molsysmt.physchem.get_mass#

molsysmt.physchem.get_mass(molecular_system, element='system', selection='all', syntax='MolSysMT', definition='physical', skip_digestion=False)[source]#

Total mass of the selected elements.

Returns the mass aggregated at the requested hierarchical level. Two definitions are available: a table of standard atomic masses ('physical') and mass values read directly from an OpenMM object ('OpenMM').

Parameters:

  • molecular_system (molecular system) – Input system in any supported form.

  • element ({'atom', 'group', 'component', 'molecule', 'chain', 'entity', 'system'}, default 'system') – Hierarchical element for which mass is returned. For elements coarser than 'atom', the masses of all constituent atoms are summed.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Selection of elements to include in the output.

  • syntax (str, default 'MolSysMT') – Selection syntax.

  • definition ({'physical', 'OpenMM'}, default 'physical') –

    Mass definition to use.

    • 'physical': standard atomic masses from the periodic table (IUPAC values), summed per element.

    • 'OpenMM': masses extracted from an openmm.Topology, openmm.Modeller, pdbfixer.PDBFixer, or openmm.System object. Element-level aggregation above 'atom' is supported for topology-based forms only.

  • skip_digestion (bool, default False) – If True, bypass argument validation (for internal use only).

Returns:

Mass as a PyUnitWizard quantity in dalton (amu). Shape is (n_elements,) for atom/group/component/molecule/chain/entity elements, or a scalar for element='system'.

Return type:

quantity

Raises:

NotImplementedError – If the requested combination of element and form is not supported under the 'OpenMM' definition.

Notes

Standard atomic masses ('physical') follow IUPAC 2021 values. Results are converted to pint units and standardized through PyUnitWizard before being returned.

Added in version 1.0.0.

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