Assigning charges before a bounded export#

Calculating and retaining a named mechanical charge assignment on prepared chemistry.

Added in version 1.0.0.

Calculating a prepared ligand#

The bundled caffeine SDF already includes all indexed hydrogens and full covalent orders. This recipe neither adds hydrogens nor changes protonation.

import molsysmt as msm

molsys = msm.build.assign_partial_charges(
    msm.systems['caffeine']['caffeine.sdf'], method='gasteiger_marsili')
report = molsys.molecular_mechanics.partial_charge_assignment
assert report['coverage'] == 'complete'
assert report['parameters']['iterations'] == 12
assert abs(report['total_charge']) < report['total_charge_tolerance']

Demo Systems Catalog

See Demo Systems Catalog for the bundled datasets.

The native partial-charge array uses elementary charge. Formal charges remain in ChemicalStates; the total check does not establish electrostatic accuracy. Save the report with the result for provenance. H5MSM 0.5 does not persist the experimental mechanical domain; full mechanical persistence is planned for 0.6.

Querying a subset#

selected = msm.physchem.get_partial_charges(
    molsys, method='gasteiger_marsili', selection=[14, 16], return_report=True)
assert selected['report']['atom_indices'].tolist() == [14, 16]
assert selected['report']['n_atoms'] == 24

The full graph is calculated before filtering. Extraction instead retains the previous numerical charges as a projection, with original source indices. Neither operation treats a fragment as a newly parameterized isolated molecule.

Checking a receptor#

For an already hydrogenated conventional protein, choose an explicit force field and declare the expected total if formal charges are absent:

receptor = msm.build.assign_partial_charges(
    msm.systems['chicken villin HP35']['1vii.pdb'], method='forcefield',
    forcefield='AMBER14', expected_total_charge=2)
assert receptor.molecular_mechanics.partial_charge_assignment['coverage'] == 'complete'

The +2 e declaration applies to this bundled structure and its supplied H inventory; it is not a default for another receptor. Model/template matching fails clearly for unsupported or unprepared chemistry. The calculator does not generate H, repair residues or substitute a ligand charge scheme for receptor parameters.

Before PDBQT export, independently assign chemically valid AutoDock labels and choose an explicit torsion tree where required. Charges alone do not establish docking readiness. The writer checks stored assignment consistency and records a compact provenance remark plus its three-decimal charge rounding. Reading the resulting PDBQT does not recover the full chemical state or assignment report.

See also