molsysmt.physchem.get_sasa#

molsysmt.physchem.get_sasa(molecular_system, element='atom', selection='all', structure_indices='all', syntax='MolSysMT', engine='MolSysMT', probe_radius='1.4 angstroms', n_sphere_points=240, use_cell_list='auto', use_gpu=None, gpu_backend=None, parallel=None, num_threads=None, skip_digestion=False)[source]#

Solvent-accessible surface area (SASA) per atom or residue group.

Uses the Shrake–Rupley rolling-sphere algorithm. The default engine computes SASA with the bundled Rust kernels.

Parameters:

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

  • element (str, default='atom') – Structural element level to query (‘atom’, ‘group’, ‘component’, ‘molecule’, ‘chain’, ‘entity’).

  • 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 (object, default='MolSysMT') – Argument engine.

  • probe_radius (object, default='1.4 angstroms') – Argument probe_radius.

  • n_sphere_points (object, default=240) – Argument n_sphere_points.

  • use_cell_list (object, default='auto') – Argument use_cell_list.

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

  • gpu_backend (object, default=None) – Argument gpu_backend.

  • parallel (object, default=None) – Argument parallel.

  • num_threads (object, default=None) – Argument num_threads.

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

Returns:

SASA values as a PyUnitWizard quantity in area units (nm²). Shape: (n_structures, n_elements).

Return type:

quantity

Raises:

NotImplementedMethodError – If an unsupported engine is requested.

Notes

Non-protein atoms (e.g. solvent) are included in the SASA calculation but their contribution to neighbouring atoms is accounted for.

Added in version 1.0.0.

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