schrodinger.application.phase.phase_markers module¶

Phase pharmacophore workspace markers.

schrodinger.application.phase.phase_markers.set_freestyle_site_type(site, feature_type)¶

Updates a site with the given pharmacophore feature type, and if applicable assigns projected coordinates of the corresponding free-style site type.

Returns:	pharmacophore site
Return type:	`phase.PhpSite`
Parameters:	feature_type (str) – site’s feature type

schrodinger.application.phase.phase_markers.is_site_grouped(site)¶

Get whether site is grouped

Parameters:	site (phase.PhpSite) – pharmacophore site
Returns:	whether or not site is grouped
Return type:	bool

schrodinger.application.phase.phase_markers.get_mask_name(site)¶

Get the name of the site’s mask

Parameters:	site (phase.PhpSite) – pharmacophore site
Returns:	site mask min match name
Return type:	str

class schrodinger.application.phase.phase_markers.PhaseFeatureMarker(site, entry_id, color, use_highlight, allow_picking=True)¶

Bases: object

Class defining a single Phase marker.

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)¶

MASKED_COLOR = (0.35, 0.35, 0.35)¶

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¶

__init__(site, entry_id, color, use_highlight, allow_picking=True)¶

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

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

__del__(_isinstance=<built-in function isinstance>, _module=<class 'module'>, _maestro=<module 'schrodinger.maestro.maestro' from '/scr/buildbot/savedbuilds/2018-4/NB/build-145/internal/lib/python3.6/site-packages/schrodinger/maestro/maestro.py'>)¶: Remove graphics text objects, not handled by Python garbage collector

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

setRightClickHandler(pick_category)¶

Sets right click handler for a given pick category.

Parameters:	pick_category – picking category of markers type – str

createLabels()¶: Create the labels for the sites of this feature in the Workspace.

clearLabels()¶: Remove all marker labels.

showLabels()¶: Show all marker labels.

hideLabels()¶: Hide all marker labels.

setIsGlowing(is_glowing)¶

Enables or disables glow effect for the object.

Parameters:	is_glowing (bool) – whether the object is glowing

setSelected(select)¶

Shows glow effect when this feature is selected.

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

show()¶

hide()¶

clear()¶

mask()¶: Mask the feature in workspace by setting a dull grey color to marker.

unmask()¶: Unmask the feature in workspace by setting default color to marker.

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.phase_markers', '__doc__': '\n Class defining a single Phase marker.\n ', '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), 'MASKED_COLOR': (0.35, 0.35, 0.35), '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, '__init__': <function PhaseFeatureMarker.__init__>, 'feature_type': <property object>, 'feature_name': <property object>, 'feature_coordinates': <property object>, 'is_projected': <property object>, '__del__': <function PhaseFeatureMarker.__del__>, 'getHypoID': <function PhaseFeatureMarker.getHypoID>, '_getFeatureProperties': <function PhaseFeatureMarker._getFeatureProperties>, '_createFeature': <function PhaseFeatureMarker._createFeature>, '_createAromaticFeature': <function PhaseFeatureMarker._createAromaticFeature>, '_addToMarkerGroup': <function PhaseFeatureMarker._addToMarkerGroup>, 'setRightClickHandler': <function PhaseFeatureMarker.setRightClickHandler>, 'createLabels': <function PhaseFeatureMarker.createLabels>, 'clearLabels': <function PhaseFeatureMarker.clearLabels>, 'showLabels': <function PhaseFeatureMarker.showLabels>, 'hideLabels': <function PhaseFeatureMarker.hideLabels>, 'setIsGlowing': <function PhaseFeatureMarker.setIsGlowing>, 'setSelected': <function PhaseFeatureMarker.setSelected>, '_setGlowing': <function PhaseFeatureMarker._setGlowing>, '_setColor': <function PhaseFeatureMarker._setColor>, 'show': <function PhaseFeatureMarker.show>, 'hide': <function PhaseFeatureMarker.hide>, 'clear': <function PhaseFeatureMarker.clear>, 'mask': <function PhaseFeatureMarker.mask>, 'unmask': <function PhaseFeatureMarker.unmask>, '__dict__': <attribute '__dict__' of 'PhaseFeatureMarker' objects>, '__weakref__': <attribute '__weakref__' of 'PhaseFeatureMarker' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.phase.phase_markers'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

class schrodinger.application.phase.phase_markers.PhaseSphere(*args, **kwargs)¶

Bases: schrodinger.graphics3d.sphere.MaestroSphere

Phase sphere graphics object.

__init__(*args, **kwargs)¶

Constructor requires:

x, y, z: coordinate specifying center of sphere in Angstroms.

color: One of:: Color object Color name (string) Tuple of (R, G, B) (each 0.0-1.0)

radius: radius of the sphere in Angstroms

Optional arguments:

opacity: 0.0 (transparent) through 1.0 (opaque): Defaults to 1.0
resolution: 4 to 50: Defaults to 16

setSelected(selected, color=None)¶

Shows sphere as selected (with a glow effect). Glow effect color only needs to be specified when turning it ‘on’.

Parameters:	selected (bool) – whether sphere should be selected color (tuple) – color used for selected glow effect.

__class__¶: alias of builtins.type

__del__(_hasattr=<built-in function hasattr>, _maestro=<module 'schrodinger.maestro.maestro' from '/scr/buildbot/savedbuilds/2018-4/NB/build-145/internal/lib/python3.6/site-packages/schrodinger/maestro/maestro.py'>)¶

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.phase_markers', '__doc__': '\n Phase sphere graphics object.\n ', '__init__': <function PhaseSphere.__init__>, 'setSelected': <function PhaseSphere.setSelected>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.phase.phase_markers'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

b¶: Blue value in RGB triplet

g¶: Green value in RGB triplet

groupHidden()¶: Called when the group of this object is hidden. Hide the Maestro object(s).

groupShown()¶: Called when the group of this object is shown. Show the Maestro object, if we are being shown.

hide()¶: Hide the object. It will not be drawn when the group is drawn.

isGroupShown()¶: Returns True if this object’s group is shown. False otherwise.

isShown()¶: Returns True if this object shown. False otherwise.

material¶: Sphere’s material

opacity¶: Sphere’s opacity

pick_category¶: Sphere’s picking category

pick_id¶: Sphere object’s pick ID

r¶: Red value in RGB triplet

radius¶: Sphere’s radius

setColors()¶

setCoords()¶

setEntryID(entry_id)¶

Sets entry ID for Maestro object (necessary to render in tile-by-entry mode.

Parameters:	entry_id (str) – Object’s entry ID.

setGlowColor(r, g, b)¶

Sets glow color for the object.

Parameters:	r (float) – Red component of glow color [0.0 .. 1.0] g (float) – Green component of glow color [0.0 .. 1.0] b (float) – Blue component of glow color [0.0 .. 1.0]

setIsGlowing(is_glowing)¶

Enables or disables glow effect for the object.

Parameters:	is_glowing (bool) – Whether the object is glowing.

setRGBColors(r, g, b)¶

setRightClickOnGObject(pymodule, pyfunc)¶

Sets the python callback which should be called whenever given graphics object is right clicked.

Parameters:	pymodule (str) – Python module pyfunc (str) – Python function

setXYZCoords(x, y, z)¶

show()¶: Display this object, if it was hidden

x¶: X coordinate

y¶: Y coordinate

z¶: Z coordinate

class schrodinger.application.phase.phase_markers.PhaseSphereMarkers(entry_id)¶

Bases: object

Base class that defines group of sphere markers.

SPHERE_COLOR = (1.0, 1.0, 0.0)¶

SELECTED_COLOR = (0.25, 0.5, 0.95)¶

SPHERE_OPACITY = 0.1¶

SPHERE_RESOLUTION = 20¶

ANGLE_DEP_TRANSPARENCY = True¶

next_sphere_id = 1¶

__init__(entry_id)¶

Marker initializer.

Parameters:	entry_id (int) – hypothesis entry ID

addSphere(xyz, radius)¶

Adds spehere to marker group.

Parameters:	xyz ((float, float, float)) – sphere coordinates radius (float) – sphere radius

setSphereRadiusAndCoords(sphere_index, r, x, y, z)¶

Sets sphere radius and coordinates.

Parameters:	sphere_index (int) – index of sphere in self.spheres list r (float) – sphere radius x – sphere x-coordinate x – float y – sphere y-coordinate y – float z – sphere z-coordinate z – float

removeSpheres(sphere_indices)¶

Removes spheres from the group.

Parameters:	sphere_indices (list) – list of indices to the self.sphere list

setSelected(sphere_indices)¶

Shows the specified spheres as selected (with a glow effect).

Parameters:	sphere_indices (list) – list of indices to the self.sphere list

resetSelected()¶: Resets current selection.

show()¶: Show all spheres for this group.

hide()¶: Hide all spheres for this group.

showSphere(sphere_idx)¶

Show the specified sphere.

Parameters:	sphere_idx (int) – index of the sphere in self.spheres list to show.

hideSphere(sphere_idx)¶

Hide the specified sphere.

Parameters:	sphere_idx (int) – index of the sphere in self.spheres list to hide.

clear()¶: Deletes all spheres for this group.

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.phase_markers', '__doc__': '\n Base class that defines group of sphere markers.\n ', 'SPHERE_COLOR': (1.0, 1.0, 0.0), 'SELECTED_COLOR': (0.25, 0.5, 0.95), 'SPHERE_OPACITY': 0.1, 'SPHERE_RESOLUTION': 20, 'ANGLE_DEP_TRANSPARENCY': True, 'next_sphere_id': 1, '__init__': <function PhaseSphereMarkers.__init__>, 'addSphere': <function PhaseSphereMarkers.addSphere>, 'setSphereRadiusAndCoords': <function PhaseSphereMarkers.setSphereRadiusAndCoords>, 'removeSpheres': <function PhaseSphereMarkers.removeSpheres>, 'setSelected': <function PhaseSphereMarkers.setSelected>, 'resetSelected': <function PhaseSphereMarkers.resetSelected>, 'show': <function PhaseSphereMarkers.show>, 'hide': <function PhaseSphereMarkers.hide>, 'showSphere': <function PhaseSphereMarkers.showSphere>, 'hideSphere': <function PhaseSphereMarkers.hideSphere>, 'clear': <function PhaseSphereMarkers.clear>, '__dict__': <attribute '__dict__' of 'PhaseSphereMarkers' objects>, '__weakref__': <attribute '__weakref__' of 'PhaseSphereMarkers' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.phase.phase_markers'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

class schrodinger.application.phase.phase_markers.PhaseXvolMarkers(entry_id, x_vol, interactive=False)¶

Bases: schrodinger.application.phase.phase_markers.PhaseSphereMarkers

Class that defines group of spheres for the excluded volume.

SPHERE_COLOR = (0.2, 0.9, 0.95)¶

SPHERE_OPACITY = 0.2¶

__init__(entry_id, x_vol, interactive=False)¶

Marker initializer.

Parameters:	entry_id (int) – hypothesis entry ID x_vol (`phase.PhpExclVol`) – excluded volume object

addExcludedVolumes(x_vol)¶

Adds excluded volume spheres to the current group.

Parameters:	x_vol (`phase.PhpExclVol`) – excluded volume object

ANGLE_DEP_TRANSPARENCY = True¶

SELECTED_COLOR = (0.25, 0.5, 0.95)¶

SPHERE_RESOLUTION = 20¶

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.phase_markers', '__doc__': '\n Class that defines group of spheres for the excluded volume.\n ', 'SPHERE_COLOR': (0.2, 0.9, 0.95), 'SPHERE_OPACITY': 0.2, '__init__': <function PhaseXvolMarkers.__init__>, 'addExcludedVolumes': <function PhaseXvolMarkers.addExcludedVolumes>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.phase.phase_markers'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

addSphere(xyz, radius)¶

Adds spehere to marker group.

Parameters:	xyz ((float, float, float)) – sphere coordinates radius (float) – sphere radius

clear()¶: Deletes all spheres for this group.

hide()¶: Hide all spheres for this group.

hideSphere(sphere_idx)¶

Hide the specified sphere.

Parameters:	sphere_idx (int) – index of the sphere in self.spheres list to hide.

next_sphere_id = 1¶

removeSpheres(sphere_indices)¶

Removes spheres from the group.

Parameters:	sphere_indices (list) – list of indices to the self.sphere list

resetSelected()¶: Resets current selection.

setSelected(sphere_indices)¶

Shows the specified spheres as selected (with a glow effect).

Parameters:	sphere_indices (list) – list of indices to the self.sphere list

setSphereRadiusAndCoords(sphere_index, r, x, y, z)¶

Sets sphere radius and coordinates.

Parameters:	sphere_index (int) – index of sphere in self.spheres list r (float) – sphere radius x – sphere x-coordinate x – float y – sphere y-coordinate y – float z – sphere z-coordinate z – float

show()¶: Show all spheres for this group.

showSphere(sphere_idx)¶

Show the specified sphere.

Parameters:	sphere_idx (int) – index of the sphere in self.spheres list to show.

class schrodinger.application.phase.phase_markers.PhaseTolMarkers(entry_id, sites)¶

Bases: schrodinger.application.phase.phase_markers.PhaseSphereMarkers

Class that defines group of tolerance spheres.

SPHERE_COLOR = (0.5, 0.5, 0.5)¶

SPHERE_OPACITY = 0.5¶

__init__(entry_id, sites)¶

Marker initializer.

Parameters:	entry_id (int) – hypothesis entry ID sites (list of `phase.PhpSite`) – Phase hypothesis sites

showTolMarker(site)¶

Show tolerance marker for the given site.

Parameters:	site (`phase.PhpSite`) – Phase hypothesis site

hideTolMarker(site)¶

Hide tolerance marker for the given site.

Parameters:	site (`phase.PhpSite`) – Phase hypothesis site

ANGLE_DEP_TRANSPARENCY = True¶

SELECTED_COLOR = (0.25, 0.5, 0.95)¶

SPHERE_RESOLUTION = 20¶

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.phase_markers', '__doc__': '\n Class that defines group of tolerance spheres.\n ', 'SPHERE_COLOR': (0.5, 0.5, 0.5), 'SPHERE_OPACITY': 0.5, '__init__': <function PhaseTolMarkers.__init__>, 'showTolMarker': <function PhaseTolMarkers.showTolMarker>, 'hideTolMarker': <function PhaseTolMarkers.hideTolMarker>, '_genTolMarkerKey': <function PhaseTolMarkers._genTolMarkerKey>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.phase.phase_markers'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

addSphere(xyz, radius)¶

Adds spehere to marker group.

Parameters:	xyz ((float, float, float)) – sphere coordinates radius (float) – sphere radius

clear()¶: Deletes all spheres for this group.

hide()¶: Hide all spheres for this group.

hideSphere(sphere_idx)¶

Hide the specified sphere.

Parameters:	sphere_idx (int) – index of the sphere in self.spheres list to hide.

next_sphere_id = 1¶

removeSpheres(sphere_indices)¶

Removes spheres from the group.

Parameters:	sphere_indices (list) – list of indices to the self.sphere list

resetSelected()¶: Resets current selection.

setSelected(sphere_indices)¶

Shows the specified spheres as selected (with a glow effect).

Parameters:	sphere_indices (list) – list of indices to the self.sphere list

setSphereRadiusAndCoords(sphere_index, r, x, y, z)¶

Sets sphere radius and coordinates.

Parameters:	sphere_index (int) – index of sphere in self.spheres list r (float) – sphere radius x – sphere x-coordinate x – float y – sphere y-coordinate y – float z – sphere z-coordinate z – float

show()¶: Show all spheres for this group.

showSphere(sphere_idx)¶

Show the specified sphere.

Parameters:	sphere_idx (int) – index of the sphere in self.spheres list to show.

class schrodinger.application.phase.phase_markers.PhaseMarkers(*args, **kwargs)¶

Bases: PyQt5.QtCore.QObject

Class for adding pharmacophore feature markers and controlling their visibility.

Variables:	editingFinished (`QtCore.pyqtSignal`) – signal that gets emitted when feature editing is finished. This signal is emitted regardless of whether feature was changed or not. closeFeatureEditDialog (`QtCore.pyqtSignal`) – signal that gets emitted when any open edit feature dialog should be closed. This signal is emitted when the Phase GUI workflow changes, or the panel is closed.

editingFinished¶

closeFeatureEditDialog¶

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

featureExists(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:	True if features were already added and False otherwise
Return type:	bool

addStructureFeatures(st, mapper, entry_id, allow_picking=True)¶

Add all pharmacophore feature markers for a given structure.

Parameters:	st (`structure.Structure`) – molecule structure mapper (phase.PhpSiteMapper) – Site mapper entry_id (int) – structure entry id allow_picking (bool) – whether this marker can be ‘picked’, which allows showing a context menu when right-clicked
Returns:	list of sites that were added for this structure
Return type:	list

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

Add pharmacophore features for given sites.

Parameters:	sites (list of `phase.PhpSite`) – list of pharmacophore sites entry_id (int) – structure entry id use_highlight (list) – indicates whether sites should be ‘highlighted’ allow_picking (bool) – whether this marker can be ‘picked’, which allows showing a context menu when right-clicked

getFeature(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 that contains pharmacophore and projected points marker
Return type:	tuple

getAllFeatures()¶

Retrieve markers for all features.

Returns:	list of pharmacophore markers
Return type:	list

getSites(entry_id)¶

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

Parameters:	entry_id (int) – entry_id
Returns:	list of sites
Return type:	list

getFeatureNames(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) – entry_id

:return; list of feature names :rtype: list

addFeaturesForWorkspaceLigands(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

Return type:	list of ints
Returns:	List of entry IDs for the included ligands.

removeFeature(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

removeAllFeatures()¶: Removes markers for all pharmacophore features.

removeAllFeaturesForEntry(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(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

showAllFeatures()¶: Shows markers for all pharmacophore features.

showAllFeaturesForEntry(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

showAllFeaturesForEntryByType(entry_id, feature_types)¶

Show markers for all given feature types associated with a given entry.

Parameters:	entry_id (int) – entry id of the structure that these features are associated with. feature_types (List of str) – list of feature types that markers should be shown for.

hideFeature(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

hideAllFeatures()¶: Hide markers for all pharmacophore features.

hideAllFeaturesForEntry(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

hasXvolMarkers(entry_id)¶

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

Parameters:	entry_id (int) – entry ID

removeXvolMarkers(entry_id)¶

Removes all excluded volume markers for a given entry.

Parameters:	entry_id (int) – entry ID

removeXvolMarkersWithIDs(entry_id, sphere_indices)¶

Removes excluded volume markers with specified sphere ids for a given entry.

Parameters:	entry_id (int) – entry ID sphere_indices (list) – list of sphere indices

removeAllXvolMarkers()¶: Removes all excluded volume markers.

addXvolMarkers(entry_id, x_vol, interactive=False)¶

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 interactive (bool) – indicates whether markers should be ‘interactive’

findXvolSphereIndex(entry_id, pick_id)¶

Finds excluded volume sphere index for a given sphere pick id. Pick id is used to identify graphics3d objects picked in the Workspace.

Parameters:	entry_id (int) – entry ID pick_id (int) – pick id of graphics3d object
Returns:	index of sphere with a given pick id in the list that PhaseXvolMarkers object maintains.
Return type:	int

setXvolSelected(entry_id, sphere_indices)¶

Selects spheres with given sphere ids for a given entry id.

Parameters:	entry_id (int) – entry ID sphere_indices (list) – list of sphere indices

updateXvolMarker(entry_id, sphere_index, r, x, y, z)¶

This function is called to change radius and coordinates of excluded volume with a given sphere id and entry id.

Parameters:	entry_id (int) – entry ID sphere_index (int) – sphere index r (float) – new radius x (float) – new x-coordinate y (float) – new y-coordinate z (float) – new z-coordinate

hasTolMarkers(entry_id)¶

Checks whether tolerance markers for a given entry ID exist.

Parameters:	entry_id (int) – entry ID

removeTolMarkers(entry_id)¶

Removes all tolerance markers for a given entry.

Parameters:	entry_id (int) – entry ID

removeAllTolMarkers()¶: Removes all tolerance markers.

addTolMarkers(entry_id, sites)¶

Adds tolerance markers for a given entry ID.

Parameters:	entry_id (int) – entry ID sites (list of `phase.PhpSite`) – Phase hypothesis sites

showTolMarker(entry_id, site)¶

Show tolerance marker for the given entry ID and site.

Parameters:	entry_id (int) – hypothesis entry ID site (`phase.PhpSite`) – Phase hypothesis site

hideTolMarker(entry_id, site)¶

Hide tolerance marker for the given entry ID and site.

Parameters:	entry_id (int) – hypothesis entry ID site (`phase.PhpSite`) – Phase hypothesis site

projectModel()¶

Returns a Maestro project object.

Return type:	`schrodinger.MM_Project`
Returns:	Maestro project object.

hasRefCtMarker(entry_id)¶

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

Parameters:	entry_id (int) – entry ID

removeRefCtMarker(entry_id)¶

Removes all reference ligand markers for a given entry.

Parameters:	entry_id (int) – entry ID

removeAllRefCtMarkers()¶: Removes all reference ligand markers.

addRefCtMarker(entry_id, ref_ct)¶

Adds reference ligand markers for a given entry ID.

Parameters:	entry_id (str) – entry ID ref_ct (int) – data object that contains reference ligands

:note ownership is transferred to maestro project.

setSelection(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(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

clearSelection()¶: Clear ‘selection’ for all pharmacophore features.

setPropertyLabelVisible(entry_id, visible)¶

Shows or hides detailed (property) label for all feature markers.

Parameters:	entry_id (int) – entry id of the structure that these features are associated with visible (bool) – whether to make property labels visible or not

getFeatureFromId(marker_id)¶

Return the marker with the given ID.

Parameters:	marker_id (int) – ID of the marker (.id attribute)

:return Marker object :rtype PhaseFeatureMarker

__class__¶: alias of sip.wrappertype

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.phase_markers', '__doc__': '\n Class for adding pharmacophore feature markers and controlling their\n visibility.\n\n :cvar editingFinished: signal that gets emitted when feature editing is\n finished. This signal is emitted regardless of whether feature was changed\n or not.\n :vartype editingFinished: `QtCore.pyqtSignal`\n\n :cvar closeFeatureEditDialog: signal that gets emitted when any open edit\n feature dialog should be closed. This signal is emitted when the Phase GUI\n workflow changes, or the panel is closed.\n :vartype closeFeatureEditDialog: `QtCore.pyqtSignal`\n ', 'editingFinished': <unbound PYQT_SIGNAL PhaseMarkers.editingFinished[]>, 'closeFeatureEditDialog': <unbound PYQT_SIGNAL PhaseMarkers.closeFeatureEditDialog[]>, '__init__': <function PhaseMarkers.__init__>, 'featureExists': <function PhaseMarkers.featureExists>, 'addStructureFeatures': <function PhaseMarkers.addStructureFeatures>, 'addSites': <function PhaseMarkers.addSites>, 'getFeature': <function PhaseMarkers.getFeature>, 'getAllFeatures': <function PhaseMarkers.getAllFeatures>, 'getSites': <function PhaseMarkers.getSites>, 'getFeatureNames': <function PhaseMarkers.getFeatureNames>, 'addFeaturesForWorkspaceLigands': <function PhaseMarkers.addFeaturesForWorkspaceLigands>, '_updateFeatures': <function PhaseMarkers._updateFeatures>, 'removeFeature': <function PhaseMarkers.removeFeature>, 'removeAllFeatures': <function PhaseMarkers.removeAllFeatures>, 'removeAllFeaturesForEntry': <function PhaseMarkers.removeAllFeaturesForEntry>, 'showFeature': <function PhaseMarkers.showFeature>, 'showAllFeatures': <function PhaseMarkers.showAllFeatures>, 'showAllFeaturesForEntry': <function PhaseMarkers.showAllFeaturesForEntry>, 'showAllFeaturesForEntryByType': <function PhaseMarkers.showAllFeaturesForEntryByType>, '_showFeatureForKey': <function PhaseMarkers._showFeatureForKey>, 'hideFeature': <function PhaseMarkers.hideFeature>, 'hideAllFeatures': <function PhaseMarkers.hideAllFeatures>, 'hideAllFeaturesForEntry': <function PhaseMarkers.hideAllFeaturesForEntry>, '_hideFeatureForKey': <function PhaseMarkers._hideFeatureForKey>, 'hasXvolMarkers': <function PhaseMarkers.hasXvolMarkers>, 'removeXvolMarkers': <function PhaseMarkers.removeXvolMarkers>, 'removeXvolMarkersWithIDs': <function PhaseMarkers.removeXvolMarkersWithIDs>, 'removeAllXvolMarkers': <function PhaseMarkers.removeAllXvolMarkers>, 'addXvolMarkers': <function PhaseMarkers.addXvolMarkers>, 'findXvolSphereIndex': <function PhaseMarkers.findXvolSphereIndex>, 'setXvolSelected': <function PhaseMarkers.setXvolSelected>, 'updateXvolMarker': <function PhaseMarkers.updateXvolMarker>, 'hasTolMarkers': <function PhaseMarkers.hasTolMarkers>, 'removeTolMarkers': <function PhaseMarkers.removeTolMarkers>, 'removeAllTolMarkers': <function PhaseMarkers.removeAllTolMarkers>, 'addTolMarkers': <function PhaseMarkers.addTolMarkers>, 'showTolMarker': <function PhaseMarkers.showTolMarker>, 'hideTolMarker': <function PhaseMarkers.hideTolMarker>, 'projectModel': <function PhaseMarkers.projectModel>, 'hasRefCtMarker': <function PhaseMarkers.hasRefCtMarker>, 'removeRefCtMarker': <function PhaseMarkers.removeRefCtMarker>, 'removeAllRefCtMarkers': <function PhaseMarkers.removeAllRefCtMarkers>, 'addRefCtMarker': <function PhaseMarkers.addRefCtMarker>, 'setSelection': <function PhaseMarkers.setSelection>, 'setFeatureSelection': <function PhaseMarkers.setFeatureSelection>, 'clearSelection': <function PhaseMarkers.clearSelection>, 'setPropertyLabelVisible': <function PhaseMarkers.setPropertyLabelVisible>, '_genFeatureKey': <function PhaseMarkers._genFeatureKey>, '_getKeysForEntry': <function PhaseMarkers._getKeysForEntry>, '_getEntryIDs': <function PhaseMarkers._getEntryIDs>, 'getFeatureFromId': <function PhaseMarkers.getFeatureFromId>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattr__(self, str) → object¶

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.phase.phase_markers'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → object¶

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → object¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

inherits(self, str) → bool¶

installEventFilter(self, QObject)¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

parent(self) → QObject¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

signalsBlocked(self) → bool¶

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

tr(self, str, disambiguation: str = None, n: int = -1) → str¶

schrodinger.application.phase.phase_markers.get_phase_markers()¶

This function returns global PhaseMarkers object that should be used to generate Phase marker throughout Maestro session.

Returns:	PhaseMarkers object
Return type:	`PhaseMarkers`

schrodinger.application.phase.phase_markers.update_hypothesis_entry(hypo, entry_id)¶

Updates the structure in the project table for the given entry ID with the current PhaseHypothesis, updating the reference ligand if needed.

Parameters:	hypo (`hypothesis.PhaseHypothesis`) – hypothesis to assign to the given PT entry entry_id (int or str) – entry id to set hypothesis to

schrodinger.application.phase.phase_markers.show_workspace_phase_markers(entry_ids, include_Q=False)¶

Delays the call to show workspace phase markers with a single shot to allow for the project table project_model to update appropriately.

Parameters:	entry_ids (list of int) – list of Phase hypothesis entries include_Q (bool) – whether to include Q site phase markers

schrodinger.application.phase.phase_markers.hide_workspace_phase_markers(entry_ids)¶

Removes Phase pharmacophore site markers for given entries.

Parameters:	entry_ids (list) – list of Phase hypothesis entries

schrodinger.application.phase.phase_markers.project_close()¶: Delete all Phase feature markers.

schrodinger.application.phase.phase_markers.setup_project_close()¶: Sets up function that should be called when project is closed.

schrodinger.application.phase.phase_markers.set_entry_property(entry_id, prop_name, value)¶

Sets entry ct property to a given value. This function is used to set special hypothesis properties that define whether excluded volumes, tolerances and reference structure should be visible.

Parameters:	entry_id (int) – hypothesis entry id prop_name (str) – property name value (float or int or str) – property value

schrodinger.application.phase.phase_markers.set_excluded_volume_visible(entry_id, visible, hypo=None)¶

Toggles hypothesis properties which can be shown in the workspace for hypothesis with a given entry id.

Parameters:	entry_id (int) – Phase hypothesis entry id visible (bool) – whether to make visible in the workspace or not hypo (hypothesis.PhaseHypothesis) – the hypothesis or None. If None, the hypothesis will be obtained from the project entry id.

schrodinger.application.phase.phase_markers.set_reference_ligand_visible(entry_id, visible, hypo=None)¶

Toggles display of reference ligand in the Workspace for hypothesis with a given entry id.

Parameters:	entry_id (int) – Phase hypothesis entry id visible (bool) – whether to make visible in the workspace or not hypo (hypothesis.PhaseHypothesis) – the hypothesis or None. If None, the hypothesis will be obtained from the project entry id.

schrodinger.application.phase.phase_markers.set_feature_tolerance_visible(entry_id, visible, hypo=None)¶

Toggles display of feature tolerance spheres in the Workspace for hypothesis with a given entry id.

Parameters:	entry_id (int) – Phase hypothesis entry id visible (bool) – whether to make visible in the workspace or not hypo (hypothesis.PhaseHypothesis) – the hypothesis or None. If None, the hypothesis will be obtained from the project entry id.

schrodinger.application.phase.phase_markers.set_property_labels_visible(entry_id, visible, hypo=None)¶

Toggles display of feature property labels for hypothesis with a given entry_id.

Parameters:	entry_id (int) – Phase hypothesis entry id visible (bool) – whether to make property labels visible or not hypo (hypothesis.PhaseHypothesis) – the hypothesis or None. If None, the hypothesis will be obtained from the project entry id.

schrodinger.application.phase.phase_markers.show_phase_hover_markers(pick_id)¶

Show glow effect when mouse is hovered on a phase marker.

Parameters:	pick_id (int) – Phase marker pick id

schrodinger.application.phase.phase_markers.hide_phase_hover_markers(pick_id)¶

Remove glow effect when mouse is moved away from a phase marker.

Parameters:	pick_id (int) – Phase marker pick id

schrodinger.application.phase.phase_markers module¶

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