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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/Molecule.php";
/**
* Base class representing a Molecule from a XYZ format file
*
* @author Jesus M. Castagnetto <jmcastagnetto@php.net>
* @version 1.0
* @access public
* @package Science_Chemistry
*/
class Science_Chemistry_Molecule_XYZ extends Science_Chemistry_Molecule {
/**
* Energy of the molecule. Optional value in XYZ file format.
*
* @var float
* @access public
*/
var $energy = 0.0;
/**
* Constructor for the class, accepts 2 optional parameters:
* the data and its source. Possible values for $src: "file", "string"
*
* @param optional string $xyzdata
* @param optional string $src one of "file" or "string"
* @return object Science_Chemistry_Molecule_XYZ
* @access public
* @see parseXYZ()
*/
function Science_Chemistry_Molecule_XYZ($xyzdata="", $src="file") {
if (!empty($xyzdata))
if (!$this->parseXYZ($xyzdata, $src))
return null;
}
/**
* method that does the parsing of the XYZ data itself
*
* @param string $xyzdata
* @param string $src
* @return boolean
* @access public
* @see Science_Chemistry_Molecule_XYZ()
*/
function parseXYZ($xyzdata, $src) {
if ($src == "file") {
$line = file($xyzdata);
} elseif ($src == "string") {
$line = explode("\n", $xyzdata);
} else {
return false;
}
unset($this->atoms);
// first line is number of atoms
$this->num_atoms = trim($line[0]);
// second line is molecule name and energy
preg_match("/^([[:alnum:].]+)[[:space:]]+([[:digit:].-]+)/",trim($line[1]),$re);
$this->name = trim($re[1]);
$this->energy = trim($re[2]);
for ($i=2; $i<count($line); $i++) {
if (!preg_match("/^#/",$line[$i]) && !preg_match("/^$/", $line[$i])) {
$this->atoms[] = $this->parseAtom($line[$i]);
}
}
}
/**
* Parses an XYZ atom record
*
* @param string $line
* @return object Science_Chemistry_Atom
* @access public
* @see parseXYZ()
*/
function parseAtom($line) {
list($element, $x, $y, $z) = preg_split("/[\t ]+/",trim($line));
return new Science_Chemistry_Atom($element, array($x, $y, $z));
}
/**
* Generates a string representation of the XYZ molecule
* Overrides parent Science_Chemistry_Molecule::toString() method
*
* @return string
* @access public
*/
function toString() {
if (!$this->atoms)
return false;
$out[] = $this->num_atoms;
$out[] = $this->name."\t".sprintf("%15f",$this->energy);
reset($this->atoms);
for ($i=0; $i<$this->num_atoms; $i++)
$out[] = $this->atoms[$i]->toString();
return implode("\n",$out)."\n";
}
} // end of class Science_Chemistry_Molecule_XYZ
// vim: expandtab: ts=4: sw=4
?>
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