jmcastagnetto Tue Apr 10 11:33:21 2001 EDT
Modified files:
/pear/Science Chemistry.php
/pear/Science/Chemistry Atom.php Atom_PDB.php Coordinates.php
Element.php Macromolecule.php
Macromolecule_PDB.php Molecule.php
Molecule_XYZ.php PDBFile.php PDBParser.php
Periodic_Table.php Residue_PDB.php
/pear/Science/Chemistry/test chi_crawler.php testChem.php
testPDB.php xyz2cml.php
Log:
Renamning of classes from Chem_* to Science_Chemistry_*
Index: pear/Science/Chemistry.php
diff -u pear/Science/Chemistry.php:1.1 pear/Science/Chemistry.php:1.2
--- pear/Science/Chemistry.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Chemistry.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Chemistry.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "PEAR.php";
@@ -24,7 +24,7 @@
/**
* Package version constant
*/
-define (CHEM_VERSION, 1.0);
+define (SCIENCE_CHEMISTRY_VERSION, 1.0);
require_once "Science/Chemistry/Element.php";
require_once "Science/Chemistry/Periodic_Table.php";
Index: pear/Science/Chemistry/Atom.php
diff -u pear/Science/Chemistry/Atom.php:1.1 pear/Science/Chemistry/Atom.php:1.2
--- pear/Science/Chemistry/Atom.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/Atom.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Atom.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Atom.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "Science/Chemistry.php";
@@ -29,7 +29,7 @@
* @access public
* @package Science_Chemistry
*/
-class Chem_Atom {
+class Science_Chemistry_Atom {
/**
* Element symbol
@@ -42,9 +42,9 @@
var $element="";
/**
- * Chem_Coordinates object
+ * Science_Chemistry_Coordinates object
*
- * @var object Chem_Coordinates
+ * @var object Science_Chemistry_Coordinates
* @access private
*
* @see getCoordinates();
@@ -58,17 +58,17 @@
* @param string $element chemical symbol
* @param optional array $coords array of coordinates (x, y, z)
* @access public
- * @return object Chem_Atom
+ * @return object Science_Chemistry_Atom
*
* @see setCoordinates()
*/
- function Chem_Atom($element, $coords="") {
+ function Science_Chemistry_Atom($element, $coords="") {
if ($element && ereg("[[:alpha:]]{1,2}", $element))
$this->element = $element;
else
return null;
if (is_array($coords) && count($coords) == 3)
- if (!$this->xyz = new Chem_Coordinates($coords))
+ if (!$this->xyz = new Science_Chemistry_Coordinates($coords))
return null;
}
@@ -80,7 +80,7 @@
* @access public
*/
function setCoordinates($coords) {
- $this->xyz = new Chem_Coordinates($coords);
+ $this->xyz = new Science_Chemistry_Coordinates($coords);
return (is_object($this->xyz) && !empty($this->xyz));
}
@@ -99,7 +99,7 @@
/**
* Returns the coordinates object for the atom
*
- * @return object Chem_Coordinates
+ * @return object Science_Chemistry_Coordinates
* @access public
*
* @see $xyz;
@@ -112,34 +112,34 @@
* Calculates the cartesian distance from this atom
* instance to another
*
- * @param object Chem_Atom $atom2
+ * @param object Science_Chemistry_Atom $atom2
* @return float distance
* @access public
*/
function distance($atom2) {
- if (!empty($this->xyz) && Chem_Coordinates::areCoordinates($this->xyz)
- && Chem_Atom::isAtom($atom2))
+ if (!empty($this->xyz) &&
+Science_Chemistry_Coordinates::areCoordinates($this->xyz)
+ && Science_Chemistry_Atom::isAtom($atom2))
return $this->xyz->distance($atom2->xyz);
else
return -1.0;
}
/**
- * Checks if the object is an instance of Chem_Atom
+ * Checks if the object is an instance of Science_Chemistry_Atom
*
- * @param object Chem_Atom $obj
+ * @param object Science_Chemistry_Atom $obj
* @return boolean
* @access public
*/
function isAtom($obj) {
return (is_object($obj) &&
- (strtolower(get_class($obj)) == strtolower("Chem_Atom")
- || is_subclass_of($obj, strtolower("Chem_Atom")))
+ (strtolower(get_class($obj)) == strtolower("Science_Chemistry_Atom")
+ || is_subclass_of($obj, strtolower("Science_Chemistry_Atom")))
);
}
/**
- * Returns a string representation of the Chem_Atom object
+ * Returns a string representation of the Science_Chemistry_Atom object
*
* @return string
* @access public
@@ -150,7 +150,7 @@
}
/**
- * Returns a CML representation of the Chem_Atom object
+ * Returns a CML representation of the Science_Chemistry_Atom object
* Accepts an optional id
*
* @param optional string $id
@@ -165,7 +165,7 @@
return $out;
}
-} // end of class Chem_Atom
+} // end of class Science_Chemistry_Atom
// vim: expandtab: ts=4: sw=4
?>
Index: pear/Science/Chemistry/Atom_PDB.php
diff -u pear/Science/Chemistry/Atom_PDB.php:1.1 pear/Science/Chemistry/Atom_PDB.php:1.2
--- pear/Science/Chemistry/Atom_PDB.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/Atom_PDB.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Atom_PDB.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Atom_PDB.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "Science/Chemistry/Atom.php" ;
@@ -30,7 +30,7 @@
* @access public
* @package Science_Chemistry
*/
-class Chem_Atom_PDB extends Chem_Atom {
+class Science_Chemistry_Atom_PDB extends Science_Chemistry_Atom {
/**
* PDB Atom record type, one of ATOM or HETATM
@@ -158,7 +158,7 @@
var $parent_residue;
- function Chem_Atom_PDB($atomrec, $residue="") {
+ function Science_Chemistry_Atom_PDB($atomrec, $residue="") {
// reference to containing residue
if (!empty($residue))
$this->parent_residue =& $residue;
@@ -180,7 +180,7 @@
$x = (double) trim(substr($atomrec,30,8));
$y = (double) trim(substr($atomrec,38,8));
$z = (double) trim(substr($atomrec,46,8));
- $this->xyz = new Chem_Coordinates(array($x, $y, $z));
+ $this->xyz = new Science_Chemistry_Coordinates(array($x, $y, $z));
$element = trim(substr($atomrec,76,2));
$this->element = $element;
}
Index: pear/Science/Chemistry/Coordinates.php
diff -u pear/Science/Chemistry/Coordinates.php:1.1
pear/Science/Chemistry/Coordinates.php:1.2
--- pear/Science/Chemistry/Coordinates.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/Coordinates.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Coordinates.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Coordinates.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
/**
@@ -28,7 +28,7 @@
* @access public
* @package Science_Chemistry
*/
-class Chem_Coordinates {
+class Science_Chemistry_Coordinates {
/**
* Array of tridimensional coordinates: (x, y, z)
@@ -43,10 +43,10 @@
* not an array with 3 entries
*
* @param array $coords array of three floats (x, y, z)
- * @return object Chem_Coordinates
+ * @return object Science_Chemistry_Coordinates
* @access public
*/
- function Chem_Coordinates($coords) {
+ function Science_Chemistry_Coordinates($coords) {
if (is_array($coords) && count($coords) == 3)
$this->coords = $coords;
else
@@ -56,12 +56,12 @@
/**
* Castesian distance calculation method
*
- * @param object Chem_Coordinates $coord
+ * @param object Science_Chemistry_Coordinates $coord
* @return float distance
* @access public
*/
function distance($coord) {
- if (Chem_Coordinates::areCoordinates($coord)) {
+ if (Science_Chemistry_Coordinates::areCoordinates($coord)) {
$xyz2 = $coord->getCoordinates();
for ($i=0; $i<count($xyz2); $i++)
$sum2 += pow(($xyz2[$i] - $this->coords[$i]),2);
@@ -70,16 +70,16 @@
}
/**
- * Checks if the object is an instance of Chem_Coordinates
+ * Checks if the object is an instance of Science_Chemistry_Coordinates
*
- * @param object Chem_Coordinates $obj
+ * @param object Science_Chemistry_Coordinates $obj
* @return boolean
* @access public
*/
function areCoordinates($obj) {
return ( is_object($obj) &&
- (strtolower(get_class($obj)) == strtolower("Chem_Coordinates")
- || is_subclass_of($obj, strtolower("Chem_Coordinates")))
+ (strtolower(get_class($obj)) ==
+strtolower("Science_Chemistry_Coordinates")
+ || is_subclass_of($obj,
+strtolower("Science_Chemistry_Coordinates")))
);
}
@@ -121,7 +121,7 @@
return $out;
}
-} // end of class Chem_Coordinates
+} // end of class Science_Chemistry_Coordinates
// vim: expandtab: ts=4: sw=4
?>
Index: pear/Science/Chemistry/Element.php
diff -u pear/Science/Chemistry/Element.php:1.1 pear/Science/Chemistry/Element.php:1.2
--- pear/Science/Chemistry/Element.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/Element.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Element.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Element.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
/**
@@ -27,7 +27,7 @@
* @access public
* @package Science_Chemistry
*/
-class Chem_Element {
+class Science_Chemistry_Element {
/**
* Element's symbol, one or two characters, case sensitive
@@ -95,10 +95,10 @@
* @param string $mp melting point (with comments)
* @param string $bp boiling point (with comments)
* @param string $fam family
- * @return object Chem_Element
+ * @return object Science_Chemistry_Element
* @access public
*/
- function Chem_Element ($sym, $name, $num, $wgt, $mp, $bp, $fam) {
+ function Science_Chemistry_Element ($sym, $name, $num, $wgt, $mp, $bp, $fam) {
$this->symbol = $sym;
$this->name = $name;
$this->number = $num;
@@ -109,20 +109,20 @@
}
/**
- * Checks if an object is a Chem_Element instance
+ * Checks if an object is a Science_Chemistry_Element instance
*
- * @param object Chem_Element $obj
+ * @param object Science_Chemistry_Element $obj
* @return boolean
* @access public
*/
function isElement($obj) {
return (is_object($obj) &&
- (get_class($obj) == "Chem_Element" ||
- is_subclass_of($obj, "Chem_Element"))
+ (get_class($obj) == "Science_Chemistry_Element" ||
+ is_subclass_of($obj, "Science_Chemistry_Element"))
);
}
-} // end of Chem_Element
+} // end of Science_Chemistry_Element
// vim: expandtab: ts=4: sw=4
?>
Index: pear/Science/Chemistry/Macromolecule.php
diff -u pear/Science/Chemistry/Macromolecule.php:1.1
pear/Science/Chemistry/Macromolecule.php:1.2
--- pear/Science/Chemistry/Macromolecule.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/Macromolecule.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Macromolecule.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Macromolecule.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "Science/Chemistry.php";
@@ -25,14 +25,14 @@
/**
* Represents a macromolecule, composed of several
- * Chem_Molecule objects
+ * Science_Chemistry_Molecule objects
*
* @author Jesus M. Castagnetto <[EMAIL PROTECTED]>
* @version 1.0
* @access public
* @package Science_Chemistry
*/
-class Chem_Macromolecule {
+class Science_Chemistry_Macromolecule {
/**
* Macromolecule's name
@@ -60,16 +60,16 @@
/**
* Constructor for the class, requires a macromolecule name
- * and an optional array of Chem_Molecule objects
+ * and an optional array of Science_Chemistry_Molecule objects
*
* @param string $name
* @param optional array $molecules
- * @return object Chem_Macromolecule
+ * @return object Science_Chemistry_Macromolecule
* @access public
* @see $name
* @see initMacromolecule()
*/
- function Chem_Macromolecule($name, $molecules="") {
+ function Science_Chemistry_Macromolecule($name, $molecules="") {
$this->name = $name;
if (!empty($molecules))
if (!$this->initMacromolecule($molecules))
@@ -78,7 +78,7 @@
/**
- * Initializes the array of Chem_Molecule objects
+ * Initializes the array of Science_Chemistry_Molecule objects
*
* @param array $molecules
* @return boolean
@@ -97,15 +97,15 @@
}
/**
- * Adds a Chem_Molecule object to the list of molecules in the macromolecule
+ * Adds a Science_Chemistry_Molecule object to the list of molecules in the
+macromolecule
*
- * @param object Chem_Molecule $mol
+ * @param object Science_Chemistry_Molecule $mol
* @return boolean
* @access public
* @see initMacromolecule()
*/
function addMolecule($mol) {
- if (Chem_Molecule::isMolecule($mol)) {
+ if (Science_Chemistry_Molecule::isMolecule($mol)) {
$this->molecules[] = $mol;
$this->num_molecules++;
return true;
@@ -115,7 +115,7 @@
}
/**
- * Returns an array of Chem_Molecule objects
+ * Returns an array of Science_Chemistry_Molecule objects
*
* @return array
* @access public
@@ -126,16 +126,16 @@
}
/**
- * Checks if the object is an instance of Chem_Macromolecule
+ * Checks if the object is an instance of Science_Chemistry_Macromolecule
*
- * @param object Chem_Macromolecule $obj
+ * @param object Science_Chemistry_Macromolecule $obj
* @return boolean
* @access public
*/
function isMacromolecule($obj) {
return (is_object($obj) &&
- (strtolower(get_class($obj)) == strtolower("Chem_Macromolecule") ||
- is_subclass_of($obj, strtolower("Chem_Macromolecule")))
+ (strtolower(get_class($obj)) ==
+strtolower("Science_Chemistry_Macromolecule") ||
+ is_subclass_of($obj, strtolower("Science_Chemistry_Macromolecule")))
);
}
@@ -175,7 +175,7 @@
return $out;
}
-} // end of Chem_Macromolecule
+} // end of Science_Chemistry_Macromolecule
// vim: expandtab: ts=4: sw=4
?>
Index: pear/Science/Chemistry/Macromolecule_PDB.php
diff -u pear/Science/Chemistry/Macromolecule_PDB.php:1.1
pear/Science/Chemistry/Macromolecule_PDB.php:1.2
--- pear/Science/Chemistry/Macromolecule_PDB.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/Macromolecule_PDB.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Macromolecule_PDB.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Macromolecule_PDB.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "Science/Chemistry/Macromolecule.php";
@@ -24,14 +24,14 @@
/**
* Represents a PDB macromolecule, composed of several
- * Chem_Residue_PDB objects
+ * Science_Chemistry_Residue_PDB objects
*
* @author Jesus M. Castagnetto <[EMAIL PROTECTED]>
* @version 1.0
* @access public
* @package Science_Chemistry
*/
-class Chem_Macromolecule_PDB extends Chem_Macromolecule {
+class Science_Chemistry_Macromolecule_PDB extends Science_Chemistry_Macromolecule {
/**
* Constructor for the class
@@ -39,12 +39,12 @@
* @param string $pdb PDB ID of the containing file
* @param array $records Array of lines comprising the macromolecule
* @param object PDBFile $pdbfile reference to the PDB file object
- * @return object Chem_Macromolecule_PDB
+ * @return object Science_Chemistry_Macromolecule_PDB
* @access public
* @see $pdb
* @see parseResidues()
*/
- function Chem_Macromolecule_PDB($pdb, $records, $pdbfile="") {
+ function Science_Chemistry_Macromolecule_PDB($pdb, $records, $pdbfile="") {
$this->pdb =& $pdb;
$this->pdbfile =& $pdbfile;
$this->parseResidues($records);
@@ -55,7 +55,7 @@
*
* @param array $records
* @access private
- * @see Chem_Macromolecule_PDB()
+ * @see Science_Chemistry_Macromolecule_PDB()
*/
function parseResidues($records) {
$curr_res_id = "";
@@ -71,7 +71,7 @@
$res_atoms[] = $atomrec;
} else {
if (!empty($res_atoms)) {
- $this->molecules[] = new Chem_Residue_PDB(&$this->pdb,
+ $this->molecules[] = new
+Science_Chemistry_Residue_PDB(&$this->pdb,
&$res_atoms, &$this);
$this->num_molecules++;
}
@@ -80,7 +80,7 @@
}
}
}
-} // end of Chem_Macromolecule_PDB
+} // end of Science_Chemistry_Macromolecule_PDB
// vim: expandtab: ts=4: sw=4
?>
Index: pear/Science/Chemistry/Molecule.php
diff -u pear/Science/Chemistry/Molecule.php:1.1 pear/Science/Chemistry/Molecule.php:1.2
--- pear/Science/Chemistry/Molecule.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/Molecule.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Molecule.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Molecule.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "Science/Chemistry.php";
@@ -30,7 +30,7 @@
* @access public
* @package Science_Chemistry
*/
-class Chem_Molecule {
+class Science_Chemistry_Molecule {
/**
* Molecule name
@@ -89,16 +89,16 @@
/**
* Constructor for the class, requires a molecule name
- * and an optional array of Chem_Atom objects
+ * and an optional array of Science_Chemistry_Atom objects
*
* @param string $name
* @param optional array $atoms
- * @return object Chem_Molecule
+ * @return object Science_Chemistry_Molecule
* @access public
* @see $name
* @see initMolecule()
*/
- function Chem_Molecule($name, $atoms="") {
+ function Science_Chemistry_Molecule($name, $atoms="") {
if ($name)
$this->name = $name;
else
@@ -109,7 +109,7 @@
}
/**
- * Initializes the array of Chem_Atom objects
+ * Initializes the array of Science_Chemistry_Atom objects
*
* @param array $atoms
* @return boolean
@@ -131,15 +131,15 @@
}
/**
- * Adds a Chem_Atom object to the list of atoms in the molecule
+ * Adds a Science_Chemistry_Atom object to the list of atoms in the molecule
*
- * @param object Chem_Atom $atom
+ * @param object Science_Chemistry_Atom $atom
* @return boolean
* @access public
* @see initMolecule()
*/
function addAtom($atom) {
- if (Chem_Atom::isAtom($atom)) {
+ if (Science_Chemistry_Atom::isAtom($atom)) {
$this->atoms[] = $atom;
$this->num_atoms++;
// unset the distance matrix and
@@ -169,16 +169,16 @@
}
/**
- * Checks if the object is an instance of Chem_Molecule
+ * Checks if the object is an instance of Science_Chemistry_Molecule
*
- * @param object Chem_Molecule $obj
+ * @param object Science_Chemistry_Molecule $obj
* @return boolean
* @access public
*/
function isMolecule($obj) {
return (is_object($obj) &&
- (strtolower(get_class($obj)) == strtolower("Chem_Molecule") ||
- is_subclass_of($obj, strtolower("Chem_Molecule")))
+ (strtolower(get_class($obj)) ==
+strtolower("Science_Chemistry_Molecule") ||
+ is_subclass_of($obj, strtolower("Science_Chemistry_Molecule")))
);
}
@@ -396,7 +396,7 @@
return $ctable;
}
-} // end of class Chem_Molecule
+} // end of class Science_Chemistry_Molecule
// vim: expandtab: ts=4: sw=4
Index: pear/Science/Chemistry/Molecule_XYZ.php
diff -u pear/Science/Chemistry/Molecule_XYZ.php:1.1
pear/Science/Chemistry/Molecule_XYZ.php:1.2
--- pear/Science/Chemistry/Molecule_XYZ.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/Molecule_XYZ.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Molecule_XYZ.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Molecule_XYZ.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "Science/Chemistry.php";
@@ -30,7 +30,7 @@
* @access public
* @package Science_Chemistry
*/
-class Chem_Molecule_XYZ extends Chem_Molecule {
+class Science_Chemistry_Molecule_XYZ extends Science_Chemistry_Molecule {
/**
* Energy of the molecule. Optional value in XYZ file format.
@@ -46,11 +46,11 @@
*
* @param optional string $xyzdata
* @param optional string $src one of "file" or "string"
- * @return object Chem_Molecule_XYZ
+ * @return object Science_Chemistry_Molecule_XYZ
* @access public
* @see parseXYZ()
*/
- function Chem_Molecule_XYZ($xyzdata="", $src="file") {
+ function Science_Chemistry_Molecule_XYZ($xyzdata="", $src="file") {
if (!empty($xyzdata))
if (!$this->parseXYZ($xyzdata, $src))
return null;
@@ -63,7 +63,7 @@
* @param string $src
* @return boolean
* @access public
- * @see Chem_Molecule_XYZ()
+ * @see Science_Chemistry_Molecule_XYZ()
*/
function parseXYZ($xyzdata, $src) {
if ($src == "file") {
@@ -91,18 +91,18 @@
* Parses an XYZ atom record
*
* @param string $line
- * @return object Chem_Atom
+ * @return object Science_Chemistry_Atom
* @acess public
* @see parseXYZ()
*/
function parseAtom($line) {
list($element, $x, $y, $z) = split("[\t ]+",trim($line));
- return new Chem_Atom($element, array($x, $y, $z));
+ return new Science_Chemistry_Atom($element, array($x, $y, $z));
}
/**
* Generates a string representation of the XYZ molecule
- * Overrides parent Chem_Molecule::toString() method
+ * Overrides parent Science_Chemistry_Molecule::toString() method
*
* @return string
* @access public
@@ -118,7 +118,7 @@
return implode("\n",$out)."\n";
}
-} // end of class Chem_Molecule_XYZ
+} // end of class Science_Chemistry_Molecule_XYZ
// vim: expandtab: ts=4: sw=4
?>
Index: pear/Science/Chemistry/PDBFile.php
diff -u pear/Science/Chemistry/PDBFile.php:1.1 pear/Science/Chemistry/PDBFile.php:1.2
--- pear/Science/Chemistry/PDBFile.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/PDBFile.php Tue Apr 10 11:33:20 2001
@@ -16,21 +16,21 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: PDBFile.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: PDBFile.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "Science/Chemistry/Macromolecule_PDB.php";
/**
- * Represents a PDB file, composed of one or more Chem_Macromolecule_PDB objects
+ * Represents a PDB file, composed of one or more Science_Chemistry_Macromolecule_PDB
+objects
*
* @author Jesus M. Castagnetto <[EMAIL PROTECTED]>
* @version 1.0
* @access public
* @package Science_Chemistry
- * @see Chem_PDBParser
+ * @see Science_Chemistry_PDBParser
*/
-class Chem_PDBFile {
+class Science_Chemistry_PDBFile {
/**
* PDB ID
@@ -98,7 +98,7 @@
* @see $file
* @see mkArrays()
*/
- function Chem_PDBFile($filename) {
+ function Science_Chemistry_PDBFile($filename) {
if (!file_exists($filename))
return null;
list($pdb,) = explode(".",basename($filename));
@@ -112,7 +112,7 @@
*
* @param array $arr array of lines
* @access private
- * @see Chem_Macromolecule_PDB()
+ * @see Science_Chemistry_Macromolecule_PDB()
*/
function parseFile($arr) {
$month = array (
@@ -159,7 +159,7 @@
// of a model, if so, create new macromolecule and change
// the flag
if ($rectype == "ENDMDL") {
- $this->macromolecules[] = new Chem_Macromolecule_PDB($this->pdb,
+ $this->macromolecules[] = new
+Science_Chemistry_Macromolecule_PDB($this->pdb,
$tmparr, &$this);
$this->num_macromolecules++;
$flag = "endmodel";
@@ -169,7 +169,7 @@
// if we got to the end without hitting a MODEL ... ENDMDL pair
// add the only macromolecule in this file to the array
if ($flag == "nomodel") {
- $this->macromolecules[] = new Chem_Macromolecule_PDB(&$this->pdb,
+ $this->macromolecules[] = new
+Science_Chemistry_Macromolecule_PDB(&$this->pdb,
&$tmparr, &$this);
$this->num_macromolecules++;
}
Index: pear/Science/Chemistry/PDBParser.php
diff -u pear/Science/Chemistry/PDBParser.php:1.1
pear/Science/Chemistry/PDBParser.php:1.2
--- pear/Science/Chemistry/PDBParser.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/PDBParser.php Tue Apr 10 11:33:20 2001
@@ -16,23 +16,23 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: PDBParser.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: PDBParser.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
/**
* A self-contained class to parse a PDB file into an array of residues
* each containing an array of atoms
* <br>
- * Useful when dealing with big PDB files, where using the Chem_PDBFile
+ * Useful when dealing with big PDB files, where using the Science_Chemistry_PDBFile
* class will generate out of memory errors.
*
* @author Jesus M. Castagnetto <[EMAIL PROTECTED]>
* @version 1.0
* @access public
* @package Science_Chemistry
- * @see Chem_PDBFile
+ * @see Science_Chemistry_PDBFile
*/
-class Chem_PDBParser {
+class Science_Chemistry_PDBParser {
/**
* PDB ID
@@ -93,7 +93,7 @@
* @access public
* @see parseResidues()
*/
- function Chem_PDBParser($filename, $multi=false, $meta=false, $full=false) {
+ function Science_Chemistry_PDBParser($filename, $multi=false, $meta=false,
+$full=false) {
if (!file_exists($filename))
return null;
list($pdb,) = explode(".",basename($filename));
Index: pear/Science/Chemistry/Periodic_Table.php
diff -u pear/Science/Chemistry/Periodic_Table.php:1.1
pear/Science/Chemistry/Periodic_Table.php:1.2
--- pear/Science/Chemistry/Periodic_Table.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/Periodic_Table.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Periodic_Table.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Periodic_Table.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "Science/Chemistry.php";
@@ -29,7 +29,7 @@
* @access public
* @package Science_Chemistry
*/
-class Chem_Periodic_Table {
+class Science_Chemistry_Periodic_Table {
/**
* The associative array containing the chemical elements
@@ -40,27 +40,27 @@
var $periodic_table = array();
/**
- * Returns a Chem_Element object correspoding to the symbol (case sensitive)
+ * Returns a Science_Chemistry_Element object correspoding to the symbol (case
+sensitive)
*
* @param string $symbol
- * @return object Chem_Element
+ * @return object Science_Chemistry_Element
* @access public
*/
function getElement($symbol) {
if (empty($this->periodic_table))
initTable();
$elem = $this->periodic_table[$symbol];
- if (Chem_Element::isElement($elem))
+ if (Science_Chemistry_Element::isElement($elem))
return $elem;
else
return null;
}
/**
- * Returns an array of Chem_Element objects belonging to an element family
+ * Returns an array of Science_Chemistry_Element objects belonging to an element
+family
*
* @param string $family
- * @return array Chem_Element objects
+ * @return array Science_Chemistry_Element objects
* @access public
*/
function getElementFamily($family) {
@@ -299,7 +299,7 @@
109,-1, "unknown", "unknown", "");
}
-} // end of Chem_Periodic_Table
+} // end of Science_Chemistry_Periodic_Table
// vim: expandtab: ts=4: sw=4
?>
Index: pear/Science/Chemistry/Residue_PDB.php
diff -u pear/Science/Chemistry/Residue_PDB.php:1.1
pear/Science/Chemistry/Residue_PDB.php:1.2
--- pear/Science/Chemistry/Residue_PDB.php:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/Residue_PDB.php Tue Apr 10 11:33:20 2001
@@ -16,7 +16,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: Residue_PDB.php,v 1.1 2001/04/10 16:44:39 jmcastagnetto Exp $
+// $Id: Residue_PDB.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "Science/Chemistry.php";
@@ -31,7 +31,7 @@
* @access public
* @package Science_Chemistry
*/
-class Chem_Residue_PDB extends Chem_Molecule {
+class Science_Chemistry_Residue_PDB extends Science_Chemistry_Molecule {
/**
* PDB Residue sequence number
@@ -80,7 +80,7 @@
* Reference to the protein
* to which this residue belongs
*
- * @var object Chem_Macromolecule_PDB
+ * @var object Science_Chemistry_Macromolecule_PDB
* @access public
*/
var $macromol;
@@ -90,13 +90,13 @@
*
* @param string $pdb PDB if of the protein/nucleic acid/etc.
* @param array $atomrec_arr Array of PDB atom record lines
- * @param object Chem_Macromolecule_PDB $macromol reference to the
containing macromolecule
- * @return object Chem_Residue_PDB
+ * @param object Science_Chemistry_Macromolecule_PDB $macromol reference to
+the containing macromolecule
+ * @return object Science_Chemistry_Residue_PDB
* @access public
*/
- function Chem_Residue_PDB($pdb, $atomrec_arr, $macromol="") {
+ function Science_Chemistry_Residue_PDB($pdb, $atomrec_arr, $macromol="") {
for ($i=0; $i < count($atomrec_arr); $i++)
- $this->atoms[] = new Chem_Atom_PDB(&$atomrec_arr[$i], &$this);
+ $this->atoms[] = new Science_Chemistry_Atom_PDB(&$atomrec_arr[$i],
+&$this);
if (!empty($this->atoms)) {
$this->VALID = true;
$this->macromol =& $macromol;
@@ -144,7 +144,7 @@
}
*/
-} // end of Chem_Residue_PDB class
+} // end of Science_Chemistry_Residue_PDB class
// vim: expandtab: ts=4: sw=4
?>
Index: pear/Science/Chemistry/test/chi_crawler.php
diff -u pear/Science/Chemistry/test/chi_crawler.php:1.1
pear/Science/Chemistry/test/chi_crawler.php:1.2
--- pear/Science/Chemistry/test/chi_crawler.php:1.1 Tue Apr 10 09:44:42 2001
+++ pear/Science/Chemistry/test/chi_crawler.php Tue Apr 10 11:33:20 2001
@@ -122,7 +122,7 @@
continue;
}
exec("grep HIS ".$filepath." > ".$tmpfile);
- $f = new Chem_PDBParser($tmpfile);
+ $f = new Science_Chemistry_PDBParser($tmpfile);
$histidines = $f->getResidueList(0,"HIS");
unset($f);
if (empty($histidines)) {
Index: pear/Science/Chemistry/test/testChem.php
diff -u pear/Science/Chemistry/test/testChem.php:1.1
pear/Science/Chemistry/test/testChem.php:1.2
--- pear/Science/Chemistry/test/testChem.php:1.1 Tue Apr 10 09:44:42 2001
+++ pear/Science/Chemistry/test/testChem.php Tue Apr 10 11:33:20 2001
@@ -17,7 +17,7 @@
// | Authors: Jesus M. Castagnetto <[EMAIL PROTECTED]> |
// +----------------------------------------------------------------------+
//
-// $Id: testChem.php,v 1.1 2001/04/10 16:44:42 jmcastagnetto Exp $
+// $Id: testChem.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
//
require_once "Science/Chemistry.php";
@@ -25,18 +25,18 @@
require_once "Science/Chemistry/Macromolecule.php";
echo "Creating and printing an atom\n";
-$a = new Chem_Atom("N", array(2.3,4.5,-2.1));
+$a = new Science_Chemistry_Atom("N", array(2.3,4.5,-2.1));
echo $a->toString()."\n";
echo "Creating a second atom and calculating distance to first one\n";
-$b = new Chem_Atom("C", array(1.2,3.4,-1.6));
+$b = new Science_Chemistry_Atom("C", array(1.2,3.4,-1.6));
echo $b->toString()."\n";
echo "\nDistance N to C: ".sprintf("%.4f", $a->distance($b))." Angstroms\n";
//print_r($a);
//print_r($b);
echo "\n=====\nReading a molecule:\n";
-$m = new Chem_Molecule_XYZ("his.xyz");
-echo "\$m is a molecule: ".(int)Chem_Molecule::isMolecule($m)."\n";
+$m = new Science_Chemistry_Molecule_XYZ("his.xyz");
+echo "\$m is a molecule: ".(int)Science_Chemistry_Molecule::isMolecule($m)."\n";
echo $m->toString();
//echo "Calculating Distance Matrix\n";
//$m->printDistanceMatrix();
@@ -50,11 +50,11 @@
//$big = implode("",file("7AHL.xyz")) ;
//echo "It took: ".(time() - $start)." seconds\n";
-$n = new Chem_Molecule_XYZ("lys.xyz");
+$n = new Science_Chemistry_Molecule_XYZ("lys.xyz");
$mols = array($m, $n);
-$big = new Chem_Macromolecule("big one", $mols);
+$big = new Science_Chemistry_Macromolecule("big one", $mols);
echo $big->toString();
echo $big->toCML("biggie", "big", true);
Index: pear/Science/Chemistry/test/testPDB.php
diff -u pear/Science/Chemistry/test/testPDB.php:1.1
pear/Science/Chemistry/test/testPDB.php:1.2
--- pear/Science/Chemistry/test/testPDB.php:1.1 Tue Apr 10 09:44:42 2001
+++ pear/Science/Chemistry/test/testPDB.php Tue Apr 10 11:33:20 2001
@@ -4,24 +4,24 @@
$start = time();
require "Science/Chemistry/PDBParser.php";
-//$file = new Chem_PDBParser("1hca.pdb");
+//$file = new Science_Chemistry_PDBParser("1hca.pdb");
// small fragment from 1hca.pdb
-//$file = new Chem_PDBParser("small.pdb");
+//$file = new Science_Chemistry_PDBParser("small.pdb");
// The file below, breaks it
-//$file = new Chem_PDBParser("7AHL.pdb");
+//$file = new Science_Chemistry_PDBParser("7AHL.pdb");
// muti-model file
-//$file = new Chem_PDBParser("1b1g.pdb");
-$file = new Chem_PDBParser("1b1g.pdb", true);
+//$file = new Science_Chemistry_PDBParser("1b1g.pdb");
+$file = new Science_Chemistry_PDBParser("1b1g.pdb", true);
print_r($file);
//echo "Took: ".( time() - $start )."seconds\n";
*/
require "Science/Chemistry/PDBFile.php";
-//$file = new Chem_PDBFile("small.pdb");
-$file = new Chem_PDBFile("1b1g.pdb");
+//$file = new Science_Chemistry_PDBFile("small.pdb");
+$file = new Science_Chemistry_PDBFile("1b1g.pdb");
for ($j=0; $j < $file->num_macromolecules; $j++) {
$mol =& $file->macromolecules[$j];
echo $mol->toCML("model", ($j + 1));
Index: pear/Science/Chemistry/test/xyz2cml.php
diff -u pear/Science/Chemistry/test/xyz2cml.php:1.1
pear/Science/Chemistry/test/xyz2cml.php:1.2
--- pear/Science/Chemistry/test/xyz2cml.php:1.1 Tue Apr 10 09:44:42 2001
+++ pear/Science/Chemistry/test/xyz2cml.php Tue Apr 10 11:33:20 2001
@@ -19,7 +19,7 @@
//
// Sample script that uses the Chemistry classes to convert a XYZ file to CML
//
-// $Id: xyz2cml.php,v 1.1 2001/04/10 16:44:42 jmcastagnetto Exp $
+// $Id: xyz2cml.php,v 1.2 2001/04/10 18:33:20 jmcastagnetto Exp $
require_once "Science/Chemistry.php";
require_once "Science/Chemistry/Molecule_XYZ.php";
@@ -63,7 +63,7 @@
echo "Converting ".$argv[1]." to $cml... ";
// create the molecule object
-$mol = new Chem_Molecule_XYZ($xyz);
+$mol = new Science_Chemistry_Molecule_XYZ($xyz);
// prepare output
$out = "<?xml version=\"1.0\">
--
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