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A
absolute() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
add_argument() (protomslib.free_energy.free_energy_argument_parser.FEArgumentParser method)
add_blank_row() (protomslib.free_energy.table.Table method)
add_data() (protomslib.free_energy.free_energy_base.BAR method)
(protomslib.free_energy.free_energy_base.Estimator method)
(protomslib.free_energy.free_energy_base.MBAR method)
(protomslib.free_energy.free_energy_base.TI method)
(protomslib.free_energy.gcmc_free_energy_base.GCI method)
(protomslib.free_energy.gcmc_free_energy_base.GCMCMBAR method)
(protomslib.free_energy.table.Column method)
(protomslib.free_energy.table.SubColumn method)
add_row() (protomslib.free_energy.table.Table method)
addAtom() (protomslib.simulationobjects.Residue method)
alignhydrogens() (in module protomslib.prepare.water)
angle() (in module protomslib.simulationobjects)
angle_atms() (in module protomslib.simulationobjects)
append() (protomslib.simulationobjects.TemplateFile method)
as_floats() (protomslib.free_energy.free_energy_base.Series method)
assign_paramobj() (protomslib.simulationobjects.TemplateFile method)
Atom (class in protomslib.simulationobjects)
AtomSet (class in protomslib.simulationobjects)
B
B_to_chemical_potential() (protomslib.free_energy.gcmc_free_energy_base.GCMCMBAR method)
B_values (protomslib.free_energy.gcmc_free_energy_base.GCMCResult attribute)
BAR (class in protomslib.free_energy.free_energy_base)
BaseResult (class in protomslib.free_energy.free_energy_base)
Bs (protomslib.free_energy.gcmc_free_energy_base.GCMCMBAR attribute)
C
calculate() (protomslib.free_energy.free_energy_base.BAR method)
(protomslib.free_energy.free_energy_base.Estimator method)
(protomslib.free_energy.free_energy_base.FreeEnergyCalculation method)
(protomslib.free_energy.free_energy_base.MBAR method)
(protomslib.free_energy.free_energy_base.TI method)
(protomslib.free_energy.gcmc_free_energy_base.GCI method)
(protomslib.free_energy.gcmc_free_energy_base.GCMCMBAR method)
(protomslib.free_energy.gcmc_free_energy_base.TitrationCalculation method)
check_clashes() (protomslib.free_energy.free_energy_argument_parser.FEArgumentParser method)
clear() (protomslib.command.ProtoMSSimulation method)
clear_gcmcbox() (in module protomslib.gcmc)
color() (in module protomslib.simulationobjects)
Column (class in protomslib.free_energy.table)
convertwater() (in module protomslib.prepare.water)
copy() (protomslib.simulationobjects.PDBFile method)
D
dG (protomslib.free_energy.free_energy_base.PMF attribute)
(protomslib.free_energy.free_energy_base.Result attribute)
DihParameter (class in protomslib.simulationobjects)
DihTerm (class in protomslib.simulationobjects)
distribute_particles() (in module protomslib.gcmc)
DualTopology (class in protomslib.command)
E
EnergyResults (class in protomslib.simulationobjects)
epoch() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
Equilibration (class in protomslib.command)
equilibrium_B (protomslib.free_energy.gcmc_free_energy_base.GCMCPMF attribute)
(protomslib.free_energy.gcmc_free_energy_base.GCMCResult attribute)
equilibrium_B() (protomslib.free_energy.gcmc_free_energy_base.GCMCMBAR method)
Estimator (class in protomslib.free_energy.free_energy_base)
F
FEArgumentParser (class in protomslib.free_energy.free_energy_argument_parser)
find_box() (in module protomslib.simulationobjects)
fit_ensemble() (in module protomslib.free_energy.gcmc_free_energy_base)
fit_offset() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
fit_unit() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
ForceFieldParameter (class in protomslib.simulationobjects)
format_help() (protomslib.simulationobjects.MyArgumentParser method)
formats (protomslib.simulationobjects.ParameterSet attribute)
forward() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
forward_unit() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
FreeEnergyCalculation (class in protomslib.free_energy.free_energy_base)
from_residues() (protomslib.simulationobjects.PDBSet method)
fromData() (protomslib.free_energy.free_energy_base.Quantity static method)
G
GCAPDual (class in protomslib.command)
GCAPSingle (class in protomslib.command)
GCI (class in protomslib.free_energy.gcmc_free_energy_base)
GCMC (class in protomslib.command)
GCMCMBAR (class in protomslib.free_energy.gcmc_free_energy_base)
GCMCPMF (class in protomslib.free_energy.gcmc_free_energy_base)
GCMCResult (class in protomslib.free_energy.gcmc_free_energy_base)
generate_input() (in module protomslib.command)
get_alchemical_arg_parser() (in module protomslib.free_energy.free_energy_base)
get_base_arg_parser() (in module protomslib.free_energy.free_energy_base)
get_gci_arg_parser() (in module protomslib.free_energy.gcmc_free_energy_base)
get_par_by_index() (protomslib.simulationobjects.ParameterSet method)
get_params() (protomslib.simulationobjects.ParameterSet method)
getBox() (protomslib.simulationobjects.PDBFile method)
getCenter() (protomslib.simulationobjects.PDBFile method)
(protomslib.simulationobjects.Residue method)
getElement() (protomslib.simulationobjects.Atom method)
H
huber() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
I
insertion_pmf (protomslib.free_energy.gcmc_free_energy_base.GCMCResult attribute)
insertion_pmf() (in module protomslib.free_energy.gcmc_free_energy_base)
integrated_logistic() (in module protomslib.free_energy.gcmc_free_energy_base)
inverse_slp() (in module protomslib.free_energy.gcmc_free_energy_base)
is_solvent() (in module protomslib.simulationobjects)
isAminoacid() (protomslib.simulationobjects.Residue method)
J
Jaws1 (class in protomslib.command)
Jaws2 (class in protomslib.command)
L
lambdas (protomslib.free_energy.free_energy_base.Result attribute)
logistic() (in module protomslib.free_energy.gcmc_free_energy_base)
M
make_dummy() (in module protomslib.prepare)
make_gcmcbox() (in module protomslib.gcmc)
make_series() (protomslib.simulationobjects.ResultsFile method)
make_softcore() (protomslib.command.DualTopology method)
(protomslib.command.GCAPDual method)
MBAR (class in protomslib.free_energy.free_energy_base)
merge_pdbs() (in module protomslib.simulationobjects)
model (protomslib.free_energy.gcmc_free_energy_base.GCMCResult attribute)
MolTemplate (class in protomslib.simulationobjects)
msd() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
MyArgumentParser (class in protomslib.simulationobjects)
N
N_max (protomslib.free_energy.gcmc_free_energy_base.GCI attribute)
N_min (protomslib.free_energy.gcmc_free_energy_base.GCI attribute)
O
occupancies (protomslib.free_energy.gcmc_free_energy_base.GCMCResult attribute)
P
Parameter (class in protomslib.simulationobjects)
ParameterSet (class in protomslib.simulationobjects)
parse() (protomslib.simulationobjects.AtomSet method)
(protomslib.simulationobjects.ForceFieldParameter method)
(protomslib.simulationobjects.SnapshotResults method)
(protomslib.simulationobjects.TemplateAtom method)
(protomslib.simulationobjects.TemplateConnectivity method)
(protomslib.simulationobjects.TemplateSoluteAtom method)
parse_args() (protomslib.free_energy.free_energy_argument_parser.FEArgumentParser method)
parse_from() (protomslib.simulationobjects.MolTemplate method)
parse_line() (protomslib.simulationobjects.EnergyResults method)
pdb2pms() (in module protomslib.prepare)
PDBFile (class in protomslib.simulationobjects)
PDBSet (class in protomslib.simulationobjects)
plot() (protomslib.free_energy.free_energy_base.Series method)
plot_insertion_pmf() (in module protomslib.free_energy.gcmc_free_energy_base)
plot_titration() (in module protomslib.free_energy.gcmc_free_energy_base)
PMF (class in protomslib.free_energy.free_energy_base)
pmf (protomslib.free_energy.free_energy_base.Result attribute)
predict() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
print_bequil() (in module protomslib.gcmc)
print_fullhelp() (protomslib.simulationobjects.MyArgumentParser method)
print_help() (protomslib.simulationobjects.MyArgumentParser method)
ProteinLigandSimulation (class in protomslib.command)
protomslib.command (module)
protomslib.free_energy.free_energy_argument_parser (module)
protomslib.free_energy.free_energy_base (module)
protomslib.free_energy.gcmc_free_energy_base (module)
protomslib.free_energy.table (module)
protomslib.gcmc (module)
protomslib.prepare (module)
protomslib.prepare.scoop (module)
protomslib.prepare.water (module)
protomslib.simulationobjects (module)
protomslib.solvate (module)
protomslib.utils (module)
ProtoMSSimulation (class in protomslib.command)
pseudohuber() (in module protomslib.free_energy.gcmc_free_energy_base)
Q
Quantity (class in protomslib.free_energy.free_energy_base)
R
randomise() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
randsearch() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
read() (protomslib.simulationobjects.ParameterSet method)
(protomslib.simulationobjects.PDBFile method)
(protomslib.simulationobjects.PDBSet method)
(protomslib.simulationobjects.RestartFile method)
(protomslib.simulationobjects.ResultsFile method)
(protomslib.simulationobjects.TemplateFile method)
read_convfile() (in module protomslib.prepare)
read_from() (protomslib.simulationobjects.PDBFile method)
readCommandFile() (protomslib.command.ProtoMSSimulation method)
Residue (class in protomslib.simulationobjects)
RestartFile (class in protomslib.simulationobjects)
RestraintRelease (class in protomslib.command)
Result (class in protomslib.free_energy.free_energy_base)
result_class (protomslib.free_energy.free_energy_base.Estimator attribute)
ResultsFile (class in protomslib.simulationobjects)
rotatesolute() (in module protomslib.prepare.water)
rotatewat() (in module protomslib.prepare.water)
rotmat_x() (in module protomslib.utils)
rotmat_y() (in module protomslib.utils)
rotmat_z() (in module protomslib.utils)
run() (protomslib.command.ProtoMSSimulation method)
(protomslib.free_energy.free_energy_base.FreeEnergyCalculation method)
run_antechamber() (in module protomslib.prepare)
run_parmchk() (in module protomslib.prepare)
S
Sampling (class in protomslib.command)
scoop() (in module protomslib.prepare.scoop)
Series (class in protomslib.free_energy.free_energy_base)
set_jaws2_box() (in module protomslib.prepare.water)
setChunk() (protomslib.command.ProtoMSSimulation method)
setDump() (protomslib.command.ProtoMSSimulation method)
setForceField() (protomslib.command.ProtoMSSimulation method)
setParameter() (protomslib.command.ProtoMSSimulation method)
setProtein() (protomslib.command.ProtoMSSimulation method)
setSolute() (protomslib.command.ProtoMSSimulation method)
setSolvent() (protomslib.command.ProtoMSSimulation method)
setStream() (protomslib.command.ProtoMSSimulation method)
setup_logger() (in module protomslib.simulationobjects)
SetupError
simplex_sample() (in module protomslib.free_energy.gcmc_free_energy_base)
SingleTopology (class in protomslib.command)
Slp (class in protomslib.free_energy.gcmc_free_energy_base)
SnapshotResults (class in protomslib.simulationobjects)
solvate() (in module protomslib.solvate)
spec_string_from_user_input() (protomslib.command.DualTopology method)
(protomslib.command.GCAPDual method)
split_waters() (in module protomslib.prepare.water)
standard_filename() (in module protomslib.simulationobjects)
SubColumn (class in protomslib.free_energy.table)
subset() (protomslib.free_energy.free_energy_base.Estimator method)
T
Table (class in protomslib.free_energy.table)
TemplateAtom (class in protomslib.simulationobjects)
TemplateConnectivity (class in protomslib.simulationobjects)
TemplateFile (class in protomslib.simulationobjects)
TemplateSoluteAtom (class in protomslib.simulationobjects)
TI (class in protomslib.free_energy.free_energy_base)
TitrationCalculation (class in protomslib.free_energy.gcmc_free_energy_base)
train() (protomslib.free_energy.gcmc_free_energy_base.Slp method)
W
width (protomslib.free_energy.table.Column attribute)
write() (protomslib.simulationobjects.PDBFile method)
(protomslib.simulationobjects.PDBSet method)
(protomslib.simulationobjects.TemplateFile method)
write_box() (in module protomslib.simulationobjects)
write_to() (protomslib.simulationobjects.MolTemplate method)
write_zmat() (protomslib.simulationobjects.MolTemplate method)
writeCommandFile() (protomslib.command.ProtoMSSimulation method)
Z
zmat() (protomslib.simulationobjects.TemplateAtom method)
(protomslib.simulationobjects.TemplateSoluteAtom method)
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