Index

_

_apply_charge_correction() (ParaMol.Tasks.parametrization.Parametrization method) _calculate_a() (ParaMol.MM_engines.resp.RESP method) _calculate_b() (ParaMol.MM_engines.resp.RESP method) _calculate_regularization_derivative() (ParaMol.MM_engines.resp.RESP method) _check_cell_units() (ParaMol.QM_engines.amber_wrapper.AmberWrapper method) _create_optimizer() (ParaMol.Optimizers.optimizer.Optimizer method) _get_constraints() (ParaMol.Tasks.parametrization.Parametrization static method) _get_parameters_rmsd() (ParaMol.Tasks.adaptive_parametrization.AdaptiveParametrization static method) _get_total_charge() (ParaMol.Tasks.parametrization.Parametrization static method) _hyperbolic_regularization() (ParaMol.Objective_function.Properties.regularization.Regularization method) _l1_regularization() (ParaMol.Objective_function.Properties.regularization.Regularization method) _l2_regularization() (ParaMol.Objective_function.Properties.regularization.Regularization method) _perform_assertions() (ParaMol.Tasks.parametrization.Parametrization static method)

_perform_optimization() (ParaMol.Tasks.parametrization.Parametrization method) _plot() (ParaMol.Tasks.objective_function_plot.ObjectiveFunctionPlot static method) _prepare_work_dir() (ParaMol.QM_engines.dftb_wrapper.DFTBWrapper method) _prepare_workdir() (ParaMol.QM_engines.ase_wrapper.ASEWrapper method) _qm_engine_init() (ParaMol.QM_engines.qm_engine.QMEngine method) _regularization_derivative_hyperbolic() (ParaMol.MM_engines.resp.RESP method) _regularization_derivative_l2() (ParaMol.MM_engines.resp.RESP method) _run_parallel() (ParaMol.Tasks.ab_initio_properties.AbInitioProperties method) _run_serial() (ParaMol.Tasks.ab_initio_properties.AbInitioProperties method) _set_force_groups() (ParaMol.MM_engines.openmm.OpenMMEngine method) _write_data() (ParaMol.Tasks.objective_function_plot.ObjectiveFunctionPlot static method) _write_geometry_gen_format() (ParaMol.QM_engines.dftb_wrapper.DFTBWrapper method) _write_input_file() (ParaMol.QM_engines.dftb_wrapper.DFTBWrapper method)

A

AbInitioProperties (class in ParaMol.Tasks.ab_initio_properties) AdaptiveParametrization (class in ParaMol.Tasks.adaptive_parametrization) add_parameter() (ParaMol.Force_field.force_field_term.FFTerm method) add_system() (ParaMol.Objective_function.Properties.energy_property.EnergyProperty method) (ParaMol.Objective_function.Properties.esp_property.ESPProperty method)

add_torsion_terms() (ParaMol.MM_engines.openmm.OpenMMEngine method) AmberSymmetrizer (class in ParaMol.Utils.Symmetrizers.amber_symmetrizer) AmberWrapper (class in ParaMol.QM_engines.amber_wrapper) append_data_to_system() (ParaMol.System.system.ParaMolSystem method) ASEWrapper (class in ParaMol.QM_engines.ase_wrapper)

C

calculate_inverse_covariance_qm_forces() (ParaMol.Objective_function.Properties.force_property.ForceProperty method) calculate_inverse_distances() (ParaMol.MM_engines.resp.RESP method) calculate_objective_function() (ParaMol.Objective_function.objective_function.ObjectiveFunction method) calculate_parameters_magnitudes() (ParaMol.Parameter_space.parameter_space.ParameterSpace method) calculate_prior_widths() (ParaMol.Parameter_space.parameter_space.ParameterSpace method) calculate_property() (ParaMol.Objective_function.Properties.energy_property.EnergyProperty method) (ParaMol.Objective_function.Properties.esp_property.ESPProperty method) (ParaMol.Objective_function.Properties.force_property.ForceProperty method) (ParaMol.Objective_function.Properties.regularization.Regularization method) calculate_scaling_constants() (ParaMol.Parameter_space.parameter_space.ParameterSpace method) calculate_variance() (ParaMol.Objective_function.Properties.energy_property.EnergyProperty method) (ParaMol.Objective_function.Properties.esp_property.ESPProperty method) (ParaMol.Objective_function.Properties.force_property.ForceProperty method) (ParaMol.Objective_function.Properties.property.Property method) CharmmSymmetrizer (class in ParaMol.Utils.Symmetrizers.charmm_symmetrizer) chdir() (ParaMol.Utils.interface.ParaMolInterface method) chdir_base() (ParaMol.Utils.interface.ParaMolInterface method) chdir_previous() (ParaMol.Utils.interface.ParaMolInterface method)

check_dir_exists() (ParaMol.Utils.interface.ParaMolInterface static method) check_file_exists() (ParaMol.Utils.interface.ParaMolInterface static method) compute_conformations_weights() (ParaMol.System.system.ParaMolSystem method) conformational_sampling() (in module ParaMol.Utils.conformational_sampling) convert_system_ref_arrays_to_list() (ParaMol.System.system.ParaMolSystem method) CPUObjectiveFunction (class in ParaMol.Objective_function.cpu_objective_function) create_dir() (ParaMol.Utils.interface.ParaMolInterface method) create_force_field() (ParaMol.Force_field.force_field.ForceField method) create_force_field_from_openmm() (ParaMol.Force_field.force_field.ForceField method) create_force_field_optimizable() (ParaMol.Force_field.force_field.ForceField method) create_harmonic_angle_force_field() (ParaMol.Force_field.force_field.ForceField method) create_harmonic_bond_force_field() (ParaMol.Force_field.force_field.ForceField method) create_nonbonded_force_field() (ParaMol.Force_field.force_field.ForceField method) create_objective_function() (ParaMol.Tasks.task.Task static method) create_optimizer() (ParaMol.Tasks.task.Task static method) create_parameter_space() (ParaMol.Tasks.task.Task static method) create_periodic_torsion_force_field() (ParaMol.Force_field.force_field.ForceField method) create_properties() (ParaMol.Tasks.task.Task static method) create_qm_engines() (ParaMol.System.system.ParaMolSystem method)

D

DFTBWrapper (class in ParaMol.QM_engines.dftb_wrapper)

E

energy_statistics() (ParaMol.System.system.ParaMolSystem method)

EnergyProperty (class in ParaMol.Objective_function.Properties.energy_property) ESPProperty (class in ParaMol.Objective_function.Properties.esp_property)

F

f() (ParaMol.Objective_function.objective_function.ObjectiveFunction method) f_callback_function() (ParaMol.Objective_function.cpu_objective_function.CPUObjectiveFunction method) (ParaMol.Objective_function.gpu_objective_function.GPUObjectiveFunction method) FFTerm (class in ParaMol.Force_field.force_field_term) filter_conformations() (ParaMol.System.system.ParaMolSystem method) fit_resp_charges_explicitly() (ParaMol.MM_engines.resp.RESP method)

force_groups_dict (ParaMol.MM_engines.openmm.OpenMMEngine attribute) force_statistics() (ParaMol.System.system.ParaMolSystem method) ForceField (class in ParaMol.Force_field.force_field) ForceProperty (class in ParaMol.Objective_function.Properties.force_property) freeze_atoms() (ParaMol.Tasks.torsions_scan.TorsionScan static method) freeze_torsions() (ParaMol.Tasks.torsions_scan.TorsionScan static method)

G

gaussian_read_log() (ParaMol.Utils.gaussian_esp.GaussianESP static method) GaussianESP (class in ParaMol.Utils.gaussian_esp) generate_maxwell_boltzmann_velocities() (ParaMol.MM_engines.openmm.OpenMMEngine method) get_atom_list() (ParaMol.MM_engines.openmm.OpenMMEngine method) get_atomic_numbers() (ParaMol.MM_engines.openmm.OpenMMEngine method) get_cell() (ParaMol.MM_engines.openmm.OpenMMEngine method) get_charge_symmetries() (ParaMol.Utils.Symmetrizers.symmetrizer.Symmetrizer method) get_energies_ensemble() (ParaMol.System.system.ParaMolSystem method) get_esp_ensemble() (ParaMol.System.system.ParaMolSystem method) get_f_count() (ParaMol.Objective_function.objective_function.ObjectiveFunction method) get_forces() (ParaMol.MM_engines.openmm.OpenMMEngine method) get_forces_ensemble() (ParaMol.System.system.ParaMolSystem method) get_kinetic_energy() (ParaMol.MM_engines.openmm.OpenMMEngine method) get_masses() (ParaMol.MM_engines.openmm.OpenMMEngine method)

get_mm_relaxed_conformations() (ParaMol.Tasks.torsions_scan.TorsionScan static method) get_number_of_atoms() (ParaMol.MM_engines.openmm.OpenMMEngine method) get_optimizable_parameters() (ParaMol.Force_field.force_field.ForceField method) (ParaMol.Parameter_space.parameter_space.ParameterSpace method) get_positions() (ParaMol.MM_engines.openmm.OpenMMEngine method) get_potential_energy() (ParaMol.MM_engines.openmm.OpenMMEngine method) get_rdkit_mol_conf() (ParaMol.Tasks.torsions_scan.TorsionScan static method) get_rotatable_bonds() (ParaMol.Tasks.torsions_parametrization.TorsionsParametrization static method) get_rotatable_torsions() (ParaMol.Tasks.torsions_parametrization.TorsionsParametrization static method) get_symmetries() (ParaMol.Utils.Symmetrizers.symmetrizer.Symmetrizer method) get_velocities() (ParaMol.MM_engines.openmm.OpenMMEngine method) GPUObjectiveFunction (class in ParaMol.Objective_function.gpu_objective_function) GradientDescent (class in ParaMol.Optimizers.gradient_descent) GromacsSymmetrizer (class in ParaMol.Utils.Symmetrizers.gromacs_symmetrizer)

I

init_openmm() (ParaMol.MM_engines.openmm.OpenMMEngine method) init_parallel() (ParaMol.Objective_function.objective_function.ObjectiveFunction method)

init_worker() (ParaMol.Objective_function.cpu_objective_function.CPUObjectiveFunction static method) (ParaMol.Objective_function.gpu_objective_function.GPUObjectiveFunction static method)

J

jacobi_preconditioning() (ParaMol.Parameter_space.parameter_space.ParameterSpace method)

M

minimize_system() (ParaMol.MM_engines.openmm.OpenMMEngine method) module ParaMol ParaMol.Force_field ParaMol.Force_field.force_field ParaMol.Force_field.force_field_term ParaMol.Force_field.force_field_term_parameter ParaMol.MM_engines ParaMol.MM_engines.openmm ParaMol.MM_engines.resp ParaMol.Objective_function ParaMol.Objective_function.cpu_objective_function ParaMol.Objective_function.gpu_objective_function ParaMol.Objective_function.objective_function ParaMol.Objective_function.Properties ParaMol.Objective_function.Properties.energy_property ParaMol.Objective_function.Properties.esp_property ParaMol.Objective_function.Properties.force_property ParaMol.Objective_function.Properties.property ParaMol.Objective_function.Properties.regularization ParaMol.Optimizers ParaMol.Optimizers.gradient_descent ParaMol.Optimizers.monte_carlo ParaMol.Optimizers.optimizer ParaMol.Optimizers.scipy_optimizers ParaMol.Optimizers.simulated_annealing ParaMol.Parameter_space ParaMol.Parameter_space.parameter_space ParaMol.QM_engines ParaMol.QM_engines.amber_wrapper ParaMol.QM_engines.ase_wrapper ParaMol.QM_engines.dftb_wrapper ParaMol.QM_engines.qm_engine ParaMol.System ParaMol.System.system ParaMol.Tasks ParaMol.Tasks.ab_initio_properties ParaMol.Tasks.adaptive_parametrization ParaMol.Tasks.forces_parallel ParaMol.Tasks.objective_function_plot ParaMol.Tasks.parametrization ParaMol.Tasks.resp_fitting ParaMol.Tasks.task ParaMol.Tasks.torsions_parametrization ParaMol.Tasks.torsions_scan ParaMol.Utils ParaMol.Utils.conformational_sampling ParaMol.Utils.gaussian_esp ParaMol.Utils.interface ParaMol.Utils.settings ParaMol.Utils.Symmetrizers ParaMol.Utils.Symmetrizers.amber_symmetrizer ParaMol.Utils.Symmetrizers.charmm_symmetrizer ParaMol.Utils.Symmetrizers.gromacs_symmetrizer ParaMol.Utils.Symmetrizers.symmetrizer

MonteCarlo (class in ParaMol.Optimizers.monte_carlo)

O

ObjectiveFunction (class in ParaMol.Objective_function.objective_function) ObjectiveFunctionPlot (class in ParaMol.Tasks.objective_function_plot) OpenMMEngine (class in ParaMol.MM_engines.openmm) optimize_scaling_constants() (ParaMol.Force_field.force_field.ForceField method)

optimize_selection() (ParaMol.Force_field.force_field.ForceField method) optimize_torsions() (ParaMol.Force_field.force_field.ForceField method) optimize_torsions_by_symmetry() (ParaMol.Force_field.force_field.ForceField method) Optimizer (class in ParaMol.Optimizers.optimizer) optimizers (ParaMol.Optimizers.optimizer.Optimizer attribute)

P

Parameter (class in ParaMol.Force_field.force_field_term_parameter) ParameterSpace (class in ParaMol.Parameter_space.parameter_space) Parametrization (class in ParaMol.Tasks.parametrization) ParaMol module ParaMol.Force_field module ParaMol.Force_field.force_field module ParaMol.Force_field.force_field_term module ParaMol.Force_field.force_field_term_parameter module ParaMol.MM_engines module ParaMol.MM_engines.openmm module ParaMol.MM_engines.resp module ParaMol.Objective_function module ParaMol.Objective_function.cpu_objective_function module ParaMol.Objective_function.gpu_objective_function module ParaMol.Objective_function.objective_function module ParaMol.Objective_function.Properties module ParaMol.Objective_function.Properties.energy_property module ParaMol.Objective_function.Properties.esp_property module ParaMol.Objective_function.Properties.force_property module ParaMol.Objective_function.Properties.property module ParaMol.Objective_function.Properties.regularization module ParaMol.Optimizers module ParaMol.Optimizers.gradient_descent module ParaMol.Optimizers.monte_carlo module ParaMol.Optimizers.optimizer module ParaMol.Optimizers.scipy_optimizers module ParaMol.Optimizers.simulated_annealing module ParaMol.Parameter_space module ParaMol.Parameter_space.parameter_space module ParaMol.QM_engines module

ParaMol.QM_engines.amber_wrapper module ParaMol.QM_engines.ase_wrapper module ParaMol.QM_engines.dftb_wrapper module ParaMol.QM_engines.qm_engine module ParaMol.System module ParaMol.System.system module ParaMol.Tasks module ParaMol.Tasks.ab_initio_properties module ParaMol.Tasks.adaptive_parametrization module ParaMol.Tasks.forces_parallel module ParaMol.Tasks.objective_function_plot module ParaMol.Tasks.parametrization module ParaMol.Tasks.resp_fitting module ParaMol.Tasks.task module ParaMol.Tasks.torsions_parametrization module ParaMol.Tasks.torsions_scan module ParaMol.Utils module ParaMol.Utils.conformational_sampling module ParaMol.Utils.gaussian_esp module ParaMol.Utils.interface module ParaMol.Utils.settings module ParaMol.Utils.Symmetrizers module ParaMol.Utils.Symmetrizers.amber_symmetrizer module ParaMol.Utils.Symmetrizers.charmm_symmetrizer module ParaMol.Utils.Symmetrizers.gromacs_symmetrizer module ParaMol.Utils.Symmetrizers.symmetrizer module ParaMolInterface (class in ParaMol.Utils.interface) ParaMolSystem (class in ParaMol.System.system) pdb_file (ParaMol.Tasks.torsions_parametrization.TorsionsParametrization attribute) Property (class in ParaMol.Objective_function.Properties.property)

Q

qm_parallel() (in module ParaMol.Tasks.forces_parallel)

QMEngine (class in ParaMol.QM_engines.qm_engine)

R

read_data() (ParaMol.System.system.ParaMolSystem method) read_ff_file() (ParaMol.Force_field.force_field.ForceField method) read_log_files() (ParaMol.Utils.gaussian_esp.GaussianESP method) read_restart_pickle() (ParaMol.Tasks.task.Task static method) Regularization (class in ParaMol.Objective_function.Properties.regularization) remove_all_created_dirs() (ParaMol.Utils.interface.ParaMolInterface method) reset_f_count() (ParaMol.Objective_function.objective_function.ObjectiveFunction method) RESP (class in ParaMol.MM_engines.resp) resp_solvers (ParaMol.Tasks.resp_fitting.RESPFitting attribute) RESPFitting (class in ParaMol.Tasks.resp_fitting) run_calculation() (ParaMol.QM_engines.amber_wrapper.AmberWrapper method) (ParaMol.QM_engines.ase_wrapper.ASEWrapper method) (ParaMol.QM_engines.dftb_wrapper.DFTBWrapper method) run_md() (ParaMol.QM_engines.ase_wrapper.ASEWrapper method)

run_optimization() (ParaMol.Optimizers.gradient_descent.GradientDescent method) (ParaMol.Optimizers.monte_carlo.MonteCarlo method) (ParaMol.Optimizers.optimizer.Optimizer method) (ParaMol.Optimizers.scipy_optimizers.ScipyOptimizer method) (ParaMol.Optimizers.simulated_annealing.SimulatedAnnealing method) run_subprocess() (ParaMol.Utils.interface.ParaMolInterface static method) run_task() (ParaMol.Tasks.ab_initio_properties.AbInitioProperties method) (ParaMol.Tasks.adaptive_parametrization.AdaptiveParametrization method) (ParaMol.Tasks.objective_function_plot.ObjectiveFunctionPlot method) (ParaMol.Tasks.parametrization.Parametrization method) (ParaMol.Tasks.resp_fitting.RESPFitting method) (ParaMol.Tasks.task.Task method) (ParaMol.Tasks.torsions_parametrization.TorsionsParametrization method) (ParaMol.Tasks.torsions_scan.TorsionScan method)

S

save() (ParaMol.Utils.Symmetrizers.symmetrizer.Symmetrizer method) save_frcmod() (ParaMol.Utils.Symmetrizers.amber_symmetrizer.AmberSymmetrizer method) save_parameter_set() (ParaMol.Utils.Symmetrizers.charmm_symmetrizer.CharmmSymmetrizer method) scan_1d() (ParaMol.Tasks.torsions_scan.TorsionScan method) scan_2d() (ParaMol.Tasks.torsions_scan.TorsionScan method) ScipyOptimizer (class in ParaMol.Optimizers.scipy_optimizers) set_bonded_parameters() (ParaMol.MM_engines.openmm.OpenMMEngine method) set_charges() (ParaMol.MM_engines.resp.RESP method) set_harmonic_angle_force_parameters() (ParaMol.MM_engines.openmm.OpenMMEngine method) set_harmonic_bond_force_parameters() (ParaMol.MM_engines.openmm.OpenMMEngine method) set_initial_charges() (ParaMol.MM_engines.resp.RESP method) set_initial_parameters_values() (ParaMol.Objective_function.Properties.regularization.Regularization method) set_non_bonded_parameters_to_zero() (ParaMol.MM_engines.openmm.OpenMMEngine method) set_nonbonded_parameters() (ParaMol.MM_engines.openmm.OpenMMEngine method)

set_parameter_optimization() (ParaMol.Force_field.force_field.ForceField method) set_periodic_torsion_force_parameters() (ParaMol.MM_engines.openmm.OpenMMEngine method) set_positions() (ParaMol.MM_engines.openmm.OpenMMEngine method) set_positions_rdkit_conf() (ParaMol.Tasks.torsions_scan.TorsionScan static method) set_prior_widths() (ParaMol.Objective_function.Properties.regularization.Regularization method) set_symmetry_constraints() (ParaMol.MM_engines.resp.RESP method) set_velocities() (ParaMol.MM_engines.openmm.OpenMMEngine method) set_zero() (ParaMol.Tasks.torsions_scan.TorsionScan static method) Settings (class in ParaMol.Utils.settings) SimulatedAnnealing (class in ParaMol.Optimizers.simulated_annealing) symmetrize_force_field() (ParaMol.Utils.Symmetrizers.symmetrizer.Symmetrizer method) Symmetrizer (class in ParaMol.Utils.Symmetrizers.symmetrizer) symmetry_group_default (ParaMol.Force_field.force_field.ForceField attribute) (ParaMol.Parameter_space.parameter_space.ParameterSpace attribute)

T

Task (class in ParaMol.Tasks.task)

TorsionScan (class in ParaMol.Tasks.torsions_scan) TorsionsParametrization (class in ParaMol.Tasks.torsions_parametrization)

U

update_force_field() (ParaMol.Force_field.force_field.ForceField method)

update_systems() (ParaMol.Parameter_space.parameter_space.ParameterSpace method) update_term_types_parameters() (ParaMol.Utils.Symmetrizers.symmetrizer.Symmetrizer method)

W

wham_reweighing() (ParaMol.System.system.ParaMolSystem method) write_coordinates_xyz() (ParaMol.System.system.ParaMolSystem method) write_data() (ParaMol.System.system.ParaMolSystem method) write_esp_paramol_format() (ParaMol.Utils.gaussian_esp.GaussianESP method)

write_ff_file() (ParaMol.Force_field.force_field.ForceField method) write_restart_pickle() (ParaMol.Tasks.task.Task static method) write_scan_data() (ParaMol.Tasks.torsions_scan.TorsionScan static method) write_system_xml() (ParaMol.MM_engines.openmm.OpenMMEngine method)