molsysmt.physchem.get_chemical_readiness#

molsysmt.physchem.get_chemical_readiness(molecular_system, selection='all', structure_indices='all', chemical_state='reference', syntax='MolSysMT', skip_digestion=False)[source]#

Assessing stored chemical fields without repairing or completing chemistry.

Parameters:

molecular_system (molecular system) – Molecular system in any supported form providing an atom domain. Incomplete chemistry and coordinate-only native inputs are assessable.
selection (str, list, tuple or numpy.ndarray, default='all') – Atoms to assess. Source indices are deduplicated and sorted. Incident bonds include external endpoints; crossing bonds are reported explicitly.
structure_indices (int, list, tuple or numpy.ndarray, default='all') – Structure indices (0-based). Select exactly one when structures exist; a source without structures is assessed with missing coordinate data.
chemical_state (str, int or None, default='reference') – State to inspect. ‘structure’ uses the selected frame association. An ambiguous reference or absent association is reported as unassessed chemistry; an invalid explicit index raises.
syntax (str, default='MolSysMT') – Syntax used for atom selection.
skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

Returns:

Detached molsysmt.chemical_readiness@1 report with source atom/bond indices, selected state/frame, per-field values and coverage, explicit or inferred bond evidence when stored, connectivity boundary/integrity checks, explicit H atom indices and unassessed scientific checks. Coverage statuses are present, partial, missing, unsupported, conflict or empty. Coordinates contain finite-position booleans, assessed in nm; formal charges are in elementary charge units. No universal ready flag or chemical-validity certificate is returned.

Return type:

dict

Raises:

ArgumentError – If an atom/frame selection is invalid or selects multiple structures.
StructuralInconsistencyError – If a state index, coordinate shape or combined source axes are invalid.
FormatError – If a source uses unsupported chemical encodings in its form adapter.

Notes

A stored value does not establish its original interpretation or validation. Unknown atom-property origins remain unassessed. Bond evidence is retained as declared, without independently validating its truth. Labels missing or ‘unspecified’ do not establish achirality. Virtual/implicit H counts are distinct from explicit H atoms and their observed coordinates. The audit checks conventional covalent multiplicities 1/2/3 or declared aromatic bonds; it does not validate valence, perceive aromaticity, choose protonation or predict how many H atoms to add. Source domains remain unchanged. H5MSM 0.5 numeric selections read chemical layers and one coordinate frame; combined layers require declared identity atom-axis correspondence. Rich string selections use the existing public selection machinery.