molsysmt.build.assign_autodock_atom_types#

molsysmt.build.assign_autodock_atom_types(molecular_system, typing_scheme, structure_indices='all', chemical_state='reference', method='chemical_environment', return_report=False, skip_digestion=False)[source]#

Assigning full named AutoDock labels to a detached single-state MolSys.

Parameters:

  • molecular_system (molecular system) – Any supported form with the chosen profile’s prerequisites. Exactly one nonempty chemical state is required for current mechanical storage.

  • typing_scheme (str) – Required explicit ‘autodock4’ parameter vocabulary.

  • structure_indices (int, list, tuple or numpy.ndarray, default='all') – Structure indices (0-based) for resolving a structure-associated state. All source structures are retained, without using coordinates for typing.

  • chemical_state (str or int, default='reference') – State to classify. Reduce multi-state inputs explicitly before attachment.

  • method (str, default='chemical_environment') – Experimental chemical_environment@1 profile with auditable rule precedence.

  • return_report (bool, default=False) – Return molecular_system and detached report when True.

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

Returns:

New system retaining source atoms, IDs, structures, chemical assignments, partial charges and named analyses. Its molecular_mechanics holds atom_ff_type labels and atom_type_assignment provenance. The source is unchanged. This does not establish complete force-field parameterization.

Return type:

molsysmt.MolSys or dict

Raises:

  • ArgumentError – If a method, scheme, state or frame request is invalid.

  • StructuralInconsistencyError – If there is no nonempty single state or the profile cannot classify all atoms without guessing missing chemistry or adding virtual H.

  • ImportError – If the optional RDKit provider is unavailable.

Notes

Calls physchem.get_autodock_atom_types; chemistry remains owned by ChemicalStates. The mechanical type report binds ordered labels to source chemistry/state. Copy/pickle preserve original producer versions. Extraction retains parent labels with projected provenance; it does not classify isolated fragments. The PDBQT writer rejects stale named chemistry/labels or a different scheme. Native property replacement clears named typing attribution. Existing analyses keep their snapshots; callers invalidate analyses depending on changed mechanics. Complete native copying can materialize structures; this is not streaming. MolecularMechanics remains experimental and is excluded from H5MSM 0.5. Charge calculation, H merging and docking protocols remain separate operations.

See also

molsysmt.physchem.get_autodock_atom_types

Calculate without attachment.

molsysmt.build.assign_partial_charges

Attach a separately named charge model.

Examples

>>> import molsysmt as msm
>>> molsys = msm.build.assign_autodock_atom_types(
...     msm.systems['caffeine']['caffeine.sdf'], typing_scheme='autodock4')
>>> molsys.molecular_mechanics.atom_type_assignment['typing_scheme']
'autodock4'

User guide

See Assigning AutoDock types for attachment and export rules.

Added in version 1.0.0.