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The module that creates the actions and menus for the Pymol-like interface of BioLuminate.
Copyright Schrodinger, LLC. All rights reserved.
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ResultsWindow | |||
MWidgetAction A QAction that performs a Maestro command |
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MAction A QAction that performs a Maestro command |
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PMLMenu The base menu class we subclass from |
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PMLContextMenu The base menu class we subclass from for context menus |
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RockData Stores information about the current workspace rocking state |
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LigandActionMixin Class that contains a method to restrict the asl to Ligands only |
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ShowLines | |||
ShowLigandLines | |||
ShowTubes | |||
ShowLigandTubes | |||
ShowBAndS | |||
ShowNonBonded | |||
ShowNonBondedSpheres | |||
ShowSpheres | |||
ShowLigandSpheres | |||
ShowCartoonOrRibbon | |||
ShowCartoon | |||
ShowRibbon | |||
ShowLabel | |||
SurfaceRender Base class for actions that render a surface |
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ShowSurface | |||
ShowMesh | |||
ShowSubstructureMenu The Show->substructure submenus |
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ShowOrganicMenu The Show->Organic submenus |
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AsMenu The Show->As submenu |
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ShowMenu The Show menu |
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Zoom | |||
Orient | |||
Center | |||
Origin | |||
Clean | |||
Rename | |||
DeleteWS | |||
DeleteProject | |||
Duplicate | |||
MakeProjectEntry Copies the atoms into a new project entry and includes it in the workspace |
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Ray Use PyMOL to make a ray-traced image |
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Extend Expand the selection to the atoms within X bonds of the ASL for this object |
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InvertCompleteSelection Invert or complete the selection within an object |
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SelectWithinEntry | |||
SelectWithinChain | |||
SelectWithinResidue | |||
SelectWithinMolecule | |||
SelectWithinAny | |||
SelectWithinCalpha | |||
Expand Expand the selection to the atoms around the ASL for this object |
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Around | |||
EntrySubMenu A submenu that lists all enabled Entry objects |
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SelectionSubMenu A submenu that lists all enabled Entry objects |
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RestrictSelection Restrict the selection to a specific object |
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RestrictToVisible | |||
RestrictToPolymer | |||
RestrictToOrganic | |||
RestrictToSolvent | |||
RestrictToInorganic | |||
RestrictSubMenu The modify-restrict submenu of the action menu |
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IncludeInSelection Include a specific object in the selection |
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IncludeVisibleInSelection | |||
ExcludeFromSelection | |||
ExcludeVisibleFromSelection | |||
ExcludePolymerFromSelection | |||
ExcludeOrganicFromSelection | |||
ExcludeSolventFromSelection | |||
ExcludeInorganicFromSelection | |||
IncludeSubMenu The modify-include submenu of the action menu |
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ExcludeSubMenu The modify-exclude submenu of the action menu |
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AroundExpandSubMenu The modify-around submenu of the action menu |
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ExtendSubMenu The modify-extend submenu of the action menu |
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InvertSubMenu The modify-invert submenu of the action menu |
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CompleteSubMenu The modify-complete submenu of the action menu |
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ModifySubMenu The modify submenu of the action menu |
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PresetAction Base class for Preset Actions |
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SimplePreset | |||
BAndSPreset | |||
BFactorPreset | |||
TechnicalPreset | |||
LigandPreset | |||
PrettyPubPreset Show the object as nice-looking cartoon ribbons |
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DefaultPreset | |||
InterfaceMixin Determine the Protein-Protein interface atoms |
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InterfacePreset | |||
RegionInfo | |||
AntibodyPreset | |||
LigandSitesSubMenu The Action-Preset-Ligand Sites submenu |
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PresetSubMenu The Preset submenu |
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PolarContactsObject | |||
PolarContactsWithSidechains | |||
PolarContactsWithSolvent | |||
PolarContactsWithoutSolvent | |||
PolarContactsWithoutMainchain | |||
PolarContactsWithoutIntraMainchain | |||
PolarContactsOnlySidechain | |||
PolarContactsOnlyMainchain | |||
PolarContactsToEntry | |||
PolarContactsToEntryWithoutSolvent | |||
PolarContactsToAnyAtoms | |||
PolarContactsToAnyNonSolvent | |||
FindPCSubMenu The Find Polar Contacts submenu |
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RemovePC | |||
PolarContactsSubMenu The Polar Contacts submenu |
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GenerateSelection Select the atoms, then generate a selection object from them |
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GenerateInterfaceSelection | |||
GenerateLigandSelection | |||
GenerateSurfResSelection | |||
GenSelectionSubMenu The Action Generate Selection submenu |
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GenerateSymmetryMates Generate all the symmetry mates and show those within X angstroms |
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HideSymmetryMates | |||
GenSymMatesSubMenu The Action Generate Symmetry Mates submenu |
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GenerateSubMenu The Action Generate submenu |
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AddHydrogens | |||
RemoveHydrogens | |||
RemoveWaters | |||
DeleteAtoms | |||
HydrogenSubMenu The Action Hydrogen submenu |
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CountAtoms | |||
SumFormalCharge | |||
SumPartialCharge | |||
ComputeSurfaceArea | |||
SurfaceAreaSubMenu The Action Surface Area submenu |
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ComputeSubMenu The Action Compute submenu |
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DeleteSelections | |||
ActionMenu The Action menu |
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HideEverything | |||
HideAtoms | |||
HideNonBonded | |||
HideRibbons | |||
HideSurface | |||
HideLabel | |||
HideMainChain | |||
HideSideChain | |||
HideWaters | |||
HideHydrogens | |||
HideAllOthers | |||
HidePolarHydrogens | |||
HideHydrogenSubMenu The Hide Hydrogen submenu |
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HideMenu The Hide menu |
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LabelAtom A QAction that performs labels atoms with the given label |
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LabelAtomByProp Labels all atoms by a custom atom property |
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LabelAtomByVDW | |||
LabelAtomByOccupancy | |||
LabelAtomByNumType | |||
LabelAtomByStereo | |||
LabelAtomByEntryIndex | |||
LabelAtomByMolIndex | |||
LabelResidues | |||
LabelChains | |||
LabelOtherSubMenu The Label Other Properties submenu |
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LabelAtomIdentSubMenu The Label Atom Identifiers submenu |
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LabelMenu The Label menu |
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ColorChooserPanel A window that lets the user choose a Maestro color. |
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ColorRibbonMixin | |||
CustomColor | |||
ColorHydrogens | |||
ColorCarbons | |||
ColorHNOS | |||
ColorObject | |||
ColorRecentCarbons | |||
ColorRecentHydrogens | |||
ColorRecentObjects | |||
ColorChains | |||
ColorChainsByCarbon | |||
ColorChainsByCalpha | |||
ColorAtomsBySpectrum | |||
ColorCarbonsBySpectrum | |||
ColorCalphasBySpectrum | |||
ColorAtomsByBFactor | |||
ColorCalphasByBFactor | |||
ColorChainbows | |||
ColorLabel A label that shows off the color each element will be colored if this menu item is chosen. |
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RecentColorSubMenu A submenu that shows the most recently chosen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top. |
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RecentCarbonColorSubMenu A submenu that shows the most recently chosen carbon colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top. |
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RecentHydrogenColorSubMenu A submenu that shows the most recently chosen hydrogen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top. |
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RecentObjectColorSubMenu A submenu that shows the most recently chosen object colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top. |
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ColorByElementSubMenu The Color by Element submenu |
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ColorChainSubMenu The ColorChainSubMenu menu |
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ColorSpectrumSubMenu The ColorSpectrumSubMenu menu |
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CustomRecentColor | |||
ColorBySubstructure | |||
ColorSubstructureSubMenu The ColorSubstructureSubMenu menu |
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AutoCycleColor | |||
AutoCycleCarbonColor | |||
AutoColorObjects | |||
AutoColorCarbons | |||
AutoColorSubMenu The Color menu |
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ColorMenu The Color menu |
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ToggleState A MAction that toggles the enabled/disabled state of an object |
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DeleteAll | |||
Reinitialize | |||
Quit | |||
Select | |||
Disable | |||
CreateEntry | |||
GeneralContextSubMenu The submenu that contains all the main actions used for most context menus |
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SubstructureContextSubMenu The GeneralContextSubMenu for a right-click that is on an atom |
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ObjectFreeContextSubMenu The GeneralContextSubMenu for a right-click that is not on an object |
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ToggleStateSubMenu The submenu that allows the user to enable/disable individual objects |
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SelectedAtomContextActionSubMenu The submenu that allows the user to enable/disable individual objects |
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SelectedAtomContextMenu The context menu for right-clicks on selected atoms |
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AtomContextMenu The context menu for right-clicks on non-selected atoms |
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SpaceContextMenu The context menu for right-clicks in space |
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tuple |
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list or None |
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list |
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str |
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str |
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iterable |
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list |
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tuple |
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str |
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str or None |
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list |
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list |
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str |
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dict |
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tuple |
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str |
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str |
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float or None |
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list |
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psp_antibody = None hash(x) |
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maestro = schrodinger.get_maestro()
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SIGNAL = QtCore.SIGNAL
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TRIGGERED = SIGNAL('triggered()')
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DISULFIDE = '(fillres /S0-S0/) AND atom.ptype CA,CB,SG'
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BACKBONE = 'backbone'
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SIDECHAIN = 'sidechain'
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POLYMER = '(backbone) or (sidechain)'
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SOLVENT = 'water'
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INORGANIC = 'not atom.ele H,C,N,O,F,P,S,Cl,Br,I'
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PROT_AND_DNA_SELE = "(res. ALA,CYS,CYX,ASP,GLU,PHE,GLY,HIS,HID
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PYMOL_IONS = 'atom.ele Ca, Hg, K, Na, Zn, Mg, Cl'
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SOLVENT_AND_IONS = '(water) OR '+ PYMOL_IONS
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WATER = 'water'
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RIBBON_STYLE = 'calphatube' hash(x) |
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THIN_TRACE = 'calphaline'
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CALPHA_SCHEME = 'calphaatom'
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CHAIN_SCHEME = 'chain'
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POSITION_SCHEME = 'residueposition'
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NONE = 'none'
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TUBE = 'tube'
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CARTOON = 'cartoon' hash(x) |
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ATOM_NONE = 'none'
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BOND_NONE = 'none'
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CPK = 'cpk'
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ATOM_WIRE = 'none'
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BOND_WIRE = 'wire'
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ATOM_BALLNSTICK = 'ballnstick'
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BOND_BALLNSTICK = 'ballnstick'
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MAESTRO_TO_STRUCT_STYLE = {ATOM_WIRE: structure.ATOM_NOSTYLE,
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MMCT_TO_MAESTRO_RIBBON_STYLE = {mm.MMCT_RIBBON_STYLE_CALINE: '
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MAESTRO_TO_MMCT_RIBBON_STYLE = dict([(val, key) for(key, val)
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DARK_BLUE = 'user2'
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BLUE = 'user27'
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CYAN = 'user4'
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SEAFOAM = 'userM'
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DARK_GREEN = 'user3'
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LIME = 'user19'
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DEEPTEAL = 'user59'
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HOTPINK = 'userN'
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YELLOWORANGE = 'userT'
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SLATE = 'blue14'
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YELLOW = 'user16'
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LIGHTBLUE = 'blue9'
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GREEN = 'green'
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RED = 'red'
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WHITE = 'white'
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ORANGE = 'orange'
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PINK = 'pink'
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MAGENTA = 'purple'
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DEEPRED = 'brown'
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OLIVE = 'olive'
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GREY = 'gray'
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ATOM_RAINBOW_COLORS = [BLUE, LIGHTBLUE, SEAFOAM, LIME, DARK_GR
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RIBBON_RAINBOW_COLORS = ['blue', 'lightblue', 'turquoise', 'sp
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PYMOL_COLOR_CYCLE = [GREEN, CYAN, MAGENTA, YELLOW, PINK, WHITE
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object_color_cycles = {}
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RT_COLOR_LABEL_START = '<span style="background-color:black;fo
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RT_COLOR_LABEL_END = '</span>'
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RT_TO_MAESTRO_COLORS = {}
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PARTIAL_CHARGE_4D = '1charge - b'
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SURFACE_AREA_CUTOFF = 10.
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PML_SURFACE = 'BL_Surface'
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PML_PRESET_SURFACE = 'BL_Preset_Surface'
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DAVE_DEBUG = os.environ.get('TOGGLE_DEBUG', 0)== 1
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results_window = None hash(x) |
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toggle_table = None The parent Toggle Table widget |
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labeler = workspacelabeler.WorkspaceLabeler()
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rock_data = RockData(interval= 1, amount= 1, span= 25)
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mmshare_data = util.hunt('mmshare', dir= 'data')
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colorpath = os.path.join(mmshare_data, 'colors.res')
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colorfile = open(colorpath, 'r')
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color_dict = OrderedDict(sorted(color_dict.items(), key= _colo
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HYDROGEN_COLOR = 'hydrogen'
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CARBON_COLOR = 'carbon'
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OBJECT_COLOR = 'object'
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MAX_RECENT_COLORS = 12
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pref_dir = maestro.get_directory(maestro.PREFERENCES)
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color_path = os.path.join(pref_dir, 'bio_color_info.conf')
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custom_color_dicts = {}
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color_file = open(color_path, 'r')
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Show and restart the progress bar on the Toggle Table if the TT is defined
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Show the current progress on the progress bar on the Toggle Table if the TT is defined
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Get the atoms in the workspace structure that match the given asl
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Get the entries in the workspace structure are affected by the given asl
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Return list of the the Visible workspace atoms
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Return an ASL that represents the Visible workspace atoms
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Joins 2 asls with the given joiner (default is AND)
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Puts a modifier in front of asl - which it protects in ()'s to make sure the modifier applies to the whole asl
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Get the surfaces associated with entry_id entry
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Get the structures in the workspace referred to by a given toggle table entry
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Display atoms and bonds with the given style, and turn off ribbons and surfaces
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Display atoms and bonds with the given style, leaving ribbons as is
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Display the specified atoms and bonds for a visible entry
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Set atom display properties (without displaying the atoms) for invisible entries
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Determine all visible and invisible entries that a toggle table object refers to.
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Modify the ASL to include current entry id
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Show ribbons
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Display all ribons for a visible (i.e. toggled on) entry
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Display all ribons for an invisible (i.e. toggled off) entry
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Update the ribbon_bypos_styles dictionary, which stores ribbon display information for invisible entries
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Update the ribbon_bypca_styles dictionary, which stores ribbon display information for invisible entries
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Rotate the workspace back and forth smoothly by small degree increments over a span of degrees range. If called when rocking is currently occuring, will stop the rocking.
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Tries to display the image file in the default image viewer
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Ensure that filename ends with the proper extension
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Create a surface
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If the owner is invisible, hide the newly created surface
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Find all the entries specified by the given owner or asl
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Finds the x,y,z coordinates of the center of the atoms
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Finds all polar contacts (hydrogen bonds) between asl1 and asl2.
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Hide the atoms given by asl
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Add entry ids to an ASL
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Run the given Maestro command on the specified atoms
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If the specified ASL is blank and owner is a selection, return the selection ASL. Otherwise, return the specified ASL.
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Remove atoms from the owner.visible_atoms list
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Hide ribbons
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Hide ribbons from an invisible structure. Note that owner is a mandatory argument, but asl is optional. (The arguments are in this order to be consistent with hide_ribbons, where owner is not mandatory.)
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Remove the specified atoms from a ToggleTableEntry ribbon styles dictionary
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Remove the specified atoms from a ToggleTableEntry ribbon colors dictionary
Note: Unlike _filter_ribbon_styles, this function acts directly on the owner object and does not return anything |
Hide a surface
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Given the toggle table owner, hide a surface.
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Hide the labels
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Hide atoms, ribbons and surfaces
Note: At least one argument must be provided. |
Create the Hide menu
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Get a user-specified color from the list of known Maestro colors
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Colors the specified atoms with the given color
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Colors the specified atoms with the given RGB colors
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Form an ASL that restricts the given ASL to those atoms of a specific element
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Color H, C, N, O and S by colors
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The user has selected a new (or re-selected an existing custom set) - add it to the list of custom sets (or move it to the end) so it ends up at the top of the menu
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Maestro doesn't like blank chain names in ASL without quotes so add the quotes if necessary
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Returns the atom B-factor
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Divide atoms up into bins based on their B-factor (temperature factor). The groups are determined to span equal ranges of b-factor (some groups may therefore contain no atoms).
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Color all the atoms (and sometimes the ribbons) as chainbows
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Adds items common to many context menus
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PROT_AND_DNA_SELE
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MAESTRO_TO_STRUCT_STYLE
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MMCT_TO_MAESTRO_RIBBON_STYLE
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MAESTRO_TO_MMCT_RIBBON_STYLE
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ATOM_RAINBOW_COLORS
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RIBBON_RAINBOW_COLORS
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PYMOL_COLOR_CYCLE
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RT_COLOR_LABEL_START
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color_dict
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Trees | Indices | Help |
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