molsysmt.build.solve_atoms_with_alternate_location#

molsysmt.build.solve_atoms_with_alternate_location(molecular_system, selection='all', structure_indices='all', location_id='occupancy', syntax='MolSysMT')[source]#

Resolving alternate-location atoms in selected structures.

Parameters:

  • molecular_system (molecular system) – Molecular system carrying alternate-location metadata.

  • selection (str, list, tuple, or numpy.ndarray, default 'all') – Atoms whose alternate locations are resolved.

  • structure_indices (int, list of int, or 'all', default 'all') – Structures in which coordinates and B factors are updated.

  • location_id (str, list, tuple, or numpy.ndarray, default 'occupancy') – Location identifier to choose. 'occupancy' chooses independently in every structure. A sequence supplies one identifier per selected atom.

  • syntax (str, default 'MolSysMT') – Syntax used to interpret a string selection.

Returns:

The molecular system is modified in place.

Return type:

None

Notes

Coordinates use the units already normalized by MolSysMT, normally nm. B factors are stored in nm². When occupancies tie at 0.5, location A is preferred when available.

See also

molsysmt.basic.get()

Getting alternate-location metadata.

Examples

>>> import molsysmt as msm
>>> from importlib.resources import files
>>> filename = str(files('molsysmt.data.pdb').joinpath('1bnf.pdb'))
>>> molecular_system = msm.convert(
...     filename, to_form='molsysmt.MolSys', get_missing_bonds=False
... )
>>> solve_atoms_with_alternate_location(
...     molecular_system, selection=[480], location_id='A'
... )
>>> molecular_system.structures.coordinates.shape[0]
1

Tutorial with more examples

See Solve atoms with alternate locations.

Added in version 1.0.0.