Index

A

A_c() (in module alchemlyb.convergence) ABFE (class in alchemlyb.workflows) 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 alchemlyb.workflows.base module

B

BAR (class in alchemlyb.estimators)

C

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

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

D

d_delta_f_ (alchemlyb.estimators.BAR attribute) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.TI attribute) decorrelate_dhdl() (in module alchemlyb.preprocessing.subsampling) decorrelate_u_nk() (in module alchemlyb.preprocessing.subsampling) delta_f_ (alchemlyb.estimators.BAR attribute) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.TI attribute)

dhdl (alchemlyb.estimators.TI attribute) dhdl2series() (in module alchemlyb.preprocessing.subsampling) dHdl_list (alchemlyb.workflows.ABFE attribute) (alchemlyb.workflows.base.WorkflowBase attribute), [1] dHdl_sample_list (alchemlyb.workflows.ABFE attribute) (alchemlyb.workflows.base.WorkflowBase attribute), [1]

E

equilibrium_detection() (in module alchemlyb.preprocessing.subsampling) estimate() (alchemlyb.workflows.ABFE method) (alchemlyb.workflows.base.WorkflowBase method) estimator (alchemlyb.workflows.ABFE attribute) extract() (in module alchemlyb.parsing.amber) (in module alchemlyb.parsing.gmx) (in module alchemlyb.parsing.gomc) (in module alchemlyb.parsing.namd)

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.ABFE attribute) (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) fwdrev_cumavg_Rc() (in module alchemlyb.convergence)

G

generate_result() (alchemlyb.workflows.ABFE method) 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)

L

logger (alchemlyb.workflows.ABFE attribute)

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 alchemlyb.workflows.base

O

overlap_matrix (alchemlyb.estimators.MBAR property)

P

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

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

R

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

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

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_nk2series() (in module alchemlyb.preprocessing.subsampling) u_nk_list (alchemlyb.workflows.ABFE attribute) (alchemlyb.workflows.base.WorkflowBase attribute), [1]

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

W

WorkflowBase (class in alchemlyb.workflows.base)