Assigning partial charges#
Attaching a validated named charge assignment to a detached molecular system.
Added in version 1.0.0.
API documentation
import molsysmt as msm
molsys = msm.build.assign_partial_charges(
msm.systems['caffeine']['caffeine.sdf'], method='gasteiger_marsili')
assert molsys.molecular_mechanics.partial_charge_assignment['coverage'] == 'complete'
Demo Systems Catalog
See Demo Systems Catalog for the bundled datasets.
The input remains unchanged. The output retains its atoms, IDs, chemistry,
coordinates and analyses and stores charges in MolecularMechanics, independently
of ChemicalStates formal charges. Exactly one chemical state is required for
attachment; multiple states can be calculated separately through
molsysmt.physchem.get_partial_charges(). Existing charges are explicitly
replaced. Other force-field parameters and AutoDock labels are not assigned.
Named analyses retain their original snapshots; explicitly invalidate/recalculate
any analysis that depends on the changed mechanical parameters.
Read Getting partial charges for model prerequisites, units, total-charge checks, projected scope, provenance, stale-assignment checks and export limits. Mechanical assignments are not persisted by H5MSM 0.5.