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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: Atom_PDB.php,v 1.5 2003/05/13 01:18:17 jmcastagnetto Exp $
//
require_once "Science/Chemistry/Atom.php" ;
/**
* Represents a PDB atom record
* and contains a reference to the PDB residue to which it belongs
*
* @author Jesus M. Castagnetto <jmcastagnetto@php.net>
* @version 1.0
* @access public
* @package Science_Chemistry
*/
class Science_Chemistry_Atom_PDB extends Science_Chemistry_Atom {
/**
* PDB Atom record type, one of ATOM or HETATM
*
* @var string
* @access private
* @see getField()
*/
var $rec_name;
/**
* PDB Atom serial number
*
* @var integer
* @access private
* @see getField()
*/
var $ser_num;
/**
* PDB Atom name
*
* @var string
* @access private
* @see getField()
*/
var $atom_name;
/**
* PDB Atom alternative location
*
* @var string
* @access private
* @see getField()
*/
var $alt_loc;
/**
* PDB Atom's Residue name
*
* @var string
* @access private
* @see getField()
*/
var $res_name;
/**
* PDB Atom's Residue chain ID
*
* @var string
* @access private
* @see getField()
*/
var $chain_id;
/**
* PDB Atom's Residue sequential numnber
*
* @var string
* @access private
* @see getField()
*/
var $res_seq_num;
/**
* PDB Atom insert code
*
* @var string
* @access private
* @see getField()
*/
var $ins_code;
/**
* PDB Atom occupancy
*
* @var float
* @access private
* @see getField()
*/
var $occupancy;
/**
* PDB Atom temperature factor
*
* @var float
* @access private
* @see getField()
*/
var $temp_factor;
/**
* PDB Atom segment identifier
*
* @var string
* @access private
* @see getField()
*/
var $segment_id;
/**
* PDB Atom electronic charge
*
* @var float
* @access private
* @see getField()
*/
var $charge;
/**
* If the atom object has been initialized
*
* @var boolean
* @access public
* @see initAtom()
*/
var $VALID = false;
/**
* Reference to the containing Residue object
*
* @var object Residue_PDB
* @access public
*/
var $parent_residue;
function Science_Chemistry_Atom_PDB($atomrec, $residue="") {
// reference to containing residue
if (!empty($residue))
$this->parent_residue =& $residue;
// process PDB atom record
// no error checking, assumes correct and standard record
$this->VALID = true;
$this->rec_name = trim(substr($atomrec,0,6));
$this->ser_num = (int) trim(substr($atomrec,6,5));
$this->atom_name = trim(substr($atomrec,12,4));
$this->alt_loc = trim(substr($atomrec,16,1));
$this->res_name = trim(substr($atomrec,17,3));
$this->chain_id = trim(substr($atomrec,21,1));
$this->res_seq_num = (int) trim(substr($atomrec,22,4));
$this->ins_code = trim(substr($atomrec,26,1));
$this->occupancy = (float) trim(substr($atomrec,54,6));
$this->temp_factor = (float) trim(substr($atomrec,60,6));
$this->segment_id = trim(substr($atomrec,72,4));
$this->charge = (float)trim(substr($atomrec,78,2));
$x = (double) trim(substr($atomrec,30,8));
$y = (double) trim(substr($atomrec,38,8));
$z = (double) trim(substr($atomrec,46,8));
$this->xyz = new Science_Chemistry_Coordinates(array($x, $y, $z));
$element = trim(substr($atomrec,76,2));
// if no element is present, use the atom_name
$this->element = (preg_match('/^[A-Z]{1,2}/', $element)) ? $element : $this->atom_name;
}
function getField($field) {
// mapping needed so we follow both the PEAR
// variable naming convention, and the PDB
// standard field naming convention
$map = array (
"RecName" => "rec_name",
"SerNum" => "ser_num",
"AtomName" => "atom_name",
"AltLoc" => "alt_loc",
"ResName" => "res_name",
"ChainID" => "chain_id",
"ResSeqNum" => "res_seq_num",
"InsCode" => "ins_code",
"Ocuppancy" => "ocuppancy",
"TempFactor" => "temp_factor",
"SegmentID" => "segment_id",
"Charge" => "charge",
"Element" => "element"
);
// for coordinates index mapping
$cmap = array ("X"=>0, "Y"=>1, "Z"=>2);
if (in_array($field, array_keys($map))) {
$internal_name = $map[$field];
return $this->$internal_name;
} elseif (in_array(strtoupper($field), array_keys($cmap))) {
$index = $cmap[strtoupper($field)];
return $this->xyz->coords[$index];
} else {
return null;
}
}
}
// vim: expandtab: ts=4: sw=4
?>
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