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

Class PhaseFeatureMixin

object --+
         |
        PhaseFeatureMixin

A mixin for adding pharmacophore feature markers and controlling their visibility.

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
x.__init__(...) initializes x; see help(type(x)) for signature

closeEvent(self, event)
Remove all features when the panel is closed.

addFeature(self, sites, feature_name, color, entry_id)
Add pharmacophore feature marker.

tuple

getFeature(self, feature_name, entry_id)
Retrieve markers for the specified feature.

tuple

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

_workspaceChanged(self, what_changed)
This function is called when Maestro workspace is changed.

_updateFeatures(self)
Show or hide features for entries that are included or excluded in the workspace.

removeFeature(self, feature_name, entry_id)
Removes markers for the specified pharmacophore feature.

removeAllFeatures(self)
Removes markers for all pharmacophore features.

removeAllFeaturesForEntry(self, entry_id)
Removes markers for all features associated with a given entry.

showFeature(self, feature_name, entry_id)
Show markers for the specified pharmacophore feature.

showAllFeatures(self)
Shows markers for all pharmacophore features.

showAllFeaturesForEntry(self, entry_id)
Shows markers for all features associated with a given entry.

_showFeatureForKey(self, feature_key)
Show markers for a given feature key.

hideFeature(self, feature_name, entry_id)
Hide markers for the specified pharmacophore feature.

hideAllFeatures(self)
Hide markers for all pharmacophore features.

hideAllFeaturesForEntry(self, entry_id)
Hide markers for all features associated with a given entry.

_hideFeatureForKey(self, feature_key)
Hide markers for a given feature key.

_genFeatureKey(self, feature_name, entry_id)
Create a unique feature key.

list

_getKeysForEntry(self, entry_id)
Get a list of all feature keys for a given entry id.

set

_getEntryIDs(self)
Get a list of unique entry ids that feature markers stored in this mixin are associated with.

tuple

_calculateArrowTail(self, x, y, z, px, py, pz, rad, rcyl)
Calculate coordinates of the projected point arrow tail position.

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

Class Variables

[hide private]

int ARROW_RADII = 0.15
radius of the arrow that is drawn between pharmacophore site and projected points.

int SPHERE_RADII = 0.8
radius of the pharmacophore site

Instance Variables

[hide private]

dict

_phase_features
A dictionary containing all pharmacophore feature markers associated with this panel.

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, *args, **kwargs)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

addFeature(self, sites, feature_name, color, entry_id)

Add pharmacophore feature marker.

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.
feature_name (str) - feature name
color (list) - list of float rgb values that define color of this feature's markers
entry_id (int) - entry id of the structure that this feature is associated with

Decorators:

@markers.requires_maestro

getFeature(self, feature_name, entry_id)

Retrieve markers for the specified feature.

Parameters:

feature_name (str) - feature name
entry_id (int) - entry id of the structure that this feature is associated with

Returns: tuple

Decorators:

@markers.requires_maestro

_createFeature(self, sites, color, 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
entry_id (int) - entry id of the structure that this feature is associated with

Returns: tuple

_workspaceChanged(self, what_changed)

This function is called when Maestro workspace is changed.

Decorators:

@maestro_callback.workspace_changed_active_project

_updateFeatures(self)

Show or hide features for entries that are included or excluded in the workspace. Delete features for entries, which were deleted from the project.

removeFeature(self, feature_name, entry_id)

Removes markers for the specified pharmacophore feature.

Parameters:

feature_name - feature name
feature_name - str
entry_id (int) - entry id of the structure that this feature is associated with

Decorators:

@markers.requires_maestro

removeAllFeatures(self)

Removes markers for all pharmacophore features.

Decorators:

@markers.requires_maestro

removeAllFeaturesForEntry(self, entry_id)

Removes markers for all features associated with a given entry.

Parameters:

entry_id (int) - entry id of the structure that this feature is associated with

Decorators:

@markers.requires_maestro

showFeature(self, feature_name, entry_id)

Show markers for the specified pharmacophore feature.

Parameters:

feature_name - feature name
feature_name - str
entry_id (int) - entry id of the structure that this feature is associated with

Decorators:

@markers.requires_maestro

showAllFeatures(self)

Shows markers for all pharmacophore features.

Decorators:

@markers.requires_maestro

showAllFeaturesForEntry(self, entry_id)

Shows markers for all features associated with a given entry.

Parameters:

entry_id (int) - entry id of the structure that this feature is associated with

Decorators:

@markers.requires_maestro

_showFeatureForKey(self, feature_key)

Show markers for a given feature key.

Parameters:

feature_key (str) - unique feature key.

hideFeature(self, feature_name, entry_id)

Hide markers for the specified pharmacophore feature.

Parameters:

feature_name - feature name
feature_name - str
entry_id (int) - entry id of the structure that this feature is associated with

Decorators:

@markers.requires_maestro

hideAllFeatures(self)

Hide markers for all pharmacophore features.

Decorators:

@markers.requires_maestro

hideAllFeaturesForEntry(self, entry_id)

Hide markers for all features associated with a given entry.

Parameters:

entry_id (int) - entry id of the structure that this feature is associated with

Decorators:

@markers.requires_maestro

_hideFeatureForKey(self, feature_key)

Hide markers for a given feature key.

Parameters:

feature_key (str) - unique feature key.

_genFeatureKey(self, feature_name, entry_id)

Create a unique feature key.

Parameters:

feature_name - feature name
feature_name - str
entry_id (int) - entry id of the structure that this feature is associated with

Returns:

A tuple

_getKeysForEntry(self, entry_id)

Get a list of all feature keys for a given entry id.

Parameters:

entry_id (int) - entry id of the structure that this feature is associated with

Returns: list

list of feature keys

_getEntryIDs(self)

Get a list of unique entry ids that feature markers stored in this mixin are associated with.

Returns: set: set of unique entry ids

_calculateArrowTail(self, x, y, z, px, py, pz, rad, rcyl)

Calculate coordinates of the projected point arrow tail position. Tail position is calculated in such a way that arrow cylinder 'grows' from the surface of the pharmacophore sphere.

Parameters:

x (float) - x-coordinate of the pharmacophore site
y (float) - y-coordinate of the pharmacophore site
z (float) - z-coordinate of the pharmacophore site
px (float) - x-coordinate of the projected point (arrow end point)
py (float) - y-coordinate of the projected point (arrow end point)
pz (float) - z-coordinate of the projected point (arrow end point)
rad (float) - pharmacophore feature sphere radii
rcyl (float) - radii of the arrow cylinder

Returns: tuple

tuple that contains xyz coordinates of the arrow tail point

Instance Variable Details

[hide private]

_phase_features

A dictionary containing all pharmacophore feature markers associated with this panel. Keys are generated via _genFeatureKey function. Values contain a tuple of two markers: pharmacophore site marker (sphere) and one or more arrow markers for projected points.

Type:: dict

Class PhaseFeatureMixin

__init__(self, *args, **kwargs) (Constructor)

addFeature(self, sites, feature_name, color, entry_id)

getFeature(self, feature_name, entry_id)

_createFeature(self, sites, color, entry_id)

_workspaceChanged(self, what_changed)

_updateFeatures(self)

removeFeature(self, feature_name, entry_id)

removeAllFeatures(self)

removeAllFeaturesForEntry(self, entry_id)

showFeature(self, feature_name, entry_id)

showAllFeatures(self)

showAllFeaturesForEntry(self, entry_id)

_showFeatureForKey(self, feature_key)

hideFeature(self, feature_name, entry_id)

hideAllFeatures(self)

hideAllFeaturesForEntry(self, entry_id)

_hideFeatureForKey(self, feature_key)

_genFeatureKey(self, feature_name, entry_id)

_getKeysForEntry(self, entry_id)

_getEntryIDs(self)

_calculateArrowTail(self, x, y, z, px, py, pz, rad, rcyl)

_phase_features

init(self, *args, **kwargs)
(Constructor)