Science_Chemistry
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Class: Science_Chemistry_Molecule

Source Location: /Science_Chemistry-1.1.2/Science/Chemistry/Molecule.php

Class Overview


Base class representing a Molecule


Author(s):

Version:

  • 1.0

Variables

Methods


Child classes:

Science_Chemistry_Residue_PDB
Represents a PDB residue
Science_Chemistry_Molecule_XYZ
Base class representing a Molecule from a XYZ format file

Inherited Variables

Inherited Methods


Class Details

[line 33]
Base class representing a Molecule


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Class Variables

$name =  ""

[line 41]

Molecule name
  • Access: public

Type:   string


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$num_atoms =  0

[line 50]

Number of atoms in the molecule

Type:   integer


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Method Detail

Science_Chemistry_Molecule (Constructor)   [line 101]

object Science_Chemistry_Molecule Science_Chemistry_Molecule( string $name, [optional $atoms = ""])

Constructor for the class, requires a molecule name and an optional array of Science_Chemistry_Atom objects

Parameters:

string   $name     
optional   $atoms     array $atoms

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addAtom   [line 141]

boolean addAtom( object Science_Chemistry_Atom $atom)

Adds a Science_Chemistry_Atom object to the list of atoms in the molecule

Parameters:

object Science_Chemistry_Atom   $atom     

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calcConnectionTable   [line 358]

boolean calcConnectionTable( )

Calculates the connection table for the molecule
  • Access: public

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calcDistanceMatrix   [line 297]

boolean calcDistanceMatrix( )

Calculates the atom-atom distance matrix in Angstroms
  • Access: public

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getAtoms   [line 167]

array getAtoms( )

Returns an array of Atom objects
  • See: $atoms
  • Access: public

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getBondCutoff   [line 287]

float getBondCutoff( )

Returns the bond cutoff uses to determine bonds

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getConnectionTable   [line 396]

array getConnectionTable( )

Returns an array of connected atoms and their bond distance e.g. array ( array ($atomobj1, $atomobj2, $distance ), ... )
  • Access: public

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getDistanceMatrix   [line 345]

array getDistanceMatrix( )

Returns the atom-atom distance matrix
  • Access: public

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initMolecule   [line 121]

boolean initMolecule( array $atoms)

Initializes the array of Science_Chemistry_Atom objects

Parameters:

array   $atoms     

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isMolecule   [line 178]

boolean isMolecule( object Science_Chemistry_Molecule $obj)

Checks if the object is an instance of Science_Chemistry_Molecule
  • Access: public

Parameters:

object Science_Chemistry_Molecule   $obj     

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printConnectionTable   [line 375]

boolean printConnectionTable( )

Prints the molecule's connection table
  • Access: public

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printDistanceMatrix   [line 318]

string printDistanceMatrix( )

Prints the atom-atom distance matrix
  • Access: public

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setBondCutoff   [line 269]

boolean setBondCutoff( float $cutoff)

Sets the distance cutoff for bond determination

Parameters:

float   $cutoff     

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toCML   [line 225]

string toCML( [optional $title = "molecule"], [optional $id = "mol1"], [ $connect = false])

Returns a CML representation of the molecule Accepts an optional id, and a flag to signal printing of the connection table
  • Access: public

Parameters:

optional   $title     string $id
optional   $id     boolean $connect
   $connect     

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toString   [line 193]

string toString( )

Returns a string representation of the molecule as a XYZ-format file Alias of toXYZ()

Overridden in child classes as:

Science_Chemistry_Molecule_XYZ::toString()
Generates a string representation of the XYZ molecule Overrides parent Science_Chemistry_Molecule::toString() method

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toXYZ   [line 204]

string toXYZ( )

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

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Documentation generated on Mon, 09 Apr 2012 18:00:04 +0000 by phpDocumentor 1.4.3. PEAR Logo Copyright © PHP Group 2004.