molsysmt.physchem.get_charge#

molsysmt.physchem.get_charge(molecular_system, element='group', selection='all', definition='physical_pH7', forcefield='AMBER14', water_model=None, syntax='MolSysMT', skip_digestion=False)[source]#

Electric charge for the selected elements.

Returns the electric charge aggregated at the requested hierarchical level. Two families of definitions are supported:

  • 'physical_pH7' and 'collantes' — residue-based tabulated scales that assign a fixed charge to each amino acid group. The charge is then summed across all groups within the requested element.

  • 'OpenMM' — reads partial charges from an openmm.System or openmm.Simulation object’s NonbondedForce. If a different form is provided, the system is first converted to openmm.System using the specified forcefield.

Parameters:

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

  • element ({'atom', 'group', 'component', 'molecule', 'chain', 'entity', 'system'}, default 'group') – Hierarchical element for which charge is returned. When definition is 'physical_pH7' or 'collantes', element must be 'group' or coarser ('atom' raises an error). When definition is 'OpenMM' and the form is openmm.System, only 'atom' and 'system' are supported.

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

  • definition ({'physical_pH7', 'collantes', 'OpenMM'}, default 'physical_pH7') –

    Charge definition to use.

    • 'physical_pH7': fixed integer charges at pH 7 for the 20 standard amino acids (e.g. Arg +1, Asp −1).

    • 'collantes': alternative tabulated scale from Collantes et al.

    • 'OpenMM': partial charges extracted from an OpenMM NonbondedForce.

  • forcefield (str, default 'AMBER14') – Force field used to build the openmm.System when definition='OpenMM' and the input is not already an OpenMM system object.

  • water_model (str or None, default None) – Water model passed to the OpenMM system builder (when applicable).

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

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

Returns:

Electric charge as a PyUnitWizard quantity in elementary charge units (e). Shape is (n_elements,) for atom/group/component/ molecule/chain/entity elements, or a scalar for element='system'.

Return type:

quantity

Raises:

  • NotImplementedMethodError – If an unsupported definition is requested.

  • ArgumentChoiceError – If element='atom' is combined with a residue-based definition, or if a mid-hierarchy element is combined with the openmm.System form.

Notes

Values are rounded to 4 decimal places for the 'OpenMM' definition to avoid floating-point noise from unit conversions.

Added in version 1.0.0.

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