science_Chemistry_Macromolecule_PDB()
*/
function parseResidues($records) {
$curr_res_id = '';
$res_atoms = array();
$nrecs = count($records);
for ($i=0; $i< $nrecs; $i++) {
$atomrec = $records[$i];
$res_name = trim(substr($atomrec,17,3));
$chain = trim(substr($atomrec,21,1));
$seq_num = (int) trim(substr($atomrec,22,4));
$res_id = $res_name.":".$seq_num.":".$chain;
$res_atoms[$res_id][] = $atomrec;
}
foreach ($res_atoms as $mol_id => $atoms_list) {
$this->molecules[] =& new Science_Chemistry_Residue_PDB($this->pdb,
$atoms_list, $this);
$this->num_molecules++;
}
return true;
}
} // end of Science_Chemistry_Macromolecule_PDB
// vim: expandtab: ts=4: sw=4
?>
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