Class _AtomCollection
object --+
|
_AtomCollection
- Known Subclasses:
-
A set of atoms, usually comprising a subset of the total atoms in a
Structure. Initialize using a structure and an iterable of current atom
indices.
Important methods include extractStructure and getAtomIndices. Use the atom attribute to iterate over all contained atoms.
1-based indexed access to the atoms is also possible using atom (e.g. atom[1] gets the first atom in the
_AtomCollection). The number of atoms can be determined via
len(self.atom) or len(self).
Intended as a base class for _Ring, _Molecule, and _Chain.
|
|
__init__(self,
st,
atoms)
x.__init__(...) initializes x; see help(type(x)) for signature |
|
|
|
|
__len__(self)
Returns number of atoms. |
|
|
|
list of ints
|
getAtomIndices(self)
Return a list of atom indices for all atoms in this object. |
|
|
|
|
|
|
|
extractStructure(self,
copy_props=False)
Return a new Structure containing only the atoms associated with this
substructure. |
|
|
|
Inherited from object:
__delattr__,
__format__,
__getattribute__,
__hash__,
__new__,
__reduce__,
__reduce_ex__,
__repr__,
__setattr__,
__sizeof__,
__str__,
__subclasshook__
|
__init__(self,
st,
atoms)
(Constructor)
|
|
x.__init__(...) initializes x; see help(type(x)) for signature
- Overrides:
object.__init__
- (inherited documentation)
|
|
Return a list of atom indices for all atoms in this object.
- Returns: list of ints
- List of atom indicies.
|
|
Deprecated. Use getAtomIndices() method instead.
|
extractStructure(self,
copy_props=False)
|
|
Return a new Structure containing only the atoms associated with this
substructure. Structure properties, including the title, are inherited
only if copy_props is set to True.
|
structure
Return the parent Structure object for this atom collection.
- Get Method:
- unreachable.structure(self)
- Return the parent Structure object for this atom collection.
|
atom
Iterate over all atoms. Also allows 1-based indexed access to the
atoms.
- Get Method:
- unreachable.atom(self)
- Iterate over all atoms.
|
temperature_factor
Average B (tempearture) factor for all atoms that have it assigned.
Setting this property will set the B factor to the given value for each
atom.
- Get Method:
- unreachable.temperature_factor(self)
- Average B (tempearture) factor for all atoms that have it assigned.
- Set Method:
- unreachable.temperature_factor(self,
tfactor)
|