Index

_

__init__() (qmmmrebind.parameterize.GuestAmberXMLAmber method) (qmmmrebind.parameterize.HostAmberXMLAmber method) (qmmmrebind.parameterize.MergeHostGuestTopology method) (qmmmrebind.parameterize.ParameterizeGuest method) (qmmmrebind.parameterize.ParameterizeHost method) (qmmmrebind.parameterize.PrepareGaussianGuest method) (qmmmrebind.parameterize.PrepareGaussianHostGuest method) (qmmmrebind.parameterize.PrepareQMMM method) (qmmmrebind.parameterize.RunOpenMMSims method) (qmmmrebind.parameterize.TorsionDriveParams method) (qmmmrebind.parameterize.TorsionDriveSims method)

A

add_dim_prmtop() (in module qmmmrebind.parameterize) add_period_prmtop() (in module qmmmrebind.parameterize) add_solvent_pointers_prmtop() (in module qmmmrebind.parameterize) add_vectors_inpcrd() (in module qmmmrebind.parameterize)

analyze_diff_energies() (qmmmrebind.parameterize.GuestAmberXMLAmber method) (qmmmrebind.parameterize.HostAmberXMLAmber method) ANGSTROMS_PER_NM (in module qmmmrebind.parameterize) args (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine)

B

BOHRS_PER_ANGSTROM (in module qmmmrebind.parameterize)

C

change_names() (in module qmmmrebind.parameterize) clean_up() (qmmmrebind.parameterize.PrepareQMMM method) copy_file() (in module qmmmrebind.parameterize) create_host_guest() (qmmmrebind.parameterize.PrepareQMMM method)

create_non_H_bonded_torsion_drive_dir() (qmmmrebind.parameterize.TorsionDriveSims method) create_non_H_torsion_drive_dir() (qmmmrebind.parameterize.TorsionDriveSims method) create_solvent_pdb() (qmmmrebind.parameterize.PrepareSolvatedParams method) create_torsion_drive_dir() (qmmmrebind.parameterize.TorsionDriveSims method)

D

delete_guest_angle_params() (in module qmmmrebind.parameterize)

dihedral_energy() (in module qmmmrebind.parameterize) dot_product() (in module qmmmrebind.parameterize)

E

element_list (in module qmmmrebind.parameterize)

error_function() (in module qmmmrebind.parameterize) error_function_boltzmann() (in module qmmmrebind.parameterize)

F

fit_params() (in module qmmmrebind.parameterize) force_angle_constant() (in module qmmmrebind.parameterize)

force_angle_constant_special_case() (in module qmmmrebind.parameterize) force_constant_bond() (in module qmmmrebind.parameterize)

G

gen_init_guess() (in module qmmmrebind.parameterize) generate_mm_pdbs() (in module qmmmrebind.parameterize) generate_xml_antechamber() (qmmmrebind.parameterize.GuestAmberXMLAmber method) (qmmmrebind.parameterize.HostAmberXMLAmber method) generate_xml_from_charged_pdb_sdf() (in module qmmmrebind.parameterize) (qmmmrebind.parameterize.GuestAmberXMLAmber method) generate_xml_from_doubly_charged_pdb_sdf() (qmmmrebind.parameterize.GuestAmberXMLAmber method) generate_xml_from_pdb_sdf() (in module qmmmrebind.parameterize) (qmmmrebind.parameterize.GuestAmberXMLAmber method) (qmmmrebind.parameterize.HostAmberXMLAmber method) generate_xml_from_pdb_smi() (qmmmrebind.parameterize.GuestAmberXMLAmber method) generate_xml_from_prmtop() (qmmmrebind.parameterize.SystemAmberSystem method) (qmmmrebind.parameterize.SystemGuestAmberSystem method) get_atom_names() (qmmmrebind.parameterize.ParameterizeGuest method) (qmmmrebind.parameterize.ParameterizeHost method) get_bond_angle_params() (qmmmrebind.parameterize.ParameterizeGuest method) (qmmmrebind.parameterize.ParameterizeHost method) get_bond_angles() (qmmmrebind.parameterize.ParameterizeGuest method) (qmmmrebind.parameterize.ParameterizeHost method) get_charges() (qmmmrebind.parameterize.ParameterizeGuest method) (qmmmrebind.parameterize.ParameterizeHost method) get_dihedrals() (in module qmmmrebind.parameterize) get_fchk() (qmmmrebind.parameterize.PrepareGaussianGuest method) (qmmmrebind.parameterize.PrepareGaussianHost method) (qmmmrebind.parameterize.PrepareGaussianHostGuest method)

get_guest_coord() (qmmmrebind.parameterize.PrepareQMMM method) get_hessian() (qmmmrebind.parameterize.ParameterizeGuest method) (qmmmrebind.parameterize.ParameterizeHost method) get_host_mm_region_atoms() (qmmmrebind.parameterize.PrepareQMMM method) get_host_qm_mm_atoms() (qmmmrebind.parameterize.PrepareQMMM method) get_mm_potential_energies() (in module qmmmrebind.parameterize) get_non_torsion_mm_energy() (in module qmmmrebind.parameterize) get_num_host_atoms() (in module qmmmrebind.parameterize) get_openmm_energies() (in module qmmmrebind.parameterize) get_proper_dihedrals() (qmmmrebind.parameterize.ParameterizeGuest method) get_qm_energies() (in module qmmmrebind.parameterize) get_qm_host_guest_charges() (qmmmrebind.parameterize.PrepareGaussianHostGuest method) get_qm_mm_regions() (qmmmrebind.parameterize.PrepareQMMM method) get_qm_resids() (qmmmrebind.parameterize.PrepareQMMM method) get_tor_params() (in module qmmmrebind.parameterize) get_torsional_lines() (in module qmmmrebind.parameterize) get_unprocessed_hessian() (qmmmrebind.parameterize.ParameterizeGuest method) (qmmmrebind.parameterize.ParameterizeHost method) get_vibrational_scaling() (in module qmmmrebind.parameterize) get_xyz() (qmmmrebind.parameterize.ParameterizeGuest method) (qmmmrebind.parameterize.ParameterizeHost method) guest_torsion_params (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) guest_write_params (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) GuestAmberXMLAmber (class in qmmmrebind.parameterize), [1]

H

HARTREE_PER_KCAL_MOL (in module qmmmrebind.parameterize) HostAmberXMLAmber (class in qmmmrebind.parameterize), [1]

hostguest_system (in module qmmmrebind.run_qmmmrebind_host_guest), [1] (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine), [1]

K

KCAL_MOL_PER_KJ_MOL (in module qmmmrebind.parameterize)

L

list_diff() (in module qmmmrebind.parameterize) list_hartree_kcal() (in module qmmmrebind.parameterize)

list_kJ_kcal() (in module qmmmrebind.parameterize) list_to_dict() (in module qmmmrebind.parameterize)

M

merge_qm_params() (qmmmrebind.parameterize.SystemAmberSystem method) merge_topology_files() (qmmmrebind.parameterize.MergeHostGuestTopology method) merge_topology_files_system_solvent() (qmmmrebind.parameterize.PrepareSolvatedParams method) MergeHostGuestTopology (class in qmmmrebind.parameterize), [1] method_basis_scale_dict (in module qmmmrebind.parameterize) module qmmmrebind qmmmrebind.parameterize, [1] qmmmrebind.run_qmmmrebind_host_guest qmmmrebind.run_qmmmrebind_trypsin_benzamidine

module_path (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) move_qm_files() (in module qmmmrebind.parameterize) move_qmmmmrebind_files() (in module qmmmrebind.parameterize) move_qmmmrebind_files() (in module qmmmrebind.parameterize)

O

objective_function() (in module qmmmrebind.parameterize)

P

parameterize_solvent_pdb() (qmmmrebind.parameterize.PrepareSolvatedParams method) ParameterizeGuest (class in qmmmrebind.parameterize), [1] ParameterizeHost (class in qmmmrebind.parameterize), [1] params_guest (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) params_host (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) parser (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine)

path_join (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) PrepareGaussianGuest (class in qmmmrebind.parameterize), [1] PrepareGaussianHost (class in qmmmrebind.parameterize) PrepareGaussianHostGuest (class in qmmmrebind.parameterize), [1] PrepareQMMM (class in qmmmrebind.parameterize), [1] PrepareSolvatedParams (class in qmmmrebind.parameterize) prmtop_calibration() (in module qmmmrebind.parameterize) pwd_qmmmrebind (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine)

Q

qm_guest (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) qm_host (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) qm_system (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) qmmmrebind module

qmmmrebind.parameterize module, [1] qmmmrebind.run_qmmmrebind_host_guest module qmmmrebind.run_qmmmrebind_trypsin_benzamidine module qmmmrebindpdb (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine)

R

RADIANS_PER_DEGREE (in module qmmmrebind.parameterize) realign_guest() (qmmmrebind.parameterize.PrepareQMMM method) relax_init_structure() (in module qmmmrebind.parameterize) remove_bad_angle_params() (in module qmmmrebind.parameterize) remove_mm_files() (in module qmmmrebind.parameterize) reverse_list() (in module qmmmrebind.parameterize) run_gaussian() (qmmmrebind.parameterize.PrepareGaussianGuest method) (qmmmrebind.parameterize.PrepareGaussianHost method) (qmmmrebind.parameterize.PrepareGaussianHostGuest method) run_openmm_prmtop_inpcrd() (in module qmmmrebind.parameterize) (qmmmrebind.parameterize.RunOpenMMSims method)

run_openmm_prmtop_pdb() (in module qmmmrebind.parameterize) (qmmmrebind.parameterize.RunOpenMMSims method) run_openmm_solvent_prmtop_inpcrd() (qmmmrebind.parameterize.PrepareSolvatedParams method) run_openmm_solvent_prmtop_pdb() (qmmmrebind.parameterize.PrepareSolvatedParams method) run_openmm_system_solvent_prmtop_inpcrd() (qmmmrebind.parameterize.PrepareSolvatedParams method) run_openmm_system_solvent_prmtop_pdb() (qmmmrebind.parameterize.PrepareSolvatedParams method) run_openmm_xml_pdb() (qmmmrebind.parameterize.RunOpenMMSims method) run_torsion_sim() (qmmmrebind.parameterize.TorsionDriveSims method) RunOpenMMSims (class in qmmmrebind.parameterize), [1]

S

save_amber_params() (qmmmrebind.parameterize.GuestAmberXMLAmber method) (qmmmrebind.parameterize.HostAmberXMLAmber method) (qmmmrebind.parameterize.SystemAmberSystem method) (qmmmrebind.parameterize.SystemGuestAmberSystem method) save_amber_params_non_qm_charges() (qmmmrebind.parameterize.GuestAmberXMLAmber method) (qmmmrebind.parameterize.SystemAmberSystem method) (qmmmrebind.parameterize.SystemGuestAmberSystem method) save_host_mm_regions_pdbs() (qmmmrebind.parameterize.PrepareQMMM method) save_host_pdbs() (qmmmrebind.parameterize.PrepareQMMM method)

scale_list() (in module qmmmrebind.parameterize) search_in_file() (in module qmmmrebind.parameterize) serialize_system() (qmmmrebind.parameterize.HostAmberXMLAmber method) singular_resid() (in module qmmmrebind.parameterize) system (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) system_guest (in module qmmmrebind.run_qmmmrebind_host_guest) (in module qmmmrebind.run_qmmmrebind_trypsin_benzamidine) SystemAmberSystem (class in qmmmrebind.parameterize) SystemGuestAmberSystem (class in qmmmrebind.parameterize)

T

torsiondrive_input_to_xyz() (in module qmmmrebind.parameterize) TorsionDriveParams (class in qmmmrebind.parameterize), [1]

TorsionDriveSims (class in qmmmrebind.parameterize), [1] truncate() (in module qmmmrebind.parameterize)

U

u_PA_from_angles() (in module qmmmrebind.parameterize), [1]

uniq() (in module qmmmrebind.parameterize) unit_vector_N() (in module qmmmrebind.parameterize), [1]

V

versions (in module qmmmrebind)

W

write_guest_params_non_zero() (qmmmrebind.parameterize.SystemAmberSystem method) (qmmmrebind.parameterize.SystemGuestAmberSystem method) write_host_params() (qmmmrebind.parameterize.SystemAmberSystem method) write_input() (qmmmrebind.parameterize.PrepareGaussianGuest method) (qmmmrebind.parameterize.PrepareGaussianHost method) (qmmmrebind.parameterize.PrepareGaussianHostGuest method) write_intermediate_reparameterised_system_xml() (qmmmrebind.parameterize.GuestAmberXMLAmber method) (qmmmrebind.parameterize.SystemAmberSystem method) (qmmmrebind.parameterize.SystemGuestAmberSystem method) write_psi4_input() (qmmmrebind.parameterize.TorsionDriveSims method) write_reparameterised_system_xml() (qmmmrebind.parameterize.GuestAmberXMLAmber method) (qmmmrebind.parameterize.HostAmberXMLAmber method) (qmmmrebind.parameterize.SystemAmberSystem method) (qmmmrebind.parameterize.SystemGuestAmberSystem method)

write_reparams_torsion_lines() (qmmmrebind.parameterize.TorsionDriveParams method) write_reparams_torsion_lines_charged() (qmmmrebind.parameterize.TorsionDriveParams method) write_system_params() (qmmmrebind.parameterize.GuestAmberXMLAmber method) (qmmmrebind.parameterize.HostAmberXMLAmber method) write_tor_params_txt() (qmmmrebind.parameterize.TorsionDriveSims method) write_torsion_drive_run_file() (qmmmrebind.parameterize.TorsionDriveSims method) write_torsional_reparams() (qmmmrebind.parameterize.SystemAmberSystem method) (qmmmrebind.parameterize.SystemGuestAmberSystem method) (qmmmrebind.parameterize.TorsionDriveParams method) write_torsional_reparams_intermediate() (qmmmrebind.parameterize.SystemAmberSystem method) (qmmmrebind.parameterize.SystemGuestAmberSystem method)

X

xyz_to_pdb() (in module qmmmrebind.parameterize)