Index

A

alchemlyb.convergence module alchemlyb.convergence.convergence module alchemlyb.estimators module alchemlyb.parsing module alchemlyb.parsing.amber module alchemlyb.parsing.gmx module alchemlyb.parsing.gomc module

alchemlyb.parsing.namd module alchemlyb.postprocessors module alchemlyb.postprocessors.units module alchemlyb.preprocessing module alchemlyb.preprocessing.subsampling module alchemlyb.visualisation module AutoMBAR (class in alchemlyb.estimators)

B

BAR (class in alchemlyb.estimators)

C

check_convergence() (alchemlyb.workflows.base.WorkflowBase method)

concat() (in module alchemlyb) convergence (alchemlyb.workflows.base.WorkflowBase attribute), [1]

D

d_delta_f_ (alchemlyb.estimators.BAR attribute) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.TI attribute) delta_f_ (alchemlyb.estimators.BAR attribute) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.TI attribute)

dhdl (alchemlyb.estimators.TI attribute) dHdl_list (alchemlyb.workflows.base.WorkflowBase attribute), [1] dHdl_sample_list (alchemlyb.workflows.base.WorkflowBase attribute), [1]

E

equilibrium_detection() (in module alchemlyb.preprocessing.subsampling) estimate() (alchemlyb.workflows.base.WorkflowBase method) extract_dHdl() (in module alchemlyb.parsing.amber) (in module alchemlyb.parsing.gmx) (in module alchemlyb.parsing.gomc)

extract_u_nk() (in module alchemlyb.parsing.amber) (in module alchemlyb.parsing.gmx) (in module alchemlyb.parsing.gomc) (in module alchemlyb.parsing.namd)

F

file_list (alchemlyb.workflows.base.WorkflowBase attribute) fit() (alchemlyb.estimators.BAR method) (alchemlyb.estimators.MBAR method) (alchemlyb.estimators.TI method)

forward_backward_convergence() (in module alchemlyb.convergence)

G

get_params() (alchemlyb.estimators.BAR method) (alchemlyb.estimators.MBAR method) (alchemlyb.estimators.TI method)

get_unit_converter() (in module alchemlyb.postprocessors.units)

K

kJ2kcal (in module alchemlyb.postprocessors.units)

M

MBAR (class in alchemlyb.estimators) module alchemlyb.convergence alchemlyb.convergence.convergence alchemlyb.estimators alchemlyb.parsing alchemlyb.parsing.amber alchemlyb.parsing.gmx alchemlyb.parsing.gomc alchemlyb.parsing.namd alchemlyb.postprocessors alchemlyb.postprocessors.units alchemlyb.preprocessing alchemlyb.preprocessing.subsampling alchemlyb.visualisation

O

overlap_matrix (alchemlyb.estimators.MBAR property)

P

pass_attrs() (in module alchemlyb) plot() (alchemlyb.workflows.base.WorkflowBase method) plot_convergence() (in module alchemlyb.visualisation)

plot_dF_state() (in module alchemlyb.visualisation) plot_mbar_overlap_matrix() (in module alchemlyb.visualisation) plot_ti_dhdl() (in module alchemlyb.visualisation) preprocess() (alchemlyb.workflows.base.WorkflowBase method)

R

R_kJmol (in module alchemlyb.postprocessors.units) read() (alchemlyb.workflows.base.WorkflowBase method)

result (alchemlyb.workflows.base.WorkflowBase attribute), [1] run() (alchemlyb.workflows.base.WorkflowBase method)

S

separate_dhdl() (alchemlyb.estimators.TI method) set_params() (alchemlyb.estimators.BAR method) (alchemlyb.estimators.MBAR method) (alchemlyb.estimators.TI method)

slicing() (in module alchemlyb.preprocessing.subsampling) states_ (alchemlyb.estimators.BAR attribute) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.TI attribute) statistical_inefficiency() (in module alchemlyb.preprocessing.subsampling)

T

theta_ (alchemlyb.estimators.MBAR attribute) TI (class in alchemlyb.estimators)

to_kcalmol() (in module alchemlyb.postprocessors.units) to_kJmol() (in module alchemlyb.postprocessors.units) to_kT() (in module alchemlyb.postprocessors.units)

U

u_nk_list (alchemlyb.workflows.base.WorkflowBase attribute), [1]

u_nk_sample_list (alchemlyb.workflows.base.WorkflowBase attribute), [1]

W

WorkflowBase (class in alchemlyb.workflows.base)