Index

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)