blues
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Modules
Nonequilibrium Candidate Monte Carlo (NCMC)
ReportLangevinDynamicsMove
NCMCMove
RandomLigandRotationMove
BLUESSampler
SystemFactory
Integrators
Utilities
Storage
Formats
Developer Guide
UML Diagram
OpenMMTools Objects
Integrators and Moves
BLUESSampler
Initialization
BLUES Iterations
blues
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Index
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Index
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A
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B
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C
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D
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E
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F
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G
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I
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L
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N
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O
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P
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R
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S
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T
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Z
_
_kinetic_energy (blues.integrators.AlchemicalExternalLangevinIntegrator attribute)
A
add_alchemicalLambda() (blues.formats.NetCDF4Traj method)
add_protocolWork() (blues.formats.NetCDF4Traj method)
addBarostat() (in module blues.systemfactory)
addLoggingLevel() (in module blues.storage)
AlchemicalExternalLangevinIntegrator (class in blues.integrators)
alchemicalLambda() (blues.formats.NetCDF4Traj property)
amber_selection_to_atomidx() (in module blues.utils)
apply() (blues.ncmc.NCMCMove method)
(blues.ncmc.ReportLangevinDynamicsMove method)
atom_subset (blues.ncmc.NCMCMove attribute)
(blues.ncmc.RandomLigandRotationMove attribute)
atomidx_to_atomlist() (in module blues.utils)
atomIndexfromTop() (in module blues.utils)
B
blues.formats (module)
blues.integrators (module)
blues.ncmc (module)
blues.storage (module)
blues.systemfactory (module)
blues.utils (module)
BLUESSampler (class in blues.ncmc)
BLUESStateDataStorage (class in blues.storage)
C
check_amber_selection() (in module blues.utils)
collision_rate (blues.ncmc.ReportLangevinDynamicsMove attribute)
context_cache (blues.ncmc.NCMCMove attribute)
(blues.ncmc.RandomLigandRotationMove attribute)
(blues.ncmc.ReportLangevinDynamicsMove attribute)
D
describeNextReport() (blues.storage.BLUESStateDataStorage method)
(blues.storage.NetCDF4Storage method)
E
equil() (blues.ncmc.BLUESSampler method)
F
flush() (blues.formats.NetCDF4Traj method)
format() (blues.formats.LoggerFormatter method)
freeze_atoms() (in module blues.systemfactory)
freeze_radius() (in module blues.systemfactory)
G
generateAlchSystem() (in module blues.systemfactory)
get_data_filename() (in module blues.utils)
getCenterOfMass() (in module blues.utils)
getMasses() (in module blues.utils)
I
init_logger() (in module blues.storage)
L
logger (in module blues.utils)
LoggerFormatter (class in blues.formats)
N
n_steps (blues.ncmc.NCMCMove attribute)
(blues.ncmc.RandomLigandRotationMove attribute)
(blues.ncmc.ReportLangevinDynamicsMove attribute)
NCMCMove (class in blues.ncmc)
NetCDF4Storage (class in blues.storage)
NetCDF4Traj (class in blues.formats)
O
open_new() (blues.formats.NetCDF4Traj class method)
P
parse_unit_quantity() (in module blues.utils)
print_host_info() (in module blues.utils)
protocolWork() (blues.formats.NetCDF4Traj property)
R
RandomLigandRotationMove (class in blues.ncmc)
reassign_velocities (blues.ncmc.ReportLangevinDynamicsMove attribute)
report() (blues.storage.BLUESStateDataStorage method)
(blues.storage.NetCDF4Storage method)
reporters (blues.ncmc.NCMCMove attribute)
(blues.ncmc.RandomLigandRotationMove attribute)
(blues.ncmc.ReportLangevinDynamicsMove attribute)
ReportLangevinDynamicsMove (class in blues.ncmc)
reset() (blues.integrators.AlchemicalExternalLangevinIntegrator method)
restrain_positions() (in module blues.systemfactory)
run() (blues.ncmc.BLUESSampler method)
S
saveContextFrame() (in module blues.utils)
setup_logging() (in module blues.storage)
statistics() (blues.ncmc.NCMCMove property)
T
timestep (blues.ncmc.NCMCMove attribute)
(blues.ncmc.RandomLigandRotationMove attribute)
(blues.ncmc.ReportLangevinDynamicsMove attribute)
Z
zero_masses() (in module blues.systemfactory)