Index

_

__init__() (alchemlyb.estimators.BAR method) (alchemlyb.estimators.MBAR method) (alchemlyb.estimators.TI method) (alchemlyb.estimators.TI_GQ method) (alchemlyb.parsing.amber.FEData method) (alchemlyb.parsing.amber.SectionParser method) (alchemlyb.workflows.ABFE method) (alchemlyb.workflows.base.WorkflowBase method), [1]

__init_subclass__() (alchemlyb.estimators.BAR class method) (alchemlyb.estimators.MBAR class method) (alchemlyb.estimators.TI class method) (alchemlyb.estimators.TI_GQ class method) __next__() (alchemlyb.parsing.amber.SectionParser method)

A

A_c() (in module alchemlyb.convergence) (in module alchemlyb.convergence.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.lammps 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) bar_intervall (alchemlyb.parsing.amber.FEData attribute)

beta_from_units() (in module alchemlyb.parsing.lammps), [1] block_average() (in module alchemlyb.convergence) (in module alchemlyb.convergence.convergence)

C

check_convergence() (alchemlyb.workflows.ABFE method) (alchemlyb.workflows.base.WorkflowBase method), [1] clambda (alchemlyb.parsing.amber.FEData attribute) close() (alchemlyb.parsing.amber.SectionParser method)

concat() (in module alchemlyb) convergence (alchemlyb.workflows.ABFE attribute), [1] (alchemlyb.workflows.base.WorkflowBase attribute), [1], [2], [3] convert_to_pandas() (in module alchemlyb.parsing.amber)

D

d_delta_f_ (alchemlyb.estimators.BAR attribute) (alchemlyb.estimators.BAR property) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.MBAR property) (alchemlyb.estimators.TI attribute) (alchemlyb.estimators.TI property) (alchemlyb.estimators.TI_GQ attribute) (alchemlyb.estimators.TI_GQ property) d_delta_h_ (alchemlyb.estimators.BAR property) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.MBAR property) (alchemlyb.estimators.TI property) (alchemlyb.estimators.TI_GQ property) d_delta_sT_ (alchemlyb.estimators.BAR property) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.MBAR property) (alchemlyb.estimators.TI property) (alchemlyb.estimators.TI_GQ property) decorrelate_dhdl() (in module alchemlyb.preprocessing.subsampling), [1] decorrelate_u_nk() (in module alchemlyb.preprocessing.subsampling), [1] delta_f_ (alchemlyb.estimators.BAR attribute) (alchemlyb.estimators.BAR property) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.MBAR property) (alchemlyb.estimators.TI attribute) (alchemlyb.estimators.TI property) (alchemlyb.estimators.TI_GQ attribute) (alchemlyb.estimators.TI_GQ property)

delta_h_ (alchemlyb.estimators.BAR property) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.MBAR property) (alchemlyb.estimators.TI property) (alchemlyb.estimators.TI_GQ property) delta_sT_ (alchemlyb.estimators.BAR property) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.MBAR property) (alchemlyb.estimators.TI property) (alchemlyb.estimators.TI_GQ property) dhdl (alchemlyb.estimators.TI attribute) (alchemlyb.estimators.TI_GQ attribute) dhdl2series() (in module alchemlyb.preprocessing.subsampling), [1] dHdl_list (alchemlyb.workflows.ABFE attribute) (alchemlyb.workflows.base.WorkflowBase attribute), [1], [2], [3] dHdl_sample_list (alchemlyb.workflows.ABFE attribute) (alchemlyb.workflows.base.WorkflowBase attribute), [1], [2], [3] dt (alchemlyb.parsing.amber.FEData attribute)

E

energy_from_units() (in module alchemlyb.parsing.lammps) equilibrium_detection() (in module alchemlyb.preprocessing.subsampling), [1] estimate() (alchemlyb.workflows.ABFE method) (alchemlyb.workflows.base.WorkflowBase method), [1] estimator (alchemlyb.workflows.ABFE attribute) extract() (in module alchemlyb.parsing.amber), [1] (in module alchemlyb.parsing.gmx), [1] (in module alchemlyb.parsing.gomc), [1] (in module alchemlyb.parsing.namd), [1] extract_dHdl() (in module alchemlyb.parsing.amber), [1] (in module alchemlyb.parsing.gmx), [1] (in module alchemlyb.parsing.gomc), [1] (in module alchemlyb.parsing.lammps), [1] (in module alchemlyb.parsing.parquet)

extract_dHdl_from_u_n() (in module alchemlyb.parsing.lammps), [1] extract_H() (in module alchemlyb.parsing.lammps), [1] extract_section() (alchemlyb.parsing.amber.SectionParser method) extract_u_nk() (in module alchemlyb.parsing.amber), [1] (in module alchemlyb.parsing.gmx), [1] (in module alchemlyb.parsing.gomc), [1] (in module alchemlyb.parsing.lammps), [1] (in module alchemlyb.parsing.namd), [1] (in module alchemlyb.parsing.parquet) extract_u_nk_from_u_n() (in module alchemlyb.parsing.lammps), [1]

F

FEData (class in alchemlyb.parsing.amber) file_list (alchemlyb.workflows.ABFE attribute) (alchemlyb.workflows.base.WorkflowBase attribute), [1] file_validation() (in module alchemlyb.parsing.amber) fit() (alchemlyb.estimators.BAR method) (alchemlyb.estimators.MBAR method) (alchemlyb.estimators.TI method) (alchemlyb.estimators.TI_GQ method)

forward_backward_convergence() (in module alchemlyb.convergence) (in module alchemlyb.convergence.convergence) fwdrev_cumavg_Rc() (in module alchemlyb.convergence) (in module alchemlyb.convergence.convergence)

G

generate_result() (alchemlyb.workflows.ABFE method) get_bar_lambdas() (in module alchemlyb.parsing.lammps) get_metadata_routing() (alchemlyb.estimators.BAR method) (alchemlyb.estimators.MBAR method) (alchemlyb.estimators.TI method) (alchemlyb.estimators.TI_GQ method)

get_params() (alchemlyb.estimators.BAR method) (alchemlyb.estimators.MBAR method) (alchemlyb.estimators.TI method) (alchemlyb.estimators.TI_GQ method) get_unit_converter() (in module alchemlyb.postprocessors.units), [1] gradients (alchemlyb.parsing.amber.FEData attribute)

H

have_mbar (alchemlyb.parsing.amber.FEData attribute)

K

kJ2kcal (in module alchemlyb.postprocessors.units), [1]

L

lambda_from_filename() (in module alchemlyb.parsing.lammps)

logger (alchemlyb.workflows.ABFE attribute)

M

MBAR (class in alchemlyb.estimators) mbar_energies (alchemlyb.parsing.amber.FEData attribute) mbar_lambda_idx (alchemlyb.parsing.amber.FEData attribute) mbar_lambdas (alchemlyb.parsing.amber.FEData attribute) module alchemlyb.convergence alchemlyb.convergence.convergence alchemlyb.estimators alchemlyb.parsing alchemlyb.parsing.amber alchemlyb.parsing.gmx alchemlyb.parsing.gomc alchemlyb.parsing.lammps alchemlyb.parsing.namd alchemlyb.postprocessors alchemlyb.postprocessors.units alchemlyb.preprocessing alchemlyb.preprocessing.subsampling alchemlyb.visualisation alchemlyb.workflows.base

N

ntpr (alchemlyb.parsing.amber.FEData attribute)

O

overlap_matrix (alchemlyb.estimators.MBAR property)

P

pass_attrs() (in module alchemlyb) plot() (alchemlyb.workflows.ABFE method) (alchemlyb.workflows.base.WorkflowBase method), [1] plot_block_average() (in module alchemlyb.visualisation) 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), [1]

R

R_kJmol (in module alchemlyb.postprocessors.units), [1] read() (alchemlyb.workflows.ABFE method) (alchemlyb.workflows.base.WorkflowBase method), [1]

result (alchemlyb.workflows.base.WorkflowBase attribute), [1], [2], [3] run() (alchemlyb.workflows.ABFE method) (alchemlyb.workflows.base.WorkflowBase method), [1]

S

SectionParser (class in alchemlyb.parsing.amber) separate_dhdl() (alchemlyb.estimators.TI method) separate_mean_variance() (alchemlyb.estimators.TI_GQ static method) set_fit_request() (alchemlyb.estimators.BAR method) (alchemlyb.estimators.MBAR method) (alchemlyb.estimators.TI method) (alchemlyb.estimators.TI_GQ method) set_params() (alchemlyb.estimators.BAR method) (alchemlyb.estimators.MBAR method) (alchemlyb.estimators.TI method) (alchemlyb.estimators.TI_GQ method) skip_after() (alchemlyb.parsing.amber.SectionParser method)

skip_lines() (alchemlyb.parsing.amber.SectionParser method) slicing() (in module alchemlyb.preprocessing.subsampling), [1] special_points (alchemlyb.estimators.TI_GQ attribute) states_ (alchemlyb.estimators.BAR attribute) (alchemlyb.estimators.BAR property) (alchemlyb.estimators.MBAR attribute) (alchemlyb.estimators.MBAR property) (alchemlyb.estimators.TI attribute) (alchemlyb.estimators.TI property) (alchemlyb.estimators.TI_GQ attribute) (alchemlyb.estimators.TI_GQ property) statistical_inefficiency() (in module alchemlyb.preprocessing.subsampling), [1] summary (alchemlyb.workflows.ABFE attribute), [1]

T

T (alchemlyb.parsing.amber.FEData attribute) t0 (alchemlyb.parsing.amber.FEData attribute) theta_ (alchemlyb.estimators.MBAR attribute) TI (class in alchemlyb.estimators)

TI_GQ (class in alchemlyb.estimators) to_kcalmol() (in module alchemlyb.postprocessors.units), [1] to_kJmol() (in module alchemlyb.postprocessors.units), [1] to_kT() (in module alchemlyb.postprocessors.units), [1] tuple_from_filename() (in module alchemlyb.parsing.lammps)

U

u_nk2series() (in module alchemlyb.preprocessing.subsampling), [1] u_nk_list (alchemlyb.workflows.ABFE attribute) (alchemlyb.workflows.base.WorkflowBase attribute), [1], [2], [3]

u_nk_sample_list (alchemlyb.workflows.ABFE attribute) (alchemlyb.workflows.base.WorkflowBase attribute), [1], [2], [3] update_units() (alchemlyb.workflows.ABFE method)

W

WorkflowBase (class in alchemlyb.workflows.base), [1]