Package schrodinger :: Package application :: Package phase :: Module phase_markers :: Class PhaseFeatureMarker

Class PhaseFeatureMarker

object --+
         |
        PhaseFeatureMarker

Class defining a single Phase marker.

Instance Methods

[hide private]

__init__(self, sites, feature_index, color, entry_id, feature_name, use_highlight, allow_picking=True)
Feature marker initializer.

getHypoID(self)
Return the hypothesis name/ID for the hypothesis from which this feature is from.

setPropertyLabelVisible(self, visible)
Shows or hides detailed (property) label for this feature marker.

dict or None

_getFeatureProperties(self)
Returns feature properties such as feature rules, tolerance etc from the hypothesis.

tuple

_createFeature(self, sites, color, opacity, entry_id)
Create markers for the given pharmacophore sites.

tuple

_createAromaticFeature(self, sites, color, opacity, entry_id)
Create markers for the given aromatic feature.

setRightClickHandler(self, pick_category)
Sets right click handler for a given pick category.

drawLabels(self)
Draw the labels for the sites of this features in the Workspace.

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]

int ARROW_RADII = 0.065
radius of the arrow that is drawn between pharmacophore site and projected points.

int SPHERE_RADII = 0.4
radius of the pharmacophore site

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'

feature_counter = 1

Instance Variables

[hide private]

_phase_features
A dictionary containing all pharmacophore feature

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, sites, feature_index, color, entry_id, feature_name, use_highlight, allow_picking=True)
(Constructor)

Feature marker initializer.

Parameters:

sites (list) - list of PhpSite objects for this feature
feature_index (int) - index of this feature in a hypothesis
color (list) - feature marker color defined as a list of rgb values
entry_id (int) - entry id of structure this feature belongs to
feature_name (str) - feature name
use_highlight (bool) - flag defining whether this marker should be highlighted
allow_picking - indicates whether feature can be 'picked'. When enabled this would make possible to show context menu when feature is right-clicked. Default is True. @type allow_picking

Overrides: object.__init__

setPropertyLabelVisible(self, visible)

Shows or hides detailed (property) label for this feature marker.

Parameters:

visible (bool) - whether to make property labels visible or not

_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, sites, color, opacity, entry_id)

Create markers for the given pharmacophore sites.

Parameters:

sites (list) - list of PhpSite objects, where the first element is always pharmacophore site, which is followed by one or more sites for projected points ('Q' site type).
color (list) - list of float rgb values that define color of this feature's markers
opacity (float) - feature marker opacity
entry_id (int) - entry id of the structure that this feature is associated with

Returns: tuple

_createAromaticFeature(self, sites, color, opacity, entry_id)

Create markers for the given aromatic feature.

Parameters:

sites (list) - list of PhpSite objects, where the first element is always pharmacophore site, which is followed by one or more sites for projected points ('Q' site type).
color (list) - list of float rgb values that define color of this feature's markers
opacity (float) - feature marker opacity
entry_id (int) - entry id of the structure that this feature is associated with

Returns: tuple

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) - indicates 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) - color that should be used for the glow effect. It is given as a tuple of rgb values.

Class PhaseFeatureMarker

__init__(self, sites, feature_index, color, entry_id, feature_name, use_highlight, allow_picking=True) (Constructor)

setPropertyLabelVisible(self, visible)

_getFeatureProperties(self)

_createFeature(self, sites, color, opacity, entry_id)

_createAromaticFeature(self, sites, color, opacity, entry_id)

setRightClickHandler(self, pick_category)

setIsGlowing(self, is_glowing)

setSelected(self, select)

_setGlowing(self, is_glowing, glow_color)

init(self, sites, feature_index, color, entry_id, feature_name, use_highlight, allow_picking=True)
(Constructor)