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CaverDock
Index
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
P
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
|
Z
A
analyse() (pycaverdock.energy_profile.EnergyProfile method)
B
bound_end (pycaverdock.energy_profile.DiscRanges attribute)
bound_start (pycaverdock.energy_profile.DiscRanges attribute)
BoundaryType (class in pycaverdock.energy_profile)
C
calculate_dist_max() (in module pycaverdock.caverdock)
calculate_tunnel_gridbox() (in module pycaverdock.caverdock)
CaverDock (class in pycaverdock.caverdock)
CaverDockNotFoundError
CaverDockTrajectory (class in pycaverdock.caverdock)
center (pycaverdock.tunnel.Disk attribute)
check_args() (in module pycaverdock.experiment)
compress_files() (in module pycaverdock.experiment)
convert() (pycaverdock.energy_profile.DiscRanges method)
convert_eprofile_analysis() (in module pycaverdock.experiment)
copy() (pycaverdock.tunnel.Disk method)
(pycaverdock.tunnel.Vec3D method)
create_args_cache_value() (in module pycaverdock.experiment)
create_energy_profile() (in module pycaverdock.energy_profile)
create_key() (pycaverdock.experiment.Workdir method)
D
dE_bs (pycaverdock.energy_profile.EnergyProfileAnalysis attribute)
decompress_files() (in module pycaverdock.experiment)
direction (pycaverdock.caverdock.CaverDockTrajectory attribute)
(pycaverdock.energy_profile.EnergyProfile attribute)
(pycaverdock.energy_profile.EnergyProfileAnalysis attribute)
DISC_NUMBER (pycaverdock.energy_profile.BoundaryType attribute)
DiscRanges (class in pycaverdock.energy_profile)
discretize_tunnel() (in module pycaverdock.tunnel)
(pycaverdock.experiment.Experiment method)
DiscretizedTunnel (class in pycaverdock.tunnel)
Disk (class in pycaverdock.tunnel)
disks (pycaverdock.tunnel.DiscretizedTunnel attribute)
E
E_bound (pycaverdock.energy_profile.EnergyProfileAnalysis attribute)
E_max (pycaverdock.energy_profile.EnergyProfileAnalysis attribute)
E_surface (pycaverdock.energy_profile.EnergyProfileAnalysis attribute)
energy_profile (pycaverdock.caverdock.CaverDockTrajectory property)
energy_profile_lowerbound (pycaverdock.caverdock.CaverDockTrajectory property)
energy_profile_upperbound (pycaverdock.caverdock.CaverDockTrajectory property)
EnergyProfile (class in pycaverdock.energy_profile)
EnergyProfileAnalysis (class in pycaverdock.energy_profile)
entry_path() (pycaverdock.experiment.Workdir method)
exec() (pycaverdock.mgltoolswrapper.MGLToolsWrapper method)
Experiment (class in pycaverdock.experiment)
extend() (pycaverdock.tunnel.DiscretizedTunnel method)
F
FRACTION (pycaverdock.energy_profile.BoundaryType attribute)
frame (pycaverdock.energy_profile.EnergyProfile attribute)
G
generate_caverdock_config() (in module pycaverdock.caverdock)
get_ligand_atoms() (in module pycaverdock.caverdock)
get_result_path() (in module pycaverdock.caverdock)
H
has_entry() (pycaverdock.experiment.Workdir method)
hash_discretized_tunnel() (in module pycaverdock.experiment)
hash_file() (in module pycaverdock.experiment)
I
InputFile (class in pycaverdock.experiment)
intermediate_path() (pycaverdock.experiment.Experiment method)
K
k_off (pycaverdock.energy_profile.EnergyProfileAnalysis attribute)
k_on (pycaverdock.energy_profile.EnergyProfileAnalysis attribute)
L
lb (pycaverdock.caverdock.CaverDockTrajectory attribute)
Ligand (class in pycaverdock.mgltoolswrapper)
load_from_file() (pycaverdock.energy_profile.EnergyProfile static method)
(pycaverdock.tunnel.DiscretizedTunnel static method)
load_tunnel() (in module pycaverdock.tunnel)
log_file() (pycaverdock.experiment.Workdir method)
M
main() (in module pycaverdock.bin.analyseeprofile)
(in module pycaverdock.bin.analysis)
(in module pycaverdock.bin.energyprofile)
(in module pycaverdock.bin.extendtunnel)
(in module pycaverdock.bin.prepareconf)
(in module pycaverdock.bin.reverseeprofile)
max_end (pycaverdock.energy_profile.DiscRanges attribute)
max_start (pycaverdock.energy_profile.DiscRanges attribute)
mgltools_path() (pycaverdock.mgltoolswrapper.MGLToolsWrapper method)
MGLToolsNotFoundError
MGLToolsWrapper (class in pycaverdock.mgltoolswrapper)
module
pycaverdock.bin
pycaverdock.bin.analyseeprofile
pycaverdock.bin.analysis
pycaverdock.bin.energyprofile
pycaverdock.bin.extendtunnel
pycaverdock.bin.prepareconf
pycaverdock.bin.reverseeprofile
pycaverdock.caverdock
pycaverdock.energy_profile
pycaverdock.experiment
pycaverdock.mgltoolswrapper
pycaverdock.tunnel
N
normal (pycaverdock.tunnel.Disk attribute)
P
path (pycaverdock.experiment.InputFile attribute)
(pycaverdock.mgltoolswrapper.Ligand attribute)
(pycaverdock.mgltoolswrapper.Receptor attribute)
prepare_ligand() (pycaverdock.experiment.Experiment method)
(pycaverdock.mgltoolswrapper.MGLToolsWrapper method)
prepare_receptor() (pycaverdock.experiment.Experiment method)
(pycaverdock.mgltoolswrapper.MGLToolsWrapper method)
pycaverdock.bin
module
pycaverdock.bin.analyseeprofile
module
pycaverdock.bin.analysis
module
pycaverdock.bin.energyprofile
module
pycaverdock.bin.extendtunnel
module
pycaverdock.bin.prepareconf
module
pycaverdock.bin.reverseeprofile
module
pycaverdock.caverdock
module
pycaverdock.energy_profile
module
pycaverdock.experiment
module
pycaverdock.mgltoolswrapper
module
pycaverdock.tunnel
module
R
radius (pycaverdock.tunnel.Disk attribute)
Receptor (class in pycaverdock.mgltoolswrapper)
resolve_entry() (pycaverdock.experiment.Workdir method)
result_path() (pycaverdock.experiment.Experiment method)
reverse() (pycaverdock.energy_profile.EnergyProfile method)
(pycaverdock.tunnel.DiscretizedTunnel method)
run() (pycaverdock.caverdock.CaverDock method)
run_caverdock() (pycaverdock.experiment.Experiment method)
run_with_config() (pycaverdock.caverdock.CaverDock method)
S
STDERR (pycaverdock.experiment.Stream attribute)
STDOUT (pycaverdock.experiment.Stream attribute)
store_input_file() (pycaverdock.experiment.Experiment method)
Stream (class in pycaverdock.experiment)
surface_end (pycaverdock.energy_profile.DiscRanges attribute)
surface_start (pycaverdock.energy_profile.DiscRanges attribute)
T
to_tuple() (pycaverdock.tunnel.Vec3D method)
trajectory_type (pycaverdock.energy_profile.EnergyProfileAnalysis attribute)
tunnel (pycaverdock.caverdock.CaverDockTrajectory attribute)
type (pycaverdock.energy_profile.DiscRanges attribute)
U
ub (pycaverdock.caverdock.CaverDockTrajectory attribute)
V
Vec3D (class in pycaverdock.tunnel)
W
Workdir (class in pycaverdock.experiment)
write() (pycaverdock.energy_profile.EnergyProfile method)
(pycaverdock.tunnel.DiscretizedTunnel method)
write_to_dat() (pycaverdock.energy_profile.EnergyProfile method)
write_to_file() (pycaverdock.tunnel.DiscretizedTunnel method)
X
x (pycaverdock.tunnel.Vec3D attribute)
Y
y (pycaverdock.tunnel.Vec3D attribute)
Z
z (pycaverdock.tunnel.Vec3D attribute)