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 in any supported MolSysMT format.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.

  • structure_indices (int, list, tuple, or numpy.ndarray, default='all') – Structure indices (0-based) to include or process.

  • location_id (object, default='occupancy') – Argument location_id.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

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 UserGuide_Tools_Build_SolveAtomsWithAlternateLocations.

Added in version 1.0.0.