Index

_

__init__() (janus.mm_wrapper.MMWrapper method) (janus.mm_wrapper.OpenMMWrapper method) (janus.qm_wrapper.Psi4Wrapper method) (janus.qm_wrapper.QMWrapper method) (janus.qmmm.AQMMM method) (janus.qmmm.DAS method) (janus.qmmm.HotSpot method) (janus.qmmm.OniomXS method) (janus.qmmm.PAP method) (janus.qmmm.QMMM method) (janus.qmmm.SAP method)

A

AQMMM (class in janus.qmmm), [1]

au_bohr_to_kjmol_nm (janus.mm_wrapper.MMWrapper attribute)

B

Buffer (class in janus.system) build_qm_param() (janus.mm_wrapper.MMWrapper method) (janus.qm_wrapper.Psi4Wrapper method) (janus.qm_wrapper.QMWrapper method)

C

compute_COM() (janus.qmmm.AQMMM method) compute_energy() (janus.qm_wrapper.Psi4Wrapper method) compute_energy_and_charges() (janus.qm_wrapper.Psi4Wrapper method) compute_gradient() (janus.qm_wrapper.Psi4Wrapper method) compute_gradients() (janus.qmmm.QMMM method) compute_info() (janus.mm_wrapper.MMWrapper method) (janus.mm_wrapper.OpenMMWrapper method) (janus.qm_wrapper.Psi4Wrapper method) (janus.qm_wrapper.QMWrapper method) compute_lamda_i() (janus.qmmm.AQMMM method) (janus.qmmm.DAS method) (janus.qmmm.HotSpot method) compute_scale_factor_g() (janus.system.System method) compute_scf_charges() (janus.qm_wrapper.Psi4Wrapper method)

compute_sf_gradient() (janus.qmmm.PAP method) (janus.qmmm.SAP method) compute_zero_energy() (janus.qmmm.AQMMM method) convert_input() (janus.mm_wrapper.MMWrapper method) (janus.mm_wrapper.OpenMMWrapper method) (janus.qm_wrapper.QMWrapper method) (janus.qmmm.QMMM method) convert_trajectory() (janus.mm_wrapper.MMWrapper method) (janus.mm_wrapper.OpenMMWrapper method) (janus.qm_wrapper.QMWrapper method) create_modeller() (janus.mm_wrapper.OpenMMWrapper method) create_new_residue_template() (janus.mm_wrapper.OpenMMWrapper method) create_openmm_simulation() (janus.mm_wrapper.OpenMMWrapper method) create_openmm_system() (janus.mm_wrapper.OpenMMWrapper method)

D

DAS (class in janus.qmmm), [1]

define_buffer_zone() (janus.qmmm.AQMMM method) delete_atoms() (janus.mm_wrapper.OpenMMWrapper method)

E

edit_atoms() (janus.qmmm.AQMMM method)

electrostatic() (janus.qmmm.QMMM method)

F

find_boundary_bonds() (janus.qmmm.QMMM method)

find_buffer_atoms() (janus.qmmm.AQMMM method)

G

get_combos() (janus.qmmm.DAS method) (janus.qmmm.PAP method) (janus.qmmm.SAP method) get_energy_and_gradient() (janus.mm_wrapper.MMWrapper method) (janus.qm_wrapper.QMWrapper method) get_external_charges() (janus.qmmm.QMMM method) get_forces() (janus.qmmm.QMMM method) get_geom_from_trajectory() (janus.mm_wrapper.MMWrapper method) (janus.qm_wrapper.QMWrapper method) get_main_charges() (janus.mm_wrapper.MMWrapper method) (janus.mm_wrapper.OpenMMWrapper method) (janus.qm_wrapper.QMWrapper method)

get_main_info() (janus.mm_wrapper.MMWrapper method) (janus.mm_wrapper.OpenMMWrapper method) (janus.qm_wrapper.QMWrapper method) get_redistributed_positions() (janus.qmmm.QMMM method) get_residue_info() (janus.qmmm.AQMMM method) get_Rmax() (janus.qmmm.AQMMM method) get_Rmin() (janus.qmmm.AQMMM method) get_state_info() (janus.mm_wrapper.OpenMMWrapper method) get_switching_function() (janus.qmmm.OniomXS method) get_switching_functions() (janus.qmmm.SAP method) get_wrappers() (janus.initializer.Initializer method) get_zero_energy() (janus.qmmm.AQMMM method)

H

HotSpot (class in janus.qmmm), [1]

I

initialize() (janus.mm_wrapper.MMWrapper method) (janus.mm_wrapper.OpenMMWrapper method) (janus.qm_wrapper.QMWrapper method)

initialize_wrappers() (janus.initializer.Initializer method) Initializer (class in janus.initializer)

J

janus.driver (module), [1]

janus.initializer (module) janus.system (module)

K

keep_atoms() (janus.mm_wrapper.OpenMMWrapper method)

kjmol_nm_to_au_bohr (janus.mm_wrapper.MMWrapper attribute) kjmol_to_au (janus.mm_wrapper.MMWrapper attribute)

L

load_param() (janus.initializer.Initializer method)

M

make_primary_subsys_trajectory() (janus.qmmm.QMMM method) make_second_subsys_trajectory() (janus.qmmm.QMMM method)

mechanical() (janus.qmmm.QMMM method) MMWrapper (class in janus.mm_wrapper), [1]

N

nm_to_angstrom (janus.mm_wrapper.MMWrapper attribute) (janus.qmmm.AQMMM attribute)

nm_to_bohr (janus.mm_wrapper.MMWrapper attribute)

O

OniomXS (class in janus.qmmm), [1] OpenMMWrapper (class in janus.mm_wrapper), [1]

optimize_geometry() (janus.mm_wrapper.MMWrapper method) (janus.qm_wrapper.Psi4Wrapper method) (janus.qm_wrapper.QMWrapper method)

P

PAP (class in janus.qmmm), [1] partition() (janus.qmmm.AQMMM method) (janus.qmmm.DAS method) (janus.qmmm.HotSpot method) (janus.qmmm.OniomXS method) (janus.qmmm.PAP method) (janus.qmmm.SAP method)

prepare_link_atom() (janus.qmmm.QMMM method) Psi4Wrapper (class in janus.qm_wrapper), [1]

Q

QMMM (class in janus.qmmm), [1]

QMWrapper (class in janus.qm_wrapper), [1]

R

restart() (janus.mm_wrapper.OpenMMWrapper method) run_aqmmm() (janus.qmmm.AQMMM method) (janus.qmmm.DAS method) (janus.qmmm.HotSpot method) (janus.qmmm.OniomXS method) (janus.qmmm.PAP method) (janus.qmmm.SAP method)

run_janus() (in module janus.driver) run_qmmm() (janus.qmmm.AQMMM method) (janus.qmmm.QMMM method) run_simulation() (in module janus.driver) run_single_point() (in module janus.driver)

S

SAP (class in janus.qmmm), [1] set_attributes() (janus.initializer.Initializer method) set_charge_zero() (janus.mm_wrapper.OpenMMWrapper method) set_external_charges() (janus.mm_wrapper.MMWrapper method) (janus.mm_wrapper.OpenMMWrapper method) (janus.qm_wrapper.QMWrapper method) set_LJ_zero() (janus.mm_wrapper.OpenMMWrapper method) set_qm_geometry() (janus.mm_wrapper.MMWrapper method) (janus.qm_wrapper.QMWrapper method)

set_Rmax() (janus.qmmm.AQMMM method) set_Rmin() (janus.qmmm.AQMMM method) set_up_psi4() (janus.qm_wrapper.Psi4Wrapper method) set_up_reporters() (janus.mm_wrapper.MMWrapper method) (janus.mm_wrapper.OpenMMWrapper method) (janus.qm_wrapper.QMWrapper method) System (class in janus.system)

T

take_step() (janus.mm_wrapper.MMWrapper method) (janus.mm_wrapper.OpenMMWrapper method) (janus.qm_wrapper.QMWrapper method)

take_updated_step() (janus.mm_wrapper.OpenMMWrapper method)

U

update_forces() (janus.mm_wrapper.OpenMMWrapper method)

update_traj() (janus.qmmm.QMMM method)

W

write_pdb() (janus.mm_wrapper.OpenMMWrapper method)