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
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

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.
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

persistent_name

Sphere object’s persistent name

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 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 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.

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: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 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