molsysmt.form.molsysmt_MolecularMechanics package

Submodules

molsysmt.form.molsysmt_MolecularMechanics.add module

molsysmt.form.molsysmt_MolecularMechanics.add.add(to_item, item, atom_indices='all', skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.append_structures module

molsysmt.form.molsysmt_MolecularMechanics.append_structures.append_structures(item, structure_id=None, time=None, coordinates=None, box=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.attributes module

molsysmt.form.molsysmt_MolecularMechanics.copy module

molsysmt.form.molsysmt_MolecularMechanics.copy.copy(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.extract module

molsysmt.form.molsysmt_MolecularMechanics.extract.extract(item, copy_if_all=True, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get module

molsysmt.form.molsysmt_MolecularMechanics.get.get_atom_index_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_constraints_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_cutoff_distance_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_dispersion_correction_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_ewald_error_tolerance_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_flexible_constraints_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_forcefield_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_formal_charge_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_hydrogen_mass_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_implicit_solvent_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_kappa_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_n_atoms_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_n_atoms_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_non_bonded_method_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_partial_charge_from_atom(item, indices='all', skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_rigid_water_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_salt_concentration_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_solute_dielectric_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_solvent_dielectric_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_switch_distance_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.get.get_water_model_from_system(item, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.has_attribute module

molsysmt.form.molsysmt_MolecularMechanics.has_attribute.has_attribute(molecular_system, attribute, include_none=False, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.is_form module

molsysmt.form.molsysmt_MolecularMechanics.is_form.is_form(item)

molsysmt.form.molsysmt_MolecularMechanics.iterators module

molsysmt.form.molsysmt_MolecularMechanics.merge module

molsysmt.form.molsysmt_MolecularMechanics.merge.merge(items, atom_indices='all', skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set module

molsysmt.form.molsysmt_MolecularMechanics.set.set_constraints_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_cutoff_distance_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_dispersion_correction_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_ewald_error_tolerance_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_flexible_constraints_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_forcefield_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_formal_charge_to_atom(item, atom_indices='all', value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_hydrogen_mass_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_implicit_solvent_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_kappa_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_non_bonded_method_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_partial_charge_to_atom(item, atom_indices='all', value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_rigid_water_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_salt_concentration_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_solute_dielectric_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_solvent_dielectric_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_switch_distance_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.set.set_water_model_to_system(item, value=None, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanics module

molsysmt.form.molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanics(item, copy_if_all=True, skip_digestion=False)

molsysmt.form.molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanicsDict module

molsysmt.form.molsysmt_MolecularMechanics.to_molsysmt_MolecularMechanicsDict.to_molsysmt_MolecularMechanicsDict(item, atom_indices='all', skip_digestion=False)

Module contents