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:

VALUE:

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:

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