Chemical classes - Science_Chemistry

Science_Chemistry_Macromolecule

Represents a macromolecule, composed of several

public class Science_Chemistry_Macromolecule

Represents a macromolecule, composed of several
Science_Chemistry_Molecule objects

Authors Jesus M. Castagnetto <jmcastagnetto@php.net>

Version 1.0

Direct known subclasses: Science_Chemistry_Macromolecule_PDB

Public Method Summary
object Science_Chemistry_Macromolecule	Science_Chemistry_Macromolecule(string $name, [ string $molecules ]) Constructor for the class, requires a macromolecule name
boolean	initMacromolecule(array $molecules) Initializes the array of Science_Chemistry_Molecule objects
boolean	addMolecule(object Science_Chemistry_Molecule $mol) Adds a Science_Chemistry_Molecule object to the list of molecules in the macromolecule
array	getMolecules() Returns an array of Science_Chemistry_Molecule objects
boolean	isMacromolecule(object Science_Chemistry_Macromolecule $obj) Checks if the object is an instance of Science_Chemistry_Macromolecule
string	toString() Returns a string representation of the macromolecule
string	toCML([ string $title, string $id ], boolean $connect) Returns a CML representation of the molecule

Private Field Summary
string	$name Macromolecule's name
array	$molecules Array of molecular objects
int	$num_molecules Number of molecules/subunits

Public Method Details

Science_Chemistry_Macromolecule

public object Science_Chemistry_Macromolecule Science_Chemistry_Macromolecule( string $name, [ string $molecules ] )

Constructor for the class, requires a macromolecule name
and an optional array of Science_Chemistry_Molecule objects

Parameter

string	$name

string	$molecules	`= >>""<<`

Returns

object Science_Chemistry_Macromolecule

initMacromolecule

public boolean initMacromolecule( array $molecules )

Initializes the array of Science_Chemistry_Molecule objects

Parameter

array	$molecules

Returns

boolean

See Also $num_molecules, $molecules, addMolecule()

addMolecule

public boolean addMolecule( object Science_Chemistry_Molecule $mol )

Adds a Science_Chemistry_Molecule object to the list of molecules in the macromolecule

Parameter

object Science_Chemistry_Molecule	$mol

Returns

boolean

getMolecules

public array getMolecules( )

Returns an array of Science_Chemistry_Molecule objects

Returns

array

isMacromolecule

public boolean isMacromolecule( object Science_Chemistry_Macromolecule $obj )

Checks if the object is an instance of Science_Chemistry_Macromolecule

Parameter

object Science_Chemistry_Macromolecule	$obj

Returns

boolean

toString

public string toString( )

Returns a string representation of the macromolecule
as a multiple molecule XYZ-format file

Returns

string

toCML

public string toCML( [ string $title, string $id ], boolean $connect )

Returns a CML representation of the molecule
Accepts an optional id, and a flag to signalprinting of the connection table

Parameter

string	$title	`= >>"macromolecule"<<`

string	$id	`= >>"macromol1"<<`

boolean	$connect
	Warning: documentation is missing.

Returns

string

Private Field Details
$name
private string $name >><< Macromolecule's name

$molecules
private array $molecules >><< Array of molecular objects

$num_molecules
private int $num_molecules >><< Number of molecules/subunits