The modelcif.model
Python module¶
- class modelcif.model.Atom(asym_unit, seq_id, atom_id, type_symbol, x, y, z, het=False, biso=None, occupancy=None)[source]¶
Coordinates of part of the model represented by an atom.
See
Model.get_atoms()
for more details.- Parameters:
asym_unit (
modelcif.AsymUnit
) – The asymmetric unit that this atom representsseq_id (int) – The residue index represented by this atom (can be None for HETATM sites)
atom_id (str) – The name of the atom in the residue
type_symbol (str) – Element name
x (float) – x coordinate of the atom
y (float) – y coordinate of the atom
z (float) – z coordinate of the atom
het (bool) – True for HETATM sites, False (default) for ATOM
biso (float) – Temperature factor or equivalent (if applicable)
occupancy (float) – Fraction of the atom type present (if applicable)
- class modelcif.model.Model(assembly, name=None)[source]¶
Base class for coordinates of a single structure. Use a subclass such as
HomologyModel
orAbInitioModel
, or represent a custom model type by creating a new subclass and providing a docstring to describe it, e.g.:class CustomModel(Model): "custom model type"
- Parameters:
assembly (
modelcif.Assembly
) – Themodelcif.AsymUnit
objects that make up this model.name (str) – Short name for this model.
- get_atoms()[source]¶
Yield
Atom
objects that represent this model.The default implementation simply iterates over an internal list of atoms, but this is not very memory-efficient, particularly if the atoms are already stored somewhere else, e.g. in the software’s own data structures. It is recommended to subclass and provide a more efficient implementation. For example, the modbase_pdb_to_cif script uses a custom
MyModel
subclass that creates Atom objects on the fly from PDB ATOM or HETATM lines.
- property other_details¶
More information about a custom model type. By default it is the first line of the docstring.
- qa_metrics¶
Quality scores for the model or part of it (a simple list of metric objects; see
modelcif.qa_metric
)
- class modelcif.model.HomologyModel(assembly, name=None)[source]¶
Coordinates of a single structure generated using homology or comparative modeling.
See
Model
for a description of the parameters.
- class modelcif.model.AbInitioModel(assembly, name=None)[source]¶
Coordinates of a single structure generated using ab initio modeling.
See
Model
for a description of the parameters.
- class modelcif.model.ModelGroup(elements=(), name=None)[source]¶
A set of related models. See
Model
. It is implemented as a simple list of the models.These objects are typically stored directly in the system; see
modelcif.System.model_groups
.- Parameters:
elements – Initial set of models in the group.
name (str) – Descriptive name for the group.