schrodinger.maestro.markers module

Module for placing markers in the Workspace.

class schrodinger.maestro.markers.Icons

Bases: object

Constants for marker icons

class schrodinger.maestro.markers.Marker(name=None, asl='NOT all', color=(1, 1, 1))

Bases: object

Class to manipulate a set of markers in the Workspace by ASLs. The only parameter that can be controlled is the color of the marker.

This marker is useful for showing a picked ligand or residue, for example.

__init__(name=None, asl='NOT all', color=(1, 1, 1))

Create a Marker object

Parameters:

  • name (str) – The name of the marker group. Used for unique identification of the marker within Maestro. By default a unique string identifier is generated.

  • asl (str) – The ASL defining which atoms should be marked. By default no atoms are marked.

  • red – The amount of red, green, and blue to use, each ranging from 0.0 to 1.0. Default is white (1, 1, 1).

property name
Returns:

Marker name

Return type:

str

hide()

Hide the markers

show(asl=None)

Show the markers. If a new ASL is specified, then the previous markers get cleared and the new atoms are marked.

Parameters:

asl (str) – The ASL defining which atoms should be marked. This replaces any previous ASL marked by this Marker instance.

setVisible(show)

Show the marker if <show> is True; hide otherwise. Useful for hooking up to a slot of a QCheckBox.

setAsl(asl)

Update the ASL of this marker to the given string, without affecting the visibility of it.

setColor(color)
Parameters:

color (tuple(float, float, float)) – The amount of red, green, and blue to use, each ranging from 0.0 to 1.0.

class schrodinger.maestro.markers.AtomMarker(atom, marker_color=None, icon=_pymaecxx.MM_GRAPHICS_ICON_NONE, alt_color=None, highlight=False)

Bases: _BaseMarker

Class for marking a single atom.

SETTINGS_VARS = {'alt_color', 'color', 'highlight', 'icon'}
__init__(atom, marker_color=None, icon=_pymaecxx.MM_GRAPHICS_ICON_NONE, alt_color=None, highlight=False)
Parameters:

  • atom (schrodinger.structure._StructureAtom) – The atom to mark

  • marker_color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker. 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 Icons.* constants. If not given, no icon will be drawn.

  • 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.

setText(text)

Change the marker text

Parameters:

text (str) – The text to display next to the marker. If not given, no text will be displayed.

class schrodinger.maestro.markers.PairMarker(atom1, atom2, marker_color=None, icon=_pymaecxx.MM_GRAPHICS_ICON_NONE, text='', alt_color=None, highlight=False)

Bases: _BaseMarker

Class for marking two atoms. Useful for marking bonds and distances.

__init__(atom1, atom2, marker_color=None, icon=_pymaecxx.MM_GRAPHICS_ICON_NONE, text='', alt_color=None, highlight=False)
Parameters:

  • atom1 (schrodinger.structure._StructureAtom) – The first atom to mark

  • atom2 (schrodinger.structure._StructureAtom) – The second atom to mark

  • marker_color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker. 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 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.

  • 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.

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.

class schrodinger.maestro.markers.TripleMarker(atom1, atom2, atom3, marker_color=None, icon=_pymaecxx.MM_GRAPHICS_ICON_NONE, text='', alt_color=None, highlight=False)

Bases: _BaseMarker

Class for marking three atoms. Useful for marking bond angles.

__init__(atom1, atom2, atom3, marker_color=None, icon=_pymaecxx.MM_GRAPHICS_ICON_NONE, text='', alt_color=None, highlight=False)
Parameters:

  • atom1 (schrodinger.structure._StructureAtom) – The first atom to mark

  • atom2 (schrodinger.structure._StructureAtom) – The second atom to mark

  • atom3 (schrodinger.structure._StructureAtom) – The third atom to mark

  • marker_color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker. 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 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.

  • 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.

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.

class schrodinger.maestro.markers.QuadMarker(atom1, atom2, atom3, atom4, marker_color=None, icon=_pymaecxx.MM_GRAPHICS_ICON_NONE, text='', alt_color=None, highlight=False)

Bases: _BaseMarker

Class for marking four atoms. Useful for marking dihedral angles.

__init__(atom1, atom2, atom3, atom4, marker_color=None, icon=_pymaecxx.MM_GRAPHICS_ICON_NONE, text='', alt_color=None, highlight=False)
Parameters:

  • atom1 (schrodinger.structure._StructureAtom) – The first atom to mark

  • atom2 (schrodinger.structure._StructureAtom) – The second atom to mark

  • atom3 (schrodinger.structure._StructureAtom) – The third atom to mark

  • atom3 – The fourth atom to mark

  • marker_color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker. 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 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.

  • 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.

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.

class schrodinger.maestro.markers.LineMarker(coord1, entry_id1, coord2, entry_id2, marker_color=None, alt_color=None, line_width=1)

Bases: _BaseMarker

Class for marking two arbitrary points. Useful for marking lines between two graphics3d objects.

__init__(coord1, entry_id1, coord2, entry_id2, marker_color=None, alt_color=None, line_width=1)
Parameters:

  • coord1 (List of int) – The first coordinate to mark

  • coord1 – The second coordinate to mark

  • entry_id1 (int) – Entry ID the first coordinate is associated with. This is to simplify when the line marker should be shown and hidden.

  • entry_id2 (int) – Entry ID the second coordinate is associated with.

  • marker_color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker. May be an RGB tuple, color name, color index, or schrodinger.structutils.color instance. If not given, white will be used.

  • 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.

  • line_width (int) – Width of the line

update()

See parent class documentation.

Update the marker in response to the workspace contents changing. If either one of the entries the marker vertices belong to is no longer included in workspace, the marker will be deleted.

exception schrodinger.maestro.markers.NotInWorkspaceError

Bases: Exception

An exception when trying to display a marker covering atoms that are not currently in the workspace.