Index

A

AllProtocol (class in endstate_correction.protocol)

AllResults (class in endstate_correction.protocol) AMBERTopology (class in endstate_correction.topology)

B

BaseProtocol (class in endstate_correction.protocol)

BaseResults (class in endstate_correction.protocol) BSSProtocol (class in endstate_correction.protocol)

C

calculate_u_kn() (in module endstate_correction.equ) canvas() (in module endstate_correction) (in module endstate_correction.endstate_correction)

CHARMMTopology (class in endstate_correction.topology) convert_pickle_to_dcd_file() (in module endstate_correction.utils)

E

endstate_correction module endstate_correction.analysis module endstate_correction.constant module endstate_correction.endstate_correction module endstate_correction.equ module endstate_correction.neq module endstate_correction.protocol module endstate_correction.simulation module endstate_correction.simulation.amber module endstate_correction.simulation.base module endstate_correction.simulation.charmm module endstate_correction.smc module endstate_correction.system module endstate_correction.tests module

endstate_correction.tests.test_analysis module endstate_correction.tests.test_endstate_correction module endstate_correction.tests.test_equ module endstate_correction.tests.test_misc module endstate_correction.tests.test_neq module endstate_correction.tests.test_perform_endstate_correction module endstate_correction.tests.test_sampling module endstate_correction.tests.test_simulation module endstate_correction.tests.test_smc module endstate_correction.tests.test_system module endstate_correction.topology module endstate_correction.utils module EndstateCorrectionAMBER (class in endstate_correction.simulation.amber) EndstateCorrectionBase (class in endstate_correction.simulation.base) EndstateCorrectionCHARMM (class in endstate_correction.simulation.charmm) EquResults (class in endstate_correction.protocol)

F

FEPProtocol (class in endstate_correction.protocol)

FEPResults (class in endstate_correction.protocol)

G

gen_box() (in module endstate_correction.system)

get_energy() (in module endstate_correction.system) get_positions() (in module endstate_correction.system)

L

load_endstate_system_and_samples() (in module endstate_correction.tests.test_system)

load_equ_samples() (in module endstate_correction.tests.test_equ)

M

module endstate_correction endstate_correction.analysis endstate_correction.constant endstate_correction.endstate_correction endstate_correction.equ endstate_correction.neq endstate_correction.protocol endstate_correction.simulation endstate_correction.simulation.amber endstate_correction.simulation.base endstate_correction.simulation.charmm endstate_correction.smc endstate_correction.system endstate_correction.tests endstate_correction.tests.test_analysis endstate_correction.tests.test_endstate_correction endstate_correction.tests.test_equ endstate_correction.tests.test_misc endstate_correction.tests.test_neq endstate_correction.tests.test_perform_endstate_correction endstate_correction.tests.test_sampling endstate_correction.tests.test_simulation endstate_correction.tests.test_smc endstate_correction.tests.test_system endstate_correction.topology endstate_correction.utils

N

NEQProtocol (class in endstate_correction.protocol)

NEQResults (class in endstate_correction.protocol)

P

perform_endstate_correction() (in module endstate_correction.protocol) perform_SMC() (endstate_correction.smc.SMC method) perform_switching() (in module endstate_correction.neq)

plot_endstate_correction_results() (in module endstate_correction.analysis) plot_overlap_for_equilibrium_free_energy() (in module endstate_correction.analysis) plot_results_for_equilibrium_free_energy() (in module endstate_correction.analysis)

R

read_box() (in module endstate_correction.system)

Resampler (class in endstate_correction.smc) return_endstate_correction() (in module endstate_correction.analysis)

S

save_pickle_results() (in module endstate_correction.tests.test_endstate_correction) setup_vacuum_simulation() (in module endstate_correction.tests.test_system) setup_waterbox_simulation() (in module endstate_correction.tests.test_system) setup_ZINC00077329_system() (in module endstate_correction.tests.test_system)

SMC (class in endstate_correction.smc) SMCProtocol (class in endstate_correction.protocol) SMCResults (class in endstate_correction.protocol) stratified_resampling() (endstate_correction.smc.Resampler static method) summarize_endstate_correction_results() (in module endstate_correction.analysis)

T

test_ALL_protocol() (in module endstate_correction.tests.test_endstate_correction) test_collect_equ_samples() (in module endstate_correction.tests.test_equ) test_collect_work_values() (in module endstate_correction.tests.test_neq) test_converting() (in module endstate_correction.tests.test_misc) test_each_protocol() (in module endstate_correction.tests.test_endstate_correction) test_endstate_correction_imported() (in module endstate_correction.tests.test_endstate_correction) test_equilibrium_free_energy() (in module endstate_correction.tests.test_equ) test_FEP_protocol() (in module endstate_correction.tests.test_endstate_correction) test_generate_simulation_instances_with_charmmff() (in module endstate_correction.tests.test_system) test_initializing_ZINC00077329_system() (in module endstate_correction.tests.test_system) test_NEQ_protocol() (in module endstate_correction.tests.test_endstate_correction) test_plot_results_for_all_protocol() (in module endstate_correction.tests.test_analysis) test_plot_results_for_FEP_protocol() (in module endstate_correction.tests.test_analysis) test_plot_results_for_NEQ_protocol() (in module endstate_correction.tests.test_analysis)

test_plotting_equilibrium_free_energy() (in module endstate_correction.tests.test_analysis) test_sampling() (in module endstate_correction.tests.test_sampling) test_sanity() (endstate_correction.tests.test_simulation.TestEndstateCorrectionAmber method) (endstate_correction.tests.test_simulation.TestEndstateCorrectionCharmm method) test_simulating() (in module endstate_correction.tests.test_system) test_SMC() (in module endstate_correction.tests.test_smc) test_SMC_algorithm() (in module endstate_correction.tests.test_smc) test_smc_arguments() (in module endstate_correction.tests.test_endstate_correction) test_SMC_protocol() (in module endstate_correction.tests.test_endstate_correction) test_SMC_stratified_resampling() (in module endstate_correction.tests.test_smc) test_switching() (in module endstate_correction.tests.test_neq) TestEndstateCorrectionAmber (class in endstate_correction.tests.test_simulation) TestEndstateCorrectionCharmm (class in endstate_correction.tests.test_simulation) TestPerformCorrection (class in endstate_correction.tests.test_perform_endstate_correction)