Molecule Objects
DESCRIPTION:
Objects of the following classes resulting from selecting top atoms: molecule dwt.molecule cp.molecule wp.molecule cp.atom wp.atom
GENERATION:
Objects of classes "molecule", "cp.molecule", "wp.molecule" are returned from top.atoms(), matching.pursuit() or subscripting a "cp.crystal" or "wp.crystal" object.

Objects of class "dwt.molecule" are returned from top.atoms(), when the atoms are selected from a "dwt" object.

Objects of class "cp.atom" are returned from calling function cp.atom() or [[ subscripting an object of "cp.crystal" or "molecule".

Objects of class "wp.atom" are returned from calling function wp.atom() or [[ subscripting an object of "wp.crystal" or "molecule".

METHODS:
The class "molecule" has methods for the following generic functions: [, [<-, [[, [[<-, crystal.names, plot, print, reconstruct, eda.plot.

The classes "cp.molecule" and "wp.molecule" have methods for the following generic functions: decompose, time.freq.plot.

The class "dwt.molecule" has methods for the following generic functions: reconstruct, eda.plot.

The class "cp.atom" has methods for the following generic functions: bandwidth, center, freq.bandwidth, freq.center, plot, print, summary.

The class "wp.atom" has methods for the following generic functions: bandwidth, center, fourier.transform.plot, freq.bandwidth, freq.center, plot, print, summary, wavelet.name.

INHERITANCE:
Class "dwt.molecule" inherits from class "wp.molecule"; both "cp.molecule" and "wp.molecule" inherit from class "molecule".

Class "cp.atom" inherits from classes "cp.molecule", "molecule".

Class "wp.atom" inherits from classes "wp.molecule", "molecule".

STRUCTURE:
The "molecule" object is a numerical vector with the following attributes:
crystal.names:
names of crystals from which the atoms are selected.
atom.index:
indices of atoms in crystals.
dictionary:
the usual cp.dict or wp.dict object containing all relevant information.
basis:
for top.atoms method only, the original orthogonal basis.
method:
method for generating the molecule: top.atoms, matching.pursuit or subscript.
SEE ALSO:
cp.atom , decompose , matching.pursuit , reconstruct , top.atoms , wp.atom .