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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: PDBFile.php,v 1.5 2003/05/13 01:18:17 jmcastagnetto Exp $
//
require_once "Science/Chemistry/Macromolecule_PDB.php";
/**
* Represents a PDB file, composed of one or more Science_Chemistry_Macromolecule_PDB objects
*
* @author Jesus M. Castagnetto <jmcastagnetto@php.net>
* @version 1.0
* @access public
* @package Science_Chemistry
* @see Science_Chemistry_PDBParser
*/
class Science_Chemistry_PDBFile {
/**
* PDB ID
*
* @var string
* @access private
*/
var $pdb;
/**
* Full path to PDB file
*
* @var string
* @access private
*/
var $file;
/**
* PDB file's date
*
* @var string
* @access private
*/
var $date;
/**
* PDB macromolecule(s) class
*
* @var string
* @access private
*/
var $class;
/**
* Array of meta records
*
* @var array
* @access private
*/
var $meta;
/**
* Array of macromolecular objects
*
* @var array
* @access private
*/
var $macromolecules;
/**
* Number of molecules/subunits
*
* @var int
* @access private
*/
var $num_macromolecules;
/**
* Constructor for the class, requires a PDB filename
*
* @param string $filename
* @return object PDBFile;
* @access public
* @see $pdb
* @see $file
* @see mkArrays()
*/
function Science_Chemistry_PDBFile($filename, $usemeta=false) {
if (!file_exists($filename))
return null;
list($pdb,) = explode(".",basename($filename));
$this->pdb = $pdb;
$this->file = realpath($filename);
$this->parseFile(file($filename), $usemeta);
}
/**
* Makes the arrays of all present PDB record types
*
* @param array $arr array of lines
* @access private
* @see Science_Chemistry_Macromolecule_PDB()
*/
function parseFile($arr, $usemeta) {
$month = array (
"JAN" => "01", "FEB" => "02", "MAR" => "03",
"APR" => "04", "MAY" => "05", "JUN" => "06",
"JUL" => "07", "AUG" => "08", "SEP" => "09",
"OCT" => "10", "NOV" => "11", "DEC" => "12"
);
$header_re = "/^HEADER[[:space:]]+(([^[:space:]]+ )+)[[:space:]]+";
$header_re .= "([0-9]{2}-[A-Z]{3}-[0-9]{2,4})[[:space:]]+[A-Z0-9]{4}/";
if (preg_match($header_re, $arr[0], &$regs)) {
$this->class = trim($regs[1]);
// put date in a more standard format
$tmp = explode("-", $regs[3]);
if ($tmp[2] <= 23)
$year = 2000 + (int)$tmp[2];
else
$year = 1900 + (int)$tmp[2];
$this->date = $year."-".$month[$tmp[1]]."-".$tmp[0];
}
$flag = "nomodel";
$tmparr = array();
for ($i=0; $i < count($arr); $i++) {
if (!trim($arr[$i]))
continue;
$rectype = trim(strtok($arr[$i]," "));
// check if we have multi-model file
if ($rectype == "MODEL") {
$flag = "model";
continue;
}
// create the meta array and accumulate the atom records
if ($rectype != "ATOM" && $rectype != "HETATM") {
if ($usemeta) {
$this->meta[$rectype][] = trim($arr[$i]);
} else {
continue;
}
} else {
$tmparr[] = $arr[$i];
}
// did we get a multi-model file and are parsing the end
// of a model, if so, create new macromolecule and change
// the flag
if ($rectype == "ENDMDL") {
$this->macromolecules[] = new Science_Chemistry_Macromolecule_PDB($this->pdb,
$tmparr, &$this);
$this->num_macromolecules++;
$flag = "endmodel";
$tmparr = array();
}
}
// if we got to the end without hitting a MODEL ... ENDMDL pair
// add the only macromolecule in this file to the array
if ($flag == "nomodel") {
$this->macromolecules[] = new Science_Chemistry_Macromolecule_PDB(&$this->pdb,
&$tmparr, &$this);
$this->num_macromolecules++;
}
}
/**
* Returns a CML representation of the PDB file
* TODO
*
* @return string
* @access public
*/
function toCML() {
// TODO
}
} // end of PDBFile
// vim: expandtab: ts=4: sw=4
?>
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