alchemlyb
User Documentation
Installing alchemlyb
Tutorial
Parsing data files
Preprocessing datasets
Using estimators to obtain free energies
Assessing convergence
Tools for postprocessing
Visualisation of the results
Automatic workflow
Miscellaneous
References
For Developers
API principles
alchemlyb
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
W
_
__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]