molsysmt.pbc.unwrap#

molsysmt.pbc.unwrap(molecular_system, selection='all', structure_indices='all', syntax='MolSysMT', engine='MolSysMT', in_place=False, skip_digestion=False)[source]#

Unwrapping coordinates across periodic boundaries to produce continuous trajectories.

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.
syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).
engine (str, default='MolSysMT') – Backend used to perform the calculation.
in_place (bool, default=False) – Whether to modify the input molecular system in place.
skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

Returns:

Unwrapped system when in_place=False, otherwise None.

Return type:

molecular system or None

Raises:

NotImplementedMethodError – If an unsupported engine is requested.
StructuralInconsistencyError – If box vectors are missing, malformed, non-finite, or singular.

Notes

This operation restores temporal continuity independently for every atom. It does not reconstruct a molecule within one frame. Use molsysmt.pbc.wrap_to_pbc() or molsysmt.pbc.wrap_to_mic() with compact='component' for covalent reconstruction.

Added in version 1.0.0.