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 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: 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)

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

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(QMetaObject.Connection) → bool

disconnect(self) → None

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

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)

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.

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