schrodinger.application.phase.phase_markers module¶

Phase pharmacophore workspace markers.

class schrodinger.application.phase.phase_markers.FontStyles(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶

Bases: enum.Enum

Enum for font styles in Maestro.

This enum represents all potential font style names returned by maestro.get_command_option(“labelatom”, “font_style”).

Note: The values in this enum should be in sync with Maestro’s command options values.

NORMAL = 'normal'¶

ITALIC = 'italic'¶

BOLD = 'bold'¶

BOLD_ITALIC = 'bolditalic'¶

schrodinger.application.phase.phase_markers.get_atom_label_font() → tuple[str, int, bool, bool]¶

Fetches the font settings for atom labels from Maestro.

Returns: Font name, size, bold and italic flags to be used to render labels.
Return type: tuple

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

schrodinger.application.phase.phase_markers.update_phase_markers_label_font()¶: Update the font for all phase marker features.

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.

updateFontForAllLabels()¶: Update the font for all phase marker labels.

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.

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

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

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¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

closeFeatureEditDialog¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

workspaceMarkersChanged¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

markerTextToggled¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__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

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.