Index

A

all_forces: command line option

alternativ_name (protex.residue.Residue property)

C

ChargeReporter (class in protex.reporter) command line option all_forces: frozenset[str]]] int ionic_liquid: to_adapt:

current_charge (protex.residue.Residue property)

D

describeNextReport() (protex.reporter.ChargeReporter method) (protex.reporter.DrudeTemperatureReporter method) (protex.reporter.EnergyReporter method) DrudeTemperatureReporter (class in protex.reporter) dump() (protex.system.ProtexSystem method) (protex.system.ProtexTemplates method) (protex.update.KeepHUpdate method) (protex.update.NaiveMCUpdate method) (protex.update.StateUpdate method) (protex.update.Update method)

E

endstate_charge (protex.residue.Residue property)

EnergyReporter (class in protex.reporter)

F

force_is_valid() (protex.system.ProtexSystem class method)

frozenset[str]]] command line option

G

generate_complete_system() (in module protex.testsystems) generate_h2o_system() (in module protex.testsystems) generate_hpts_meoh_lj04_system() (in module protex.testsystems) generate_hpts_meoh_system() (in module protex.testsystems) generate_hpts_system() (in module protex.testsystems) generate_im1h_fora_system() (in module protex.testsystems) generate_im1h_oac_dummy_system() (in module protex.testsystems) generate_im1h_oac_system() (in module protex.testsystems) generate_single_hpts_meoh_system() (in module protex.testsystems) generate_single_im1h_oac_system() (in module protex.testsystems)

generate_small_box() (in module protex.testsystems) generate_tfa_system() (in module protex.testsystems) get_atom_name_for() (protex.system.ProtexTemplates method) get_charge_template_for() (protex.system.ProtexTemplates method) get_charges() (protex.update.StateUpdate method) get_current_number_of_each_residue_type() (protex.system.ProtexSystem method) get_equivalent_atom_for() (protex.system.ProtexTemplates method) get_num_residues() (protex.update.StateUpdate method) get_residue_name_for_coupled_state() (protex.system.ProtexTemplates method) get_update_value_for() (protex.system.ProtexTemplates method)

H

has_equivalent_atom (protex.residue.Residue property)

has_equivalent_atom() (protex.system.ProtexTemplates method)

I

int command line option

ionic_liquid: command line option

K

KeepHUpdate (class in protex.update)

L

load() (protex.system.ProtexSystem static method) (protex.system.ProtexTemplates static method) (protex.update.KeepHUpdate static method) (protex.update.NaiveMCUpdate static method) (protex.update.StateUpdate static method) (protex.update.Update static method)

load_charmm_files() (in module protex.testsystems) load_updates() (protex.system.ProtexSystem method) loadCheckpoint() (protex.system.ProtexSystem method) loadState() (protex.system.ProtexSystem method)

M

module protex.reporter protex.residue protex.system protex.testsystems protex.update

N

NaiveMCUpdate (class in protex.update)

P

protex.reporter module protex.residue module protex.system module

protex.testsystems module protex.update module ProtexSystem (class in protex.system) ProtexTemplates (class in protex.system)

R

report() (protex.reporter.ChargeReporter method) (protex.reporter.DrudeTemperatureReporter method) (protex.reporter.EnergyReporter method)

Residue (class in protex.residue)

S

save_updates() (protex.system.ProtexSystem method) saveCheckpoint() (protex.system.ProtexSystem method) saveState() (protex.system.ProtexSystem method)

set_update_value_for() (protex.system.ProtexTemplates method) setup_simulation() (in module protex.testsystems) setup_system() (in module protex.testsystems) StateUpdate (class in protex.update)

T

to_adapt: command line option

U

Update (class in protex.update) update() (protex.residue.Residue method) (protex.update.StateUpdate method)

update_context() (protex.system.ProtexSystem method)

W

write_charges() (protex.update.StateUpdate method)

write_psf() (protex.system.ProtexSystem method)