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):

Jesus M. Castagnetto <jmcastagnetto at php.net>

Version:

Variables

$energy

Methods

Inherited Variables

Class: Science_Chemistry_Molecule

Science_Chemistry_Molecule::$name
Science_Chemistry_Molecule::$num_atoms

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

Author: Jesus M. Castagnetto <jmcastagnetto@php.net>
Version: 1.0
Access: public

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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"

See: Science_Chemistry_Molecule_XYZ::parseXYZ()
Access: public

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

See: Science_Chemistry_Molecule_XYZ::parseXYZ()
Access: public

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

See: Science_Chemistry_Molecule_XYZ::Science_Chemistry_Molecule_XYZ()
Access: public

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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