schrodinger.application.glide.gui module¶

Classes and functions that are shared between the Glide GridGen and Docking panels.

schrodinger.application.glide.gui.find_equivalent_atoms(st, anum)¶: Given a structure atom, return a list of atoms that are identical to it. If no identical atoms are found, and empty list is returned.

class schrodinger.application.glide.gui.GlideWorkspaceMarkers¶

Bases: schrodinger.ui.qt.appframework2.markers.MarkerMixin

Class for marking constraints and excluded volumes in the Workspace. Along with the marker, optional labels are also drawn.

__init__()¶

clear()¶: Remove all added labels.

add(center=None, radius=None, atom=None, color=None, name=None, opacity=0.8)¶

Add another marker to draw.

Either center and radius need to be specified (to draw a sphere) or an atom object (to draw atom markers).

show()¶: Show the markers in the Workspace.

hide()¶: Hide the markers from the Workspace.

setVisible(visible)¶: Show the markers if “visible” is True, hide otherwise.

showLabels()¶: Enable labels.

hideLabels()¶: Disable labels.

setLabelsVisible(visible)¶: Show the labels if “visible” is True, hide otherwise.

addJaguarMarker(atoms, color=None, icon=None, text='', alt_color=None, highlight=False)¶

Add a marker to the specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to mark. A list may contain between one and four atoms (inclusive).
color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker and icon. May be an RGB tuple, color name, color index, or schrodinger.structutils.color instance. If not given, white will be used.
icon (int) – The icon to draw next to the marker. Should be one the self.MARKER_ICONS constants. If not given, no icon will be drawn.
text (str) – The text to display next to the marker. If not given, no text will be displayed. Note that this argument will be ignored when marking a single atom.
alt_color (tuple, str, int, or schrodinger.structutils.color) – The alternate marker color. This color is always used for text, and is used for the marker and icon when highlight is True. If not given, color will be used.
highlight (bool) – Whether the marker should be highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Returns

The newly created marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If a marker already exists for the specified atoms

Note

Either an icon or text may be displayed on a marker, but not both. If both are given, only the text will be shown.

addMarker(atoms, color=(1.0, 1.0, 1.0), group_name=None)¶

Generates a set of simple, dot-styled markers for a group of atoms.

Parameters

atoms (list or schrodinger.structure._StructureAtom) – List of atoms to be marked
color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

addMarkerFromAsl(asl, color=(1.0, 1.0, 1.0), group_name=None)¶

Generates a set of simple, dot-styled markers for group of Workspace atoms that match the given ASL. Same atoms continue to be marked even if the Workspace is later modified such that ASL matching changes.

Parameters

asl – ASL for the atoms to mark.
color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

Returns: Marker object
Return type: markers.Marker

closeEvent(event)¶: Hide all markers when the panel is closed.

getAllJaguarMarkers()¶

Get all markers._BaseMarker currently loaded into the panel

Returns: An iterator of markers._BaseMarker
Return type: iterator

getAllMarkers()¶

Get all markers.Marker loaded into the panel

Returns: list(markers.Marker)
Return type: list

getJaguarMarker(atoms)¶

Retrieve a marker for the specified atom(s)

Parameters: atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).
Returns: The requested marker
Return type: schrodinger.maestro.markers._BaseMarker
Raises: ValueError – If no marker exists for the specified atoms
Note: As indicated by the return type, this function only returns schrodinger.maestro.markers._BaseMarker derived markers. Multi atom schrodinger.maestro.markers.Marker type markers are not accessible in this way.

hideAllJaguarMarkers()¶: Hide all schrodinger.maestro.markers._BaseMarker markers for this panel

hideAllMarkers()¶: Hide all schrodinger.maestro.markers.Marker markers for this panel.

hideEvent(event)¶

removeAllJaguarMarkers()¶: Remove all markers schrodinger.maestro.markers._BaseMarker markers from this panel

removeAllJaguarMarkersForEntry(eid)¶

Remove all markers for the specified entry id from this panel

Parameters: eid (str) – The entry id to remove markers for

removeAllMarkers()¶: Remove all schrodinger.maestro.markers.Marker markers from this panel.

removeJaguarMarker(marker)¶

Removes the specified marker

Parameters: marker (schrodinger.maestro.markers._BaseMarker) – The marker to remove
Raises: ValueError – If there is no marker on the specified atoms

removeJaguarMarkerForAtoms(atoms)¶

Removes the marker for specified atom(s)

Parameters: atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).
Raises: ValueError – If no marker exists for the specified atoms

removeMarker(marker)¶

Remove the schrodinger.maestro.markers.Marker

Parameters: marker (schrodinger.maestro.markers.Marker) – Marker to remove
Raises: ValueError – If marker is the wrong type or is not associated with the panel.

showAllJaguarMarkers()¶: Show all schrodinger.maestro.markers._BaseMarker markers for which all marked atoms are in the workspace. Hide all other markers.

showAllMarkers()¶: Set all schrodinger.maestro.markers.Marker markers to be shown if the relevant atoms are in the workspace. These markers are hidden automatically by Maestro when atoms are excluded.

showEvent(event)¶: Re-show all panel markers when the panel is re-shown.