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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: Molecule.php,v 1.4 2003/05/13 01:18:17 jmcastagnetto Exp $
//
require_once "Science/Chemistry.php";
require_once "Science/Chemistry/Atom.php";
/**
* Base class representing a Molecule
*
* @author Jesus M. Castagnetto <jmcastagnetto@php.net>
* @version 1.0
* @access public
* @package Science_Chemistry
*/
class Science_Chemistry_Molecule {
/**
* Molecule name
*
* @var string
* @access public
*/
var $name = "";
/**
* Number of atoms in the molecule
*
* @var integer
* @access public
* @see initMolecule()
*/
var $num_atoms = 0;
/**
* Array of atom objects in the molecule
*
* @var array
* @access private
* @see initMolecule()
*/
var $atoms = array();
/**
* Atom-Atom distance matrix
*
* @var array
* @access private
* @see calcDistanceMatrix()
*/
var $dist_matrix = array();
/**
* Atom-Atom connection (bond) table
*
* @var array
* @access private
* @see calcConnectionTable()
*/
var $conn_table = array();
/**
* Distance cutoff for bond estimation
*
* @var float
* @access private
* @see setBondCutoff()
* @see getBondCutoff()
* @see calcConnectionTable()
*/
var $BONDCUTOFF = 1.8;
/**
* Constructor for the class, requires a molecule name
* and an optional array of Science_Chemistry_Atom objects
*
* @param string $name
* @param optional array $atoms
* @return object Science_Chemistry_Molecule
* @access public
* @see $name
* @see initMolecule()
*/
function Science_Chemistry_Molecule($name, $atoms="") {
if ($name)
$this->name = $name;
else
return null;
if ($atoms && is_array($atoms))
if (!$this->initMolecule($atoms))
return null;
}
/**
* Initializes the array of Science_Chemistry_Atom objects
*
* @param array $atoms
* @return boolean
* @access public
* @see $num_atoms
* @see $atoms
* @see addAtom()
*/
function initMolecule($atoms) {
if (is_array($atoms)) {
for ($i=0; $i=count($atoms); $i++) {
if (!$this->addAtom($atoms[$i]))
return false;
}
return true;
} else {
return false;
}
}
/**
* Adds a Science_Chemistry_Atom object to the list of atoms in the molecule
*
* @param object Science_Chemistry_Atom $atom
* @return boolean
* @access public
* @see initMolecule()
*/
function addAtom($atom) {
if (Science_Chemistry_Atom::isAtom($atom)) {
$this->atoms[] = $atom;
$this->num_atoms++;
// unset the distance matrix and
// connection table if they are not empty
// so next time either one is requested
// it gets calculated anew
if (!empty($this->dist_matrix))
$this->dist_matrix = array();
if (!empty($this->conn_table))
$this->conn_table = array();
return true;
} else {
return false;
}
}
/**
* Returns an array of Atom objects
*
* @return array
* @access public
* @see $atoms
*/
function getAtoms() {
return $this->atoms;
}
/**
* Checks if the object is an instance of Science_Chemistry_Molecule
*
* @param object Science_Chemistry_Molecule $obj
* @return boolean
* @access public
*/
function isMolecule($obj) {
return (is_object($obj) &&
(strtolower(get_class($obj)) == strtolower("Science_Chemistry_Molecule") ||
is_subclass_of($obj, strtolower("Science_Chemistry_Molecule")))
);
}
/**
* Returns a string representation of the molecule as a XYZ-format file
* Alias of toXYZ()
*
* @return string
* @access public
* @see toXYZ()
*/
function toString() {
return $this->toXYZ();
}
/**
* Returns a string representation of the molecule as a XYZ-format file
*
* @return string
* @access public
* @see toString()
*/
function toXYZ() {
if (!$this->atoms)
return false;
$out[] = $this->num_atoms;
$out[] = $this->name;
reset($this->atoms);
for ($i=0; $i<$this->num_atoms; $i++)
$out[] = $this->atoms[$i]->toString();
return implode("\n",$out)."\n";
}
/**
* Returns a CML representation of the molecule
* Accepts an optional id, and a flag to signal
* printing of the connection table
*
* @param optional string $id
* @param optional boolean $connect
* @return string
* @access public
*/
function toCML($title="molecule", $id="mol1", $connect=false) {
$out = " <molecule title=\"$title\" id=\"$id\">\n";
$out .= " <string title=\"name\">".$this->name."</string>\n";
$out .= " <list title=\"atoms\">\n";
for ($i=0; $i<$this->num_atoms; $i++)
$out .= $this->atoms[$i]->toCML($i+1);
$out .= " </list>\n";
if ($connect) {
// calculate the connection table if needed
// and short-circuit if we cannot do that
if (empty($this->conn_table))
if (!$this->calcConnectionTable()) {
$out .= " </molecule>\n";
return $out;
}
$out .= " <list title=\"connections\">\n";
for ($i=0; $i < count($this->conn_table); $i++) {
$tmp = array();
foreach ($this->conn_table[$i] as $atomid=>$flag) {
if ($flag)
$tmp[] = $atomid + 1;
}
if (!empty($tmp)) {
$out .= " <list title=\"connect\" id=\"".($i + 1)."\">";
$out .= implode(" ", $tmp)."</list>\n";
}
}
$out .= " </list>\n";
}
$out .= " </molecule>\n";
return $out;
}
/**
* Sets the distance cutoff for bond determination
*
* @param float $cutoff
* @return boolean
* @access public
* @see $BONDCUTOFF
* @see getBondCutoff()
* @see calcConnectionTable()
*/
function setBondCutoff($cutoff) {
if ((float)$cutoff > 0.0) {
$this->BONDCUTOFF = (float)$cutoff;
return true;
} else {
return false;
}
}
/**
* Returns the bond cutoff uses to determine bonds
*
* @return float
* @access public
* @see $BONDCUTOFF
* @see setBondCutoff()
* @see calcConnectionTable()
*/
function getBondCutoff() {
return $this->BONDCUTOFF;
}
/**
* Calculates the atom-atom distance matrix in Angstroms
*
* @return boolean
* @access public
*/
function calcDistanceMatrix() {
if (empty($this->atoms))
return false;
$this->dist_matrix = array();
for ($i=0; $i < $this->num_atoms; $i++)
for ($j=0; $j < $this->num_atoms; $j++) {
if ($i == $j) {
$this->dist_matrix[$i][$j] = 0.0;
} elseif ($i < $j) {
$this->dist_matrix[$i][$j] = $this->atoms[$i]->distance($this->atoms[$j]);
}
}
return true;
}
/**
* Prints the atom-atom distance matrix
*
* @return string
* @access public
*/
function printDistanceMatrix() {
if (empty($this->dist_matrix))
if(!$this->calcDistanceMatrix())
return false;
$dmat = &$this->dist_matrix;
echo "# Atom-Atom Distance Matrix:\n";
for ($i=0; $i < $this->num_atoms; $i++)
echo "\t".($i+1);
for ($i=0; $i < $this->num_atoms; $i++) {
echo "\n".($i+1);
for ($j=0; $j < $this->num_atoms; $j++)
if (!isset($dmat[$i][$j])) {
echo "\t";
} else {
printf("\t%.4f",$dmat[$i][$j]);
}
}
echo "\n";
return true;
}
/**
* Returns the atom-atom distance matrix
*
* @return array
* @access public
*/
function getDistanceMatrix() {
if (empty($this->dist_matrix))
if (!$this->calcDistanceMatrix())
return false;
return $this->dist_matrix;
}
/**
* Calculates the connection table for the molecule
*
* @return boolean
* @access public
*/
function calcConnectionTable(){
if (empty($this->dist_matrix))
if (!$this->calcDistanceMatrix())
return false;
$dmat = &$this->dist_matrix;
for ($i=0; $i < $this->num_atoms; $i++)
for ($j=($i+1); $j < $this->num_atoms; $j++)
$this->conn_table[$i][$j] = ($dmat[$i][$j] <= $this->BONDCUTOFF);
return true;
}
/**
* Prints the molecule's connection table
*
* @return boolean
* @access public
*/
function printConnectionTable() {
if (empty($this->conn_table))
if (!$this->calcConnectionTable())
return false;
printf("# Connection Table: (cutoff = %.4f Angstroms)\n", $this->BONDCUTOFF);
for ($i=0; $i < $this->num_atoms; $i++)
for ($j=($i+1); $j < $this->num_atoms; $j++)
if ($this->conn_table[$i][$j]) {
echo $this->atoms[$i]->element.($i+1)."\t";
echo $this->atoms[$j]->element.($j+1)."\n";
}
return true;
}
/**
* Returns an array of connected atoms and their bond distance
* e.g. array ( array ($atomobj1, $atomobj2, $distance ), ... )
*
* @return array
* @access public
*/
function getConnectionTable() {
if (empty($this->conn_table))
if (!$this->calcConnectionTable())
return false;
$ct = 0; $ctable=array();
for ($i=0; $i < $this->num_atoms; $i++)
for ($j=($i+1); $j < $this->num_atoms; $j++)
if ($this->conn_table[$i][$j]) {
$ctable[$ct] = array ($this->atoms[$i], $this->atoms[$j],
$this->dist_matrix[$i][$j]);
$ct++;
}
return $ctable;
}
} // end of class Science_Chemistry_Molecule
// vim: expandtab: ts=4: sw=4
?>
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