Viewing file:  xyz2cml.php (3.13 KB) -rw-rw-rw-
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#! /usr/local/bin/php -q
<?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> |
// +----------------------------------------------------------------------+
//
// Sample script that uses the Chemistry classes to convert a XYZ file to CML
//
// $Id: xyz2cml.php,v 1.3 2003/01/04 11:56:25 mj Exp $
require_once "Science/Chemistry.php";
require_once "Science/Chemistry/Molecule_XYZ.php";
// save the old value of "track_errors"
$oldtrack = ini_get("track_errors");
// set it so $php_errormsg will be used
ini_set("track_errors", 1);
// Use a local or the original DTD
//$DTDPATH = "http://www.xml-cml.org/cml_10.dtd";
// change the local path
$DTDPATH = "/usr/local/dtd/cml.dtd";
function usage ($extra) {
global $argv;
echo $extra;
echo "Usage:\n\t".basename($argv[0])." xyzfile cmlfile [title] \n\n";
// restore old "track_errors" value
ini_set("track_errors", $oldtrack);
exit -1;
}
if ($argc < 3)
usage("*ERROR* Wrong number of parameters\n");
// assume that any parameter after the cmlfile name
// is part of the title
if ($argc > 3)
for ($i=3; $i < $argc; $i++)
$title .= $argv[$i]." ";
else
$title = "molecule";
$date = date("Y-m-d H:i:s T");
$title = trim($title);
$xyz = realpath($argv[1]);
$id = str_replace("/","_", $xyz);
list($moltitle,) = explode(".",basename($xyz));
$cml = $argv[2];
echo "Converting ".$argv[1]." to $cml... ";
// create the molecule object
$mol = new Science_Chemistry_Molecule_XYZ($xyz);
// prepare output
$out = "<?xml version=\"1.0\">
<!DOCTYPE document SYSTEM \"$DTDPATH\" [
<!ELEMENT document ANY>
<!ELEMENT cml ANY>
<!ATTLIST cml
title CDATA #IMPLIED
id CDATA #IMPLIED
>
]>
<!--
-- CML document
-- converted from: $xyz
-- on: $date
-->\n";
$out .= "<document>\n<cml title=\"$title\" id=\"$id\">\n";
$out .= $mol->toCML($moltitle, $moltitle."1", true);
$out .= "</cml>\n</document>";
// write the output
$fp = @fopen($cml, "w");
if ($fp) {
fwrite($fp, $out);
flush();
fclose($fp);
echo " finished!\n\n";
} else {
usage("\n*ERROR* while writing to $cml\n--> $php_errormsg\n");
}
// restore old "track_errors" value
ini_set("track_errors", $oldtrack);
?>
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