Docs For Class Science_Chemistry

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

See: Science_Chemistry_Molecule::initMolecule()
See: Science_Chemistry_Molecule::$name
Access: public

Parameters:

string	`$name`	—
optional	`$atoms`	—	array $atoms

[ Top ]

addAtom [line 141]

boolean addAtom(
object Science_Chemistry_Atom
$atom)

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

See: Science_Chemistry_Molecule::initMolecule()
Access: public

Parameters:

object Science_Chemistry_Atom $atom —

[ Top ]

calcConnectionTable [line 358]

boolean calcConnectionTable(
)

Calculates the connection table for the molecule

Access: public

[ Top ]

calcDistanceMatrix [line 297]

boolean calcDistanceMatrix(
)

Calculates the atom-atom distance matrix in Angstroms

Access: public

[ Top ]

getAtoms [line 167]

array getAtoms(
)

Returns an array of Atom objects

See: $atoms
Access: public

[ Top ]

getBondCutoff [line 287]

float getBondCutoff(
)

Returns the bond cutoff uses to determine bonds

See: Science_Chemistry_Molecule::calcConnectionTable()
See: Science_Chemistry_Molecule::setBondCutoff()
See: $BONDCUTOFF
Access: public

[ Top ]

getConnectionTable [line 396]

array getConnectionTable(
)

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

Access: public

[ Top ]

getDistanceMatrix [line 345]

array getDistanceMatrix(
)

Returns the atom-atom distance matrix

Access: public

[ Top ]

initMolecule [line 121]

boolean initMolecule(
array
$atoms)

Initializes the array of Science_Chemistry_Atom objects

See: Science_Chemistry_Molecule::addAtom()
See: $atoms
See: Science_Chemistry_Molecule::$num_atoms
Access: public

Parameters:

array $atoms —

[ Top ]

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 —

[ Top ]

printConnectionTable [line 375]

boolean printConnectionTable(
)

Prints the molecule's connection table

Access: public

[ Top ]

printDistanceMatrix [line 318]

string printDistanceMatrix(
)

Prints the atom-atom distance matrix

Access: public

[ Top ]

setBondCutoff [line 269]

boolean setBondCutoff(
float
$cutoff)

Sets the distance cutoff for bond determination

See: Science_Chemistry_Molecule::calcConnectionTable()
See: Science_Chemistry_Molecule::getBondCutoff()
See: $BONDCUTOFF
Access: public

Parameters:

float $cutoff —

[ Top ]

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`	—

[ Top ]

toString [line 193]

string toString(
)

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

See: Science_Chemistry_Molecule::toXYZ()
Access: public

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

[ Top ]

toXYZ [line 204]

string toXYZ(
)

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

See: Science_Chemistry_Molecule::toString()
Access: public

[ Top ]

Class: Science_Chemistry_Molecule

Class Overview

Author(s):

Version:

Variables

Methods

Child classes:

Inherited Variables

Inherited Methods

Class Details

Class Variables

$name = ""

$num_atoms = 0

Method Detail

Science_Chemistry_Molecule (Constructor) [line 101]

Parameters:

addAtom [line 141]

Parameters:

calcConnectionTable [line 358]

calcDistanceMatrix [line 297]

getAtoms [line 167]

getBondCutoff [line 287]

getConnectionTable [line 396]

getDistanceMatrix [line 345]

initMolecule [line 121]

Parameters:

isMolecule [line 178]

Parameters:

printConnectionTable [line 375]

printDistanceMatrix [line 318]

setBondCutoff [line 269]

Parameters:

toCML [line 225]

Parameters:

toString [line 193]

toXYZ [line 204]