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2016-3 Schrodinger Python API
Package schrodinger :: Package application :: Package phase :: Module phase_markers :: Class PhaseMarkers
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Class PhaseMarkers

       object --+                
                |                
sip.simplewrapper --+            
                    |            
          sip.wrapper --+        
                        |        
     PyQt4.QtCore.QObject --+    
                            |    
            Qt.QtCore.QObject --+
                                |
                               PhaseMarkers

Class for adding pharmacophore feature markers and controlling their visibility.

Instance Methods [hide private]
 
editingFinished(...)
signal that gets emitted when feature editing is finished.
 
__init__(self, *args, **kwargs)
x.__init__(...) initializes x; see help(type(x)) for signature
 
__del__(self)
 
_workspaceDrawCallback(self)
Called by Maestro when Workspace needs to be drawn.
 
closeEvent(self, event)
Remove all features when the panel is closed.
bool
featureExists(self, entry_id)
This function checks whether pharmacophore features exist for a structure with a given entry_id and returns True or False.
list
addStructureFeatures(self, st, fds, entry_id, allow_picking=True)
Add all pharmacophore feature markers for a given structure.
 
addSites(self, sites, entry_id, use_highlight=False, allow_picking=True)
Add pharmacophore features for given sites.
 
addFeature(self, sites, feature_name, color, use_highlight, entry_id, allow_picking=True)
Add pharmacophore feature marker.
tuple
getFeature(self, feature_name, entry_id)
Retrieve markers for the specified feature.
list
getSites(self, entry_id)
Get list of sites for all features with a given entry id.
list
getFeatureNames(self, entry_id)
Get list of feature names that were found for the structure with a given entry id.
list of ints
addFeaturesForWorkspaceLigands(self, fds, allow_picking=True)
Add feature markers for each included ligand PT entry, according to the given feature definitions.
 
_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.
 
hasXvolMarkers(self, entry_id)
Checks whether excluded volume markers for a given entry ID exist.
 
removeXvolMarkers(self, entry_id)
Removes all excluded volume markers for a given entry.
 
removeAllXvolMarkers(self)
Removes all excluded volume markers.
 
addXvolMarkers(self, entry_id, x_vol)
Adds excluded volume markers for a given entry ID.
 
hasRefCtMarker(self, entry_id)
Checks whether refernce ligand marker for a given entry ID exists.
 
removeRefCtMarker(self, entry_id)
Removes all reference ligand markers for a given entry.
 
removeAllRefCtMarkers(self)
Removes all reference ligand markers.
 
addRefCtMarker(self, entry_id, ref_ct)
Adds reference ligand markers for a given entry ID.
 
setSelection(self, features, entry_id, selected)
Sets selection mode for multiple features.
 
setFeatureSelection(self, feature_name, entry_id, selected)
Set specified pharmacophore feature selection mode.
 
clearSelection(self)
Clear 'selection' for all pharmacophore features.
 
_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.
 
genFeatureName(self, feature_type, feature_num)
Generate feature name that starts with the one letter feature type and followed by the feature number.
 
getFeatureFromId(self, marker_id)
Return the marker with the given ID.

Inherited from Qt.QtCore.QObject: connect, emit

Inherited from PyQt4.QtCore.QObject: __getattr__, blockSignals, childEvent, children, connectNotify, customEvent, deleteLater, destroyed, disconnect, disconnectNotify, dumpObjectInfo, dumpObjectTree, dynamicPropertyNames, event, eventFilter, findChild, findChildren, inherits, installEventFilter, isWidgetType, killTimer, metaObject, moveToThread, objectName, parent, property, pyqtConfigure, receivers, removeEventFilter, sender, senderSignalIndex, setObjectName, setParent, setProperty, signalsBlocked, startTimer, thread, timerEvent, tr, trUtf8

Inherited from sip.simplewrapper: __new__

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

Class Variables [hide private]

Inherited from PyQt4.QtCore.QObject: staticMetaObject

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

editingFinished(...)

 
signal that gets emitted when feature editing is finished. This signal is emited regardless of whether feature was changed or not.

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

 

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

Overrides: object.__init__
(inherited documentation)

featureExists(self, entry_id)

 

This function checks whether pharmacophore features exist for a structure with a given entry_id and returns True or False.

Parameters:
  • entry_id (int) - structure entry_id
Returns: bool
True if features were already added and False otherwise

addStructureFeatures(self, st, fds, entry_id, allow_picking=True)

 

Add all pharmacophore feature markers for a given structure.

Parameters:
  • st (structure.Structure) - molecule structure
  • fds (list) - list of feature definitions
  • entry_id (int) - structure entry id
  • 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
Returns: list
list of sites that were added for this structure

addSites(self, sites, entry_id, use_highlight=False, allow_picking=True)

 

Add pharmacophore features for given sites.

Parameters:
  • sites (list) - list of pharmacophore sites
  • entry_id (int) - structure entry id
  • use_highlight (list) - indicates whether sites 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

addFeature(self, sites, feature_name, color, use_highlight, entry_id, allow_picking=True)

 

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
  • use_highlight (bool) - flag defining whether this marker should be highlighted
  • entry_id (int) - entry id of the structure that this feature is associated with
  • 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

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

getSites(self, entry_id)

 

Get list of sites for all features with a given entry id.

Parameters:
  • entry_id (int) - entry_id
Returns: list
list of sites

getFeatureNames(self, entry_id)

 

Get list of feature names that were found for the structure with a given entry id. Feature names are sorted in alphabetical order.

Parameters:
  • entry_id (int

    @return; list of feature names

    ) - entry_id
Returns: list

addFeaturesForWorkspaceLigands(self, fds, allow_picking=True)

 

Add feature markers for each included ligand PT entry, according to the given feature definitions.

Parameters:
  • fds - list of feature definitions
  • 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
  • st (list)
Returns: list of ints
List of entry IDs for the included ligands.
Decorators:
  • @maestro_required

_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

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

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

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

_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

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

_hideFeatureForKey(self, feature_key)

 

Hide markers for a given feature key.

Parameters:
  • feature_key (str) - unique feature key.

hasXvolMarkers(self, entry_id)

 

Checks whether excluded volume markers for a given entry ID exist.

Parameters:
  • entry_id (int) - entry ID

removeXvolMarkers(self, entry_id)

 

Removes all excluded volume markers for a given entry.

Parameters:
  • entry_id (int) - entry ID

addXvolMarkers(self, entry_id, x_vol)

 

Adds excluded volume markers for a given entry ID.

Parameters:
  • entry_id (int) - entry ID
  • x_vol (phase.PhpExclVol) - data object that contains excluded volumes

hasRefCtMarker(self, entry_id)

 

Checks whether refernce ligand marker for a given entry ID exists.

Parameters:
  • entry_id (int) - entry ID

removeRefCtMarker(self, entry_id)

 

Removes all reference ligand markers for a given entry.

Parameters:
  • entry_id (int) - entry ID

addRefCtMarker(self, entry_id, ref_ct)

 

Adds reference ligand markers for a given entry ID.

Parameters:
  • entry_id (int) - entry ID
  • ref_ct (phase.PhpExclVol) - data object that contains reference ligands

setSelection(self, features, entry_id, selected)

 

Sets selection mode for multiple features.

Parameters:
  • features (list) - list of feature names
  • entry_id (int) - entry id of the structure that this feature is associated with
  • selected (bool) - indicates whether feature should be selected or not

setFeatureSelection(self, feature_name, entry_id, selected)

 

Set specified pharmacophore feature selection mode. Shows glow effect around markers.

Parameters:
  • feature_name - feature name
  • feature_name - str
  • entry_id (int) - entry id of the structure that this feature is associated with
  • selected (bool) - indicates whether feature should be selected or not

_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

genFeatureName(self, feature_type, feature_num)

 

Generate feature name that starts with the one letter feature type and followed by the feature number. Note that we increment feature number by one to make it 1-based.

Parameters:
  • feature_type (str) - one letter feature type
  • feature_num (int) - feature number

getFeatureFromId(self, marker_id)

 

Return the marker with the given ID.

Parameters:
  • marker_id (int

    @return Marker object @rtype PhaseFeatureMarker

    ) - ID of the marker (.id attribute)

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2016-3 Schrodinger Python API
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