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) cleanup() (mdadash.backend.kernel.core.BufferedTrajectory method) (mdadash.backend.kernel.core.MultiArrayBuffer method) (mdadash.backend.kernel.core.UniverseManager 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) display_canvas() (mdadash.backend.widgets.base.WidgetBase method) display_fig() (mdadash.backend.widgets.base.WidgetBase 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_box_matrices() (in module mdadash.backend.analyses.utils) 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_topology() (mdadash.backend.kernel.core.UniverseManager method) (mdadash.backend.kernel.manager.KernelManager method) get_widget_details() (mdadash.backend.kernel.manager.KernelManager method) get_widget_inputs() (mdadash.backend.widgets.base.WidgetManager method) getstate() (mdadash.backend.kernel.core.MultiArrayBuffer 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() (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.analyses.utils 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.analyses.utils 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) MultiArrayBuffer (class in mdadash.backend.kernel.core)

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.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_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) ref_u (mdadash.backend.kernel.core.BufferedTrajectory property) 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) reset_frame_latest() (mdadash.backend.widgets.base.WidgetBase 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.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.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() (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) setstate() (mdadash.backend.kernel.core.MultiArrayBuffer class 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_3dview_frequency() (mdadash.backend.kernel.core.UniverseManager method) (mdadash.backend.kernel.manager.KernelManager method)

update_3dview_selection() (mdadash.backend.kernel.core.UniverseManager method) (mdadash.backend.kernel.manager.KernelManager method) update_n_jobs() (mdadash.backend.kernel.core.UniverseManager method) (mdadash.backend.kernel.manager.KernelManager method)

V

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

view3d (mdadash.backend.state.manager.StateManager property)

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)