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, alt_id=None)

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 represents

• seq_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)

Base class for coordinates of a single structure. Use a subclass such as HomologyModel or AbInitioModel, 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) – The modelcif.AsymUnit objects that make up this model.

• name (str) – Short name for this model.

get_atoms()

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.

not_modeled_residue_ranges

List of residue ranges that were explicitly not modeled. See NotModeledResidueRange.

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)

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)

Coordinates of a single structure generated using ab initio modeling.

See Model for a description of the parameters.

class modelcif.model.NotModeledResidueRange(asym_unit, seq_id_begin, seq_id_end)

A range of residues that were explicitly not modeled. See Model.not_modeled_residue_ranges. These ranges are not explicitly stored in the mmCIF file, but they will be excluded from the pdbx_poly_seq_scheme table.

Parameters:

• asym_unit (AsymUnit) – The asymmetric unit to which the residues belong.

• seq_id_begin (int) – Starting residue in the range.

• seq_id_end (int) – Ending residue in the range.

class modelcif.model.ModelGroup(elements=(), name=None, details=None)

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.

representatives

Any representative structural model(s). See ModelRepresentative.