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) – Molecular system in any supported MolSysMT format.

  • element (str, default='group') – 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.

  • definition (str, default='physical_pH7') – Reference dataset used to assign the requested physical property.

  • forcefield (str, default='AMBER14') – Force field parameter identifier or name.

  • water_model (str, default=None) – Water model parameter identifier (e.g., ‘TIP3P’).

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

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

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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