schrodinger.application.phase.phase_markers module¶

Phase pharmacophore workspace markers.

schrodinger.application.phase.phase_markers.get_atom_label_font_name() → str¶: @return: Font name to be used to render labels. Default is “Sans Serif”.

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.PhaseTextMarker(label, visible)¶

Bases: object

Class defining a single text label for a Phase marker.

__init__(label, visible)¶

Text marker initializer.

Parameters

label (int) – The handle of a Maestro text object
visible (bool) – tracks whether this marker is visible

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

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¶

property g¶

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¶

property opacity¶

property persistent_name¶

property pick_category¶

property pick_id¶

property r¶

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, a=None)¶

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: PyQt6.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.
markerTextToggled (QtCore.pyqtSignal) – signal that gets emitted when features text labels are toggled on and off.
_phase_features (dict[(int, str), PhaseFeatureMarker]) – dictionary mapping feature key tuples to markers associated with this panel

editingFinished¶

closeFeatureEditDialog¶

workspaceMarkersChanged¶

markerTextToggled¶

__init__(*args, **kwargs)¶

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

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 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.

setFeatureLabelVisible(entry_id, visible)¶

Shows or hides feature label for all markers.

Parameters

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

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

isAnyTextLabelVisible()¶

Checks whether any text labels (feature or property) are visible.

Returns: True if any label is visible and False otherwise.
Return type: bool

blockSignals(self, b: bool) → bool¶

childEvent(self, a0: QChildEvent)¶

children(self) → List[QObject]¶

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) → bool¶
disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, a0: QEvent) → bool¶

eventFilter(self, a0: QObject, a1: QEvent) → bool¶

findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject¶
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]¶
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

inherits(self, classname: str) → bool¶

installEventFilter(self, a0: QObject)¶

isSignalConnected(self, signal: QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, id: int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, thread: QThread)¶

objectName(self) → str¶

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

parent(self) → QObject¶

property(self, name: 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, signal: PYQT_SIGNAL) → int¶

removeEventFilter(self, a0: QObject)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, name: str)¶

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: Any) → bool¶

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

tr(sourceText: str, disambiguation: typing.Optional[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_feature_labels_visible(entry_id, visible, hypo=None, store_prop=True, emit_signal=True)¶

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

Parameters

entry_id (int) – Phase hypothesis entry id
visible (bool) – whether to make feature labels visible or not
hypo (hypothesis.PhaseHypothesis) – the hypothesis or None. If None, the hypothesis will be obtained from the project entry id.
store_prop (bool) – indicates whether visibility property should be set for the hypothesis entry. When set to False check state in PT hypothesis context menu will not change.
emit_signal (bool) – indicates whether signal should be emitted when this method is called. Default value is True

schrodinger.application.phase.phase_markers.show_all_feature_labels(visible)¶

Toggles display of all feature labels for hypotheses included in the Workspace.

Parameters: visible (bool) – whether to make feature labels visible or not

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

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.
store_prop (bool) – indicates whether visibility property should be set for the hypothesis entry. When set to False check state in PT hypothesis context menu will not change.
emit_signal (bool) – indicates whether signal should be emitted when this method is called. Default value is True

schrodinger.application.phase.phase_markers.show_all_property_labels(visible)¶

Toggles display of all property labels for hypotheses included in the Workspace.

Parameters: visible (bool) – whether to make property2 labels visible or not

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

Checks whether any Phase feature text label (feature or property) is visible.

Returns: True if any text label is visible.
Return type: bool

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

Returns a list of entry ids for Phase hypotheses that are included in the Workspace.

Returns: list of entry ids
Return type: List[int]

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

schrodinger.application.phase.phase_markers.any_phase_hypothesis_label_property_checked() → bool¶: Checks and returns if any feature label or property label is present for markers. :return: True if any feature/property label is present, False otherwise.

schrodinger.application.phase.phase_markers.is_feature_label_checked(pt, entry_id: int) → bool¶

Returns True if Feature Label is checked in project for entry id, False otherwise.

Parameters

pt (schrodinger.project.project.Project) – currently active project table
entry_id – is entry for which property needs to be checked.

schrodinger.application.phase.phase_markers.is_property_label_checked(pt, entry_id: int) → bool¶

Returns True if Property label is checked in project for entry id, False otherwise.

Parameters

pt (schrodinger.project.project.Project) – currently active project table
entry_id – is entry for which property needs to be checked.

schrodinger.application.phase.phase_markers.show_all_marker_labels_if_property_checked()¶: Shows feature labels and property labels for markers if corresponding property is checked in menu.