molsysmt.structure.get_contacts#

molsysmt.structure.get_contacts(molecular_system, selection=None, center_of_atoms=False, weights=None, structure_indices='all', selection_2=None, center_of_atoms_2=False, weights_2=None, structure_indices_2=None, threshold='12 angstroms', pairs=False, pbc=True, syntax='MolSysMT', output_type='numpy.ndarray', output_indices=None, use_gpu=None, gpu_backend=None, cell_list=None, parallel=None, num_threads=None, skip_digestion=False)[source]#

Compute a boolean contact map between two sets of atoms (or atom-group centers).

Internally calls get_distances and applies a distance threshold to produce a contact map. When only one selection is provided the contact map is computed between all pairs within that selection. When both selection and selection_2 are provided the map is computed between the two sets.

Parameters:

  • molecular_system (molecular system) – Molecular system in any supported MolSysMT format.

  • selection (str, list, tuple, or numpy.ndarray, default=None) – Selection string or boolean/integer array specifying elements.

  • center_of_atoms (bool, default=False) – Whether to compute distances relative to geometric centers.

  • weights (numpy.ndarray, list, or tuple, default=None) – Atomic mass weights array for center calculation.

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

  • selection_2 (str, list, tuple, or numpy.ndarray, default=None) – Second selection string or boolean/integer array.

  • center_of_atoms_2 (bool, default=False) – Whether to compute distances relative to geometric centers for selection_2.

  • weights_2 (numpy.ndarray, list, or tuple, default=None) – Atomic mass weights array for selection_2.

  • structure_indices_2 (int, list, tuple, or numpy.ndarray, default=None) – Structure indices (0-based) for the second selection.

  • threshold (float or quantity, default='12 angstroms') – Distance cutoff threshold quantity.

  • pairs (bool, default=False) – Whether corresponding selections define explicit pairs instead of a Cartesian product.

  • pbc (bool, default=True) – Whether to take periodic boundary conditions into account.

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

  • output_type (str, default='numpy.ndarray') – Representation used for the returned result.

  • output_indices ({'selection', 'atom', 'group'} or None, default=None) – Index convention included with the returned values.

  • use_gpu (bool, default=None) – Whether to perform computation using GPU acceleration.

  • gpu_backend (str or None, default=None) – GPU array backend, or None to use the configured backend.

  • cell_list ({'auto'}, bool, or None, default=None) – Whether to use cell-list acceleration for eligible contact calculations.

  • parallel (bool or None, default=None) – Whether to use CPU parallelism, or None to use the configured default.

  • num_threads (int or None, default=None) – Number of CPU worker threads, or None to use the configured default.

  • skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

Returns:

Contact map as a boolean numpy.ndarray (output_type='numpy.ndarray') or as a list of contacting pairs per frame (output_type='pairs' or 'sorted pairs').

Return type:

numpy.ndarray or list

Added in version 1.0.0.

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