Science_Chemistry
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Class: Science_Chemistry_Molecule_XYZ

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

Class Overview

Science_Chemistry_Molecule
   |
   --Science_Chemistry_Molecule_XYZ

Base class representing a Molecule from a XYZ format file


Author(s):

Version:

  • 1.0

Variables

Methods


Inherited Variables

Inherited Methods

Class: Science_Chemistry_Molecule

Science_Chemistry_Molecule::Science_Chemistry_Molecule()
Constructor for the class, requires a molecule name and an optional array of Science_Chemistry_Atom objects
Science_Chemistry_Molecule::addAtom()
Adds a Science_Chemistry_Atom object to the list of atoms in the molecule
Science_Chemistry_Molecule::calcConnectionTable()
Calculates the connection table for the molecule
Science_Chemistry_Molecule::calcDistanceMatrix()
Calculates the atom-atom distance matrix in Angstroms
Science_Chemistry_Molecule::getAtoms()
Returns an array of Atom objects
Science_Chemistry_Molecule::getBondCutoff()
Returns the bond cutoff uses to determine bonds
Science_Chemistry_Molecule::getConnectionTable()
Returns an array of connected atoms and their bond distance e.g. array ( array ($atomobj1, $atomobj2, $distance ), ... )
Science_Chemistry_Molecule::getDistanceMatrix()
Returns the atom-atom distance matrix
Science_Chemistry_Molecule::initMolecule()
Initializes the array of Science_Chemistry_Atom objects
Science_Chemistry_Molecule::isMolecule()
Checks if the object is an instance of Science_Chemistry_Molecule
Science_Chemistry_Molecule::printConnectionTable()
Prints the molecule's connection table
Science_Chemistry_Molecule::printDistanceMatrix()
Prints the atom-atom distance matrix
Science_Chemistry_Molecule::setBondCutoff()
Sets the distance cutoff for bond determination
Science_Chemistry_Molecule::toCML()
Returns a CML representation of the molecule Accepts an optional id, and a flag to signal printing of the connection table
Science_Chemistry_Molecule::toString()
Returns a string representation of the molecule as a XYZ-format file Alias of toXYZ()
Science_Chemistry_Molecule::toXYZ()
Returns a string representation of the molecule as a XYZ-format file

Class Details

[line 33]
Base class representing a Molecule from a XYZ format file


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Class Variables

$energy =  0.0

[line 41]

Energy of the molecule. Optional value in XYZ file format.
  • Access: public

Type:   float


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Method Detail

Science_Chemistry_Molecule_XYZ (Constructor)   [line 53]

object Science_Chemistry_Molecule_XYZ Science_Chemistry_Molecule_XYZ( [optional $xyzdata = ""], [optional $src = "file"])

Constructor for the class, accepts 2 optional parameters: the data and its source. Possible values for $src: "file", "string"

Parameters:

optional   $xyzdata     string $xyzdata
optional   $src     string $src one of "file" or "string"

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parseAtom   [line 98]

object Science_Chemistry_Atom parseAtom( string $line)

Parses an XYZ atom record

Parameters:

string   $line     

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parseXYZ   [line 68]

boolean parseXYZ( string $xyzdata, string $src)

method that does the parsing of the XYZ data itself

Parameters:

string   $xyzdata     
string   $src     

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toString   [line 110]

string toString( )

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

Overrides Science_Chemistry_Molecule::toString() (Returns a string representation of the molecule as a XYZ-format file Alias of toXYZ())
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Documentation generated on Mon, 09 Apr 2012 18:00:05 +0000 by phpDocumentor 1.4.3. PEAR Logo Copyright © PHP Group 2004.