Index

A

AbsoluteTemperature (class in mdadash.backend.analyses.energies) ACFAnalysis (class in mdadash.backend.analyses.acf) add_alert() (mdadash.backend.state.manager.StateManager method) add_notebook() (mdadash.backend.state.manager.StateManager method) add_widget_instance() (mdadash.backend.kernel.manager.KernelManager method) (mdadash.backend.widgets.base.WidgetManager method) alert() (in module mdadash.backend.kernel.utils) (mdadash.backend.widgets.base.WidgetBase method) alerts (mdadash.backend.state.manager.StateManager property) AnglesEnergy (class in mdadash.backend.analyses.energies)

apply_parallel_results() (mdadash.backend.analyses.acf.ACFAnalysis method) (mdadash.backend.analyses.com_distance.COMDistance method) (mdadash.backend.analyses.contacts.Contacts method) (mdadash.backend.analyses.dssp.DSSPAnalysis method) (mdadash.backend.analyses.helix_analysis.HelixAnalysis method) (mdadash.backend.analyses.hydrogen_bonds.HydrogenBonds method) (mdadash.backend.analyses.msd.MSDAnalysis method) (mdadash.backend.analyses.native_contacts.NativeContacts method) (mdadash.backend.analyses.rmsd.RMSD method) (mdadash.backend.analyses.rog.ROG method) (mdadash.backend.widgets.base.WidgetBase method)

B

BondsEnergy (class in mdadash.backend.analyses.energies) buffer_size (mdadash.backend.kernel.core.BufferedTrajectory property)

BufferedTrajectory (class in mdadash.backend.kernel.core) BufferFrameIteratorIndices (class in mdadash.backend.kernel.core)

C

check_slice_indices() (mdadash.backend.kernel.core.BufferedTrajectory method) COMDistance (class in mdadash.backend.analyses.com_distance) CommHandler (class in mdadash.backend.kernel.core) connect_to_simulations() (mdadash.backend.kernel.core.UniverseManager method) (mdadash.backend.kernel.manager.KernelManager method)

Contacts (class in mdadash.backend.analyses.contacts) CoulombInteractionEnergy (class in mdadash.backend.analyses.energies) CustomCode (class in mdadash.backend.analyses.custom_code)

D

dashboard_config (mdadash.backend.state.manager.StateManager property) data_key (mdadash.backend.analyses.energies.AbsoluteTemperature attribute) (mdadash.backend.analyses.energies.AnglesEnergy attribute) (mdadash.backend.analyses.energies.BondsEnergy attribute) (mdadash.backend.analyses.energies.CoulombInteractionEnergy attribute) (mdadash.backend.analyses.energies.DihedralsEnergy attribute) (mdadash.backend.analyses.energies.EnergyWidgetBase attribute) (mdadash.backend.analyses.energies.ImproperDihedralsEnergy attribute) (mdadash.backend.analyses.energies.PotentialEnergy attribute) (mdadash.backend.analyses.energies.TotalEnergy attribute) (mdadash.backend.analyses.energies.VanDerWaalsEnergy attribute) description (mdadash.backend.analyses.acf.ACFAnalysis attribute) (mdadash.backend.analyses.com_distance.COMDistance attribute) (mdadash.backend.analyses.contacts.Contacts attribute) (mdadash.backend.analyses.custom_code.CustomCode attribute) (mdadash.backend.analyses.dssp.DSSPAnalysis attribute) (mdadash.backend.analyses.energies.AbsoluteTemperature attribute) (mdadash.backend.analyses.energies.AnglesEnergy attribute) (mdadash.backend.analyses.energies.BondsEnergy attribute) (mdadash.backend.analyses.energies.CoulombInteractionEnergy attribute) (mdadash.backend.analyses.energies.DihedralsEnergy attribute) (mdadash.backend.analyses.energies.ImproperDihedralsEnergy attribute) (mdadash.backend.analyses.energies.PotentialEnergy attribute) (mdadash.backend.analyses.energies.TotalEnergy attribute) (mdadash.backend.analyses.energies.VanDerWaalsEnergy attribute) (mdadash.backend.analyses.helix_analysis.HelixAnalysis attribute) (mdadash.backend.analyses.hydrogen_bonds.HydrogenBonds attribute) (mdadash.backend.analyses.janin.JaninPlot attribute) (mdadash.backend.analyses.msd.MSDAnalysis attribute) (mdadash.backend.analyses.native_contacts.NativeContacts attribute) (mdadash.backend.analyses.ramachandran.RamachandranPlot attribute) (mdadash.backend.analyses.rmsd.RMSD attribute) (mdadash.backend.analyses.rog.ROG attribute)

DihedralsEnergy (class in mdadash.backend.analyses.energies) disconnect_from_simulations() (mdadash.backend.kernel.core.UniverseManager method) (mdadash.backend.kernel.manager.KernelManager method) DSSPAnalysis (class in mdadash.backend.analyses.dssp) duplicate_notebook() (mdadash.backend.state.manager.StateManager method) duplicate_widget_instance() (mdadash.backend.kernel.manager.KernelManager method) (mdadash.backend.widgets.base.WidgetManager method)

E

EMATrend (class in mdadash.backend.kernel.utils) EnergyWidgetBase (class in mdadash.backend.analyses.energies)

execute_code() (mdadash.backend.kernel.manager.KernelManager method) (mdadash.backend.widgets.base.WidgetManager method)

F

frames (mdadash.backend.kernel.core.BufferFrameIteratorIndices property)

G

get_available_widgets() (mdadash.backend.kernel.manager.KernelManager method) (mdadash.backend.widgets.base.WidgetManager method) get_parallel_job() (mdadash.backend.analyses.acf.ACFAnalysis method) (mdadash.backend.analyses.com_distance.COMDistance method) (mdadash.backend.analyses.contacts.Contacts method) (mdadash.backend.analyses.dssp.DSSPAnalysis method) (mdadash.backend.analyses.helix_analysis.HelixAnalysis method) (mdadash.backend.analyses.hydrogen_bonds.HydrogenBonds method) (mdadash.backend.analyses.msd.MSDAnalysis method) (mdadash.backend.analyses.native_contacts.NativeContacts method) (mdadash.backend.analyses.rmsd.RMSD method) (mdadash.backend.analyses.rog.ROG method) (mdadash.backend.widgets.base.WidgetBase method)

get_widget_details() (mdadash.backend.kernel.manager.KernelManager method) get_widget_inputs() (mdadash.backend.widgets.base.WidgetManager method)

H

HelixAnalysis (class in mdadash.backend.analyses.helix_analysis)

HydrogenBonds (class in mdadash.backend.analyses.hydrogen_bonds)

I

ImproperDihedralsEnergy (class in mdadash.backend.analyses.energies)

init_n_universes() (in module mdadash.backend.kernel.core) (mdadash.backend.kernel.core.UniverseManager method)

J

JaninPlot (class in mdadash.backend.analyses.janin)

K

KernelManager (class in mdadash.backend.kernel.manager)

L

load() (mdadash.backend.state.manager.StateManager method)

M

mdadash module mdadash.backend module mdadash.backend.analyses module mdadash.backend.analyses.acf module mdadash.backend.analyses.com_distance module mdadash.backend.analyses.contacts module mdadash.backend.analyses.custom_code module mdadash.backend.analyses.dssp module mdadash.backend.analyses.energies module mdadash.backend.analyses.helix_analysis module mdadash.backend.analyses.hydrogen_bonds module mdadash.backend.analyses.janin module mdadash.backend.analyses.msd module mdadash.backend.analyses.native_contacts module mdadash.backend.analyses.ramachandran module mdadash.backend.analyses.rmsd module mdadash.backend.analyses.rog module mdadash.backend.kernel module mdadash.backend.kernel.core module

mdadash.backend.kernel.manager module mdadash.backend.kernel.utils module mdadash.backend.state module mdadash.backend.state.manager module mdadash.backend.widgets module mdadash.backend.widgets.base module module mdadash mdadash.backend mdadash.backend.analyses mdadash.backend.analyses.acf mdadash.backend.analyses.com_distance mdadash.backend.analyses.contacts mdadash.backend.analyses.custom_code mdadash.backend.analyses.dssp mdadash.backend.analyses.energies mdadash.backend.analyses.helix_analysis mdadash.backend.analyses.hydrogen_bonds mdadash.backend.analyses.janin mdadash.backend.analyses.msd mdadash.backend.analyses.native_contacts mdadash.backend.analyses.ramachandran mdadash.backend.analyses.rmsd mdadash.backend.analyses.rog mdadash.backend.kernel mdadash.backend.kernel.core mdadash.backend.kernel.manager mdadash.backend.kernel.utils mdadash.backend.state mdadash.backend.state.manager mdadash.backend.widgets mdadash.backend.widgets.base MSDAnalysis (class in mdadash.backend.analyses.msd)

N

n_frames (mdadash.backend.kernel.core.BufferedTrajectory property) name (mdadash.backend.analyses.acf.ACFAnalysis attribute) (mdadash.backend.analyses.com_distance.COMDistance attribute) (mdadash.backend.analyses.contacts.Contacts attribute) (mdadash.backend.analyses.custom_code.CustomCode attribute) (mdadash.backend.analyses.dssp.DSSPAnalysis attribute) (mdadash.backend.analyses.energies.AbsoluteTemperature attribute) (mdadash.backend.analyses.energies.AnglesEnergy attribute) (mdadash.backend.analyses.energies.BondsEnergy attribute) (mdadash.backend.analyses.energies.CoulombInteractionEnergy attribute) (mdadash.backend.analyses.energies.DihedralsEnergy attribute) (mdadash.backend.analyses.energies.EnergyWidgetBase attribute) (mdadash.backend.analyses.energies.ImproperDihedralsEnergy attribute) (mdadash.backend.analyses.energies.PotentialEnergy attribute) (mdadash.backend.analyses.energies.TotalEnergy attribute) (mdadash.backend.analyses.energies.VanDerWaalsEnergy attribute) (mdadash.backend.analyses.helix_analysis.HelixAnalysis attribute) (mdadash.backend.analyses.hydrogen_bonds.HydrogenBonds attribute) (mdadash.backend.analyses.janin.JaninPlot attribute) (mdadash.backend.analyses.msd.MSDAnalysis attribute) (mdadash.backend.analyses.native_contacts.NativeContacts attribute) (mdadash.backend.analyses.ramachandran.RamachandranPlot attribute) (mdadash.backend.analyses.rmsd.RMSD attribute) (mdadash.backend.analyses.rog.ROG attribute)

NativeContacts (class in mdadash.backend.analyses.native_contacts) next() (mdadash.backend.kernel.core.BufferedTrajectory method) notebooks (mdadash.backend.state.manager.StateManager property)

O

on_input_change() (mdadash.backend.analyses.acf.ACFAnalysis method) (mdadash.backend.analyses.com_distance.COMDistance method) (mdadash.backend.analyses.contacts.Contacts method) (mdadash.backend.analyses.dssp.DSSPAnalysis method) (mdadash.backend.analyses.energies.EnergyWidgetBase method) (mdadash.backend.analyses.helix_analysis.HelixAnalysis method) (mdadash.backend.analyses.hydrogen_bonds.HydrogenBonds method) (mdadash.backend.analyses.janin.JaninPlot method) (mdadash.backend.analyses.msd.MSDAnalysis method) (mdadash.backend.analyses.native_contacts.NativeContacts method) (mdadash.backend.analyses.ramachandran.RamachandranPlot method) (mdadash.backend.analyses.rmsd.RMSD method) (mdadash.backend.analyses.rog.ROG method) (mdadash.backend.widgets.base.WidgetBase method) on_post_connect() (mdadash.backend.analyses.acf.ACFAnalysis method) (mdadash.backend.analyses.com_distance.COMDistance method) (mdadash.backend.analyses.contacts.Contacts method) (mdadash.backend.analyses.custom_code.CustomCode method) (mdadash.backend.analyses.dssp.DSSPAnalysis method) (mdadash.backend.analyses.helix_analysis.HelixAnalysis method) (mdadash.backend.analyses.hydrogen_bonds.HydrogenBonds method) (mdadash.backend.analyses.janin.JaninPlot method) (mdadash.backend.analyses.msd.MSDAnalysis method) (mdadash.backend.analyses.native_contacts.NativeContacts method) (mdadash.backend.analyses.ramachandran.RamachandranPlot method) (mdadash.backend.analyses.rmsd.RMSD method) (mdadash.backend.analyses.rog.ROG method) (mdadash.backend.widgets.base.WidgetBase method)

on_post_create() (mdadash.backend.analyses.acf.ACFAnalysis method) (mdadash.backend.analyses.com_distance.COMDistance method) (mdadash.backend.analyses.contacts.Contacts method) (mdadash.backend.analyses.dssp.DSSPAnalysis method) (mdadash.backend.analyses.energies.EnergyWidgetBase method) (mdadash.backend.analyses.helix_analysis.HelixAnalysis method) (mdadash.backend.analyses.hydrogen_bonds.HydrogenBonds method) (mdadash.backend.analyses.msd.MSDAnalysis method) (mdadash.backend.analyses.native_contacts.NativeContacts method) (mdadash.backend.analyses.rmsd.RMSD method) (mdadash.backend.analyses.rog.ROG method) (mdadash.backend.widgets.base.WidgetBase method) on_post_disconnect() (mdadash.backend.widgets.base.WidgetBase method) on_post_pause() (mdadash.backend.widgets.base.WidgetBase method) on_pre_resume() (mdadash.backend.widgets.base.WidgetBase method)

P

pause_simulation() (in module mdadash.backend.kernel.utils) (mdadash.backend.widgets.base.WidgetBase method)

pause_simulations() (mdadash.backend.kernel.core.UniverseManager method) (mdadash.backend.kernel.manager.KernelManager method) PotentialEnergy (class in mdadash.backend.analyses.energies)

R

RamachandranPlot (class in mdadash.backend.analyses.ramachandran) recreate_instances() (mdadash.backend.widgets.base.WidgetManager method) recreate_widget_instances() (mdadash.backend.kernel.manager.KernelManager method) register_class() (mdadash.backend.widgets.base.WidgetManager class method) register_handler() (mdadash.backend.kernel.core.CommHandler method) remove_notebook() (mdadash.backend.state.manager.StateManager method) remove_widget_instance() (mdadash.backend.kernel.manager.KernelManager method) (mdadash.backend.widgets.base.WidgetManager method) resume_simulations() (mdadash.backend.kernel.core.UniverseManager method) (mdadash.backend.kernel.manager.KernelManager method) RMSD (class in mdadash.backend.analyses.rmsd) ROG (class in mdadash.backend.analyses.rog) run() (mdadash.backend.analyses.acf.SlidingWindowACF method) (mdadash.backend.analyses.msd.SlidingWindowMSD method) run_batch() (mdadash.backend.analyses.com_distance.COMDistance method) (mdadash.backend.analyses.contacts.Contacts method) (mdadash.backend.analyses.custom_code.CustomCode method) (mdadash.backend.analyses.dssp.DSSPAnalysis method) (mdadash.backend.analyses.helix_analysis.HelixAnalysis method) (mdadash.backend.analyses.hydrogen_bonds.HydrogenBonds method) (mdadash.backend.analyses.native_contacts.NativeContacts method) (mdadash.backend.analyses.rmsd.RMSD method) (mdadash.backend.analyses.rog.ROG method) (mdadash.backend.widgets.base.WidgetBase method)

run_every_frame() (mdadash.backend.analyses.acf.ACFAnalysis method) (mdadash.backend.analyses.com_distance.COMDistance method) (mdadash.backend.analyses.contacts.Contacts method) (mdadash.backend.analyses.custom_code.CustomCode method) (mdadash.backend.analyses.dssp.DSSPAnalysis method) (mdadash.backend.analyses.energies.EnergyWidgetBase method) (mdadash.backend.analyses.helix_analysis.HelixAnalysis method) (mdadash.backend.analyses.hydrogen_bonds.HydrogenBonds method) (mdadash.backend.analyses.janin.JaninPlot method) (mdadash.backend.analyses.msd.MSDAnalysis method) (mdadash.backend.analyses.native_contacts.NativeContacts method) (mdadash.backend.analyses.ramachandran.RamachandranPlot method) (mdadash.backend.analyses.rmsd.RMSD method) (mdadash.backend.analyses.rog.ROG method) (mdadash.backend.widgets.base.WidgetBase method) run_notebooks() (in module mdadash.backend.kernel.core) (mdadash.backend.kernel.manager.KernelManager method) run_widgets() (mdadash.backend.widgets.base.WidgetManager method) running_state (mdadash.backend.state.manager.StateManager property)

S

save() (mdadash.backend.state.manager.StateManager method) send() (mdadash.backend.kernel.core.CommHandler method) send_message() (mdadash.backend.kernel.manager.KernelManager method) send_message_await_response() (mdadash.backend.kernel.manager.KernelManager method) set_widget_input() (mdadash.backend.kernel.manager.KernelManager method) (mdadash.backend.widgets.base.WidgetManager method)

settings (mdadash.backend.state.manager.StateManager property) SlidingWindowACF (class in mdadash.backend.analyses.acf) SlidingWindowMSD (class in mdadash.backend.analyses.msd) start() (mdadash.backend.kernel.manager.KernelManager method) state (mdadash.backend.state.manager.StateManager property) StateManager (class in mdadash.backend.state.manager) stop() (mdadash.backend.kernel.manager.KernelManager method)

T

TotalEnergy (class in mdadash.backend.analyses.energies)

U

universe_configs (mdadash.backend.state.manager.StateManager property) UniverseManager (class in mdadash.backend.kernel.core)

update() (mdadash.backend.kernel.utils.EMATrend method) update_n_jobs() (mdadash.backend.kernel.manager.KernelManager method) (mdadash.backend.widgets.base.WidgetManager method)

V

VanDerWaalsEnergy (class in mdadash.backend.analyses.energies)

W

WidgetBase (class in mdadash.backend.widgets.base) WidgetManager (class in mdadash.backend.widgets.base)

widgets (mdadash.backend.state.manager.StateManager property) widgets_layout (mdadash.backend.state.manager.StateManager property)

Y

y_label (mdadash.backend.analyses.energies.AbsoluteTemperature attribute) (mdadash.backend.analyses.energies.EnergyWidgetBase attribute)