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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.php";
require_once "Science/Chemistry/Atom_PDB.php";
require_once "Science/Chemistry/Molecule.php";
/**
* Represents a PDB residue
*
* @author Jesus M. Castagnetto <jmcastagnetto@php.net>
* @version 1.0
* @access public
* @package Science_Chemistry
*/
class Science_Chemistry_Residue_PDB extends Science_Chemistry_Molecule {
/**
* PDB Residue sequence number
*
* @var integer
* @access private
*/
var $seq_num;
/**
* PDB Residue chain
*
* @var string
* @access private
*/
var $chain;
/**
* PDB Residue ID
* $id = "$name:$seq_num:$chain"
*
* @var string
* @access private
*/
var $id;
/**
* PDB ID for the protein that contains
* this residue
*
* @var string
* @access private
*/
var $pdb;
/**
* If the PDB residue object has been initialized
*
* @var boolean
* @access public
*/
var $VALID = false;
/**
* Reference to the protein
* to which this residue belongs
*
* @var object Science_Chemistry_Macromolecule_PDB
* @access public
*/
var $macromol;
/**
* Constructor for the class
*
* @param string $pdb PDB if of the protein/nucleic acid/etc.
* @param array $atomrec_arr Array of PDB atom record lines
* @param object Science_Chemistry_Macromolecule_PDB $macromol reference to the containing macromolecule
* @return object Science_Chemistry_Residue_PDB
* @access public
*/
function Science_Chemistry_Residue_PDB($pdb, $atomrec_arr, $macromol="") {
for ($i=0; $i < count($atomrec_arr); $i++) {
$this->atoms[] = new Science_Chemistry_Atom_PDB($atomrec_arr[$i], $this);
}
if (!empty($this->atoms)) {
$this->VALID = true;
$this->macromol =& $macromol;
$this->pdb =& $pdb;
$this->num_atoms = count($this->atoms);
$line =& $atomrec_arr[0];
$this->name = trim(substr($line,17,3));
$this->chain = trim(substr($line,21,1));
$this->seq_num = (int) trim(substr($line,22,4));
$this->id = $this->name.":".$this->seq_num.":".$this->chain;
} else {
return null;
}
}
/**
* Calculates geometrical parameters for the residue
* Backbone bond distances, angles and torsions
* Sidechain Chi angles
* TODO
*
* @return boolean
* @access public
*/
/*
function calcGeomParams() {
// TODO
return true;
}
*/
/**
* Returns geometrical parameter for the residue
* One of: bonds, angles, torsions, or chis
* TODO
*
* @return array
* @access public
*/
/*
function getGeomParams($param) {
// TODO
return array();
}
*/
} // end of Science_Chemistry_Residue_PDB class
// vim: expandtab: ts=4: sw=4
?>
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