psiresp.configs.OneStageRESP
- pydantic model psiresp.configs.OneStageRESP[source]
Configuration for one-stage RESP
This corresponds to RESP-A2 in the R.E.D. server.
- field charge_constraints: charge.ChargeConstraintOptions = ChargeConstraintOptions(charge_sum_constraints=[], charge_equivalence_constraints=[], split_conformers=False, constrain_methyl_hydrogens_between_conformers=False, symmetric_methyls=True, symmetric_methylenes=True, symmetric_atoms_are_equivalent=False)
Charge constraints
- field defer_errors: bool = False
Whether to raise an error immediately, or gather all errors during ESP computation and raise at the end
- field grid_options: grid.GridOptions = GridOptions(grid_rmin=0, grid_rmax=-1, use_radii='msk', vdw_radii={}, vdw_scale_factors=[1.4, 1.6, 1.8, 2.0], vdw_point_density=1.0)
Options for generating grid for ESP computation
- field molecules: List[molecule.Molecule] [Required]
Molecules to use for the RESP job
- field n_processes: Optional[int] = None
Number of processes to use in multiprocessing during ESP computation. n_processes=None uses the number of CPUs.
- field qm_esp_options: qm.QMEnergyOptions = QMEnergyOptions(method='hf', basis='6-31g*', pcm_options=None, driver='energy', query_interval=20, protocols={'wavefunction': 'orbitals_and_eigenvalues'}, keywords={}, jobname='single_point')
QM options for ESP computation
- field qm_optimization_options: qm.QMGeometryOptimizationOptions = QMGeometryOptimizationOptions(method='hf', basis='6-31g*', pcm_options=None, driver='gradient', query_interval=20, protocols={'wavefunction': 'orbitals_and_eigenvalues'}, keywords={}, g_convergence='gau_tight', max_iter=200, full_hess_every=10, jobname='optimization')
QM options for geometry optimization
- field resp_options: resp.RespOptions = RespOptions(restraint_slope=0.1, restrained_fit=True, exclude_hydrogens=True, convergence_tolerance=1e-06, max_iter=500, restraint_height_stage_1=0.0005, restraint_height_stage_2=0.001, stage_2=True)
Options for fitting ESP for charges
- field stage_1_charges: Optional[RespCharges] = None
Stage 1 charges. These need to be computed by calling run() or compute_charges() directly.
- field stage_2_charges: Optional[RespCharges] = None
Stage 2 charges. These need to be computed by calling run() or compute_charges() directly.
- field temperature: float = 298.15
Temperature (in Kelvin) to use when Boltzmann-weighting conformers.
- field working_directory: pathlib.Path = PosixPath('psiresp_working_directory')
Working directory for saving intermediate files
- compute_charges(update_molecules=True)
Compute the charges for each molecule. Each Orientation must have had the ESP computed, and there must be at least one orientation present.
- Return type
- compute_esps()
Compute ESP on a grid for each orientation in a multiprocessing pool
- compute_esps_and_charges(client=None, update_molecules=True)
- Parameters
update_molecules (bool) –
- Return type
- compute_orientation_energies(client=None, **kwargs)
Compute wavefunction for each orientation
- construct_surface_constraint_matrix()
Construct the constraint matrix for each atom, as generated by the ESP at each grid point
- Return type
- classmethod from_smiles(smiles, order_by_map_number=False, **kwargs)
- generate_conformers()
Generate conformers for every molecule
- generate_molecule_charge_constraints()
Gather the charge constraints pertaining to the molecules in this RESP job
- Return type
- generate_orientations()
Generate orientations for every conformer of every molecule
- get_hash()
- iter_conformers()
- iter_orientations()
- optimize_geometries(client=None, **kwargs)
Compute optimized geometries
- run(client=None, update_molecules=True)
Run the whole job
- Parameters
update_molecules (bool) –
- Return type
- update_molecule_charges()
Update the molecules in the job with the calculated charges
- property charges
- property conformers
- property n_conformers
- property n_orientations
- property orientations