schrodinger.application.phase.phase_markers module¶
Phase pharmacophore workspace markers.
Copyright Schrodinger, LLC. All rights reserved.
-
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 markerentry_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
-
property
feature_type
¶ Phase type string of the pharmacophore site
-
property
feature_name
¶ Display name of the pharmacophore site
-
property
feature_coordinates
¶ List of coordinates of the main site and any projected coordinates
-
property
is_projected
¶ Whether the marker represents a Q projected feature
-
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.
-
setHovered
(hovered: bool)¶ Enable or disable hover effect for the marker.
-
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
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.
-
property
b
¶ Blue value in RGB triplet
-
property
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.
-
property
material
¶ Sphere’s material
-
property
opacity
¶ Sphere’s opacity
-
property
persistent_name
¶ Sphere object’s persistent name
-
property
pick_category
¶ Sphere’s picking category
-
property
pick_id
¶ Sphere object’s pick ID
-
property
r
¶ Red value in RGB triplet
-
property
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
-
property
x
¶ X coordinate
-
property
y
¶ Y coordinate
-
property
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
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¶
-
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¶
-
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.workspaceMarkersChanged (
QtCore.pyqtSignal
) – signal that gets emitted when features are shown or hidden in the Workspace._phase_features (dict[(int, str), PhaseFeatureMarker]) – dictionary mapping feature key tuples to markers associated with this panel
-
editingFinished
¶
-
closeFeatureEditDialog
¶
-
workspaceMarkersChanged
¶
-
__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 structuremapper (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 sitesentry_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
-
addCustomSites
(sites, entry_id, use_highlight=False, allow_picking=True, site_color_map={'A': (1.0, 0.5, 0.5), 'D': (0.5, 0.8, 0.9), 'H': (0.3, 1.0, 0.3), 'N': (1.0, 0.3, 0.3), 'P': (0.5, 0.6, 1.0), 'Q': (1.0, 0.0, 1.0), 'R': (0.92, 0.51, 0.2), 'X': (0.0, 1.0, 1.0), 'Y': (0.3, 0.0, 1.0), 'Z': (1.0, 0.0, 1.0)}, *_, marker_class)¶ Add pharmacophore features for given sites using a custom marker class.
See
addSites
for additional argument documentation.- Parameters
site_color_map (Dict {phase.InteractionType: (r, g, b)}) – Mapping of phase interaction type -> color
marker_class (PhaseFeatureMarker) – Marker class (Mandatory keyword-only argument)
-
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 volumesinteractive (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
-
blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
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
-
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 entryentry_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 hover 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 hover effect when mouse is moved away from a phase marker.
- Parameters
pick_id (int) – Phase marker pick id