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2017-2 Schrodinger Python API
Package schrodinger :: Package application :: Package phase :: Module phase_markers :: Class PhaseFeatureMarker
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Class PhaseFeatureMarker

object --+
         |
        PhaseFeatureMarker

Class defining a single Phase marker.

Instance Methods [hide private]
 
__init__(self, site, entry_id, color, use_highlight, allow_picking=True)
Feature marker initializer.
 
__del__(self)
Remove graphics text objects, not handled by Python garbage collector
 
getHypoID(self)
Return the hypothesis name/ID for the hypothesis from which this feature is from.
dict or None
_getFeatureProperties(self)
Returns feature properties such as feature rules, tolerance etc from the hypothesis.
 
_createFeature(self)
Creates a sphere marker for a pharmacophore site.
 
_createAromaticFeature(self)
Creates a torus marker for an aromatic pharmacophore site.
 
_addToMarkerGroup(self, maestro_object)
Assigns marker properties to the Maestro object, and adds it to the marker group.
 
setRightClickHandler(self, pick_category)
Sets right click handler for a given pick category.
 
createLabels(self)
Create the labels for the sites of this feature in the Workspace.
 
clearLabels(self)
Remove all marker labels.
 
setIsGlowing(self, is_glowing)
Enables or disables glow effect for the object.
 
setSelected(self, select)
Shows glow effect when this feature is selected.
 
_setGlowing(self, is_glowing, glow_color)
Enables or disables glow effect for the object.
 
show(self)
 
hide(self)
 
clear(self)

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  ARROW_RADII = 0.065
  SPHERE_RADII = 0.4
  TORUS_RADII = 0.45
  TORUS_TUBE_RADII = 0.12
  OPACITY_DEFAULT = 0.4
  OPACITY_SELECTED = 1.0
  GLOW_COLOR = (0.95, 0.5, 0.25)
  SELECTED_COLOR = (0.25, 0.5, 0.95)
  FEATURE_TYPE = 'Feature Type'
  USE_IN_SCREEN = 'Use in Screening'
  ALLOWED_TO_MATCH = 'Allowed to match'
  FORBIDDEN_TO_MATCH = 'Forbidden to match'
  TOLERANCE = 'Tolerance'
  XP_SCORE = 'XP Score'
  feature_counter = 1
Properties [hide private]
  feature_type
Phase type string of the pharmacophore site
  feature_name
Display name of the pharmacophore site
  feature_coordinates
List of coordinates of the main site and any projected coordinates
  is_projected
Whether the marker represents a Q projected feature

Inherited from object: __class__

Method Details [hide private]

__init__(self, site, entry_id, color, use_highlight, allow_picking=True)
(Constructor)

 

Feature marker initializer.

Parameters:
  • site (phase.PhpSite) - pharmacophore site for this marker
  • entry_id (int) - entry id of structure this feature belongs to
  • color (list) - feature marker color defined as a list of rgb values
  • use_highlight (bool) - whether this marker should be highlighted
  • allow_picking (bool) - whether this marker can be 'picked', which allows showing a context menu when right-clicked
Overrides: object.__init__

_getFeatureProperties(self)

 

Returns feature properties such as feature rules, tolerance etc from the hypothesis. If there is no hypothesis associated with this feature returns None.

Returns: dict or None
dictionary of feature properties keyed on the feature name

_createFeature(self)

 

Creates a sphere marker for a pharmacophore site. If the site has projected coordinates, arrows are created pointing to/from the sphere.

_addToMarkerGroup(self, maestro_object)

 

Assigns marker properties to the Maestro object, and adds it to the marker group.

Parameters:
  • maestro_object (graphics3d object) - Maestro 3D object

setRightClickHandler(self, pick_category)

 

Sets right click handler for a given pick category.

Parameters:
  • pick_category - picking category of markers
  • type - str

setIsGlowing(self, is_glowing)

 

Enables or disables glow effect for the object.

Parameters:
  • is_glowing (bool) - whether the object is glowing

setSelected(self, select)

 

Shows glow effect when this feature is selected.

Parameters:
  • select (bool) - whether this feature should be selected

_setGlowing(self, is_glowing, glow_color)

 

Enables or disables glow effect for the object.

Parameters:
  • is_glowing (bool) - whether the object is glowing
  • glow_color (tuple of rgb values) - color that should be used for the glow effect

Property Details [hide private]

feature_type

Phase type string of the pharmacophore site

Get Method:
unreachable.feature_type(self) - Phase type string of the pharmacophore site

feature_name

Display name of the pharmacophore site

Get Method:
unreachable.feature_name(self) - Display name of the pharmacophore site

feature_coordinates

List of coordinates of the main site and any projected coordinates

Get Method:
unreachable.feature_coordinates(self) - List of coordinates of the main site and any projected coordinates

is_projected

Whether the marker represents a Q projected feature

Get Method:
unreachable.is_projected(self) - Whether the marker represents a Q projected feature

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2017-2 Schrodinger Python API
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