Package Scientific :: Package IO :: Module PDB :: Class Atom

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Class Atom

Known Subclasses:: HetAtom

Atom in a PDB structure

Instance Methods

__getitem__(self, item)
Returns the property value

__init__(self, name, position, **properties)

__repr__(self)

__setitem__(self, item, value)

__str__(self)

str type(self)
Returns the six-letter record type, ATOM or HETATM

writeToFile(self, file)
Write an atom record to a file

Method Details

getitem(self, item)
(Indexing operator)

Parameters:

item (str) - the name of a property, including "name" or "position"

Returns:: the property value

init(self, name, position, **properties)
(Constructor)

Parameters:

name (str) - the atom name
position (Scientific.Geometry.Vector) - the atom position
properties - any other atom properties as keyword parameters. These properties are stored in the atom object and can be accessed by indexing, as for dictionaries.

repr(self)
(Representation operator)

setitem(self, item, value)
(Index assignment operator)

Parameters:

item (str) - the name of an existing or to be defined property
value - the new value for the property

str(self)
(Informal representation operator)

type(self)

Returns: str: the six-letter record type, ATOM or HETATM

writeToFile(self, file)

Write an atom record to a file

Parameters:

file (PDBFile or str) - a PDB file object or a filename