schrodinger.maestro.markers module

Module for placing markers in the Workspace.

class schrodinger.maestro.markers.Icons

Bases: object

Constants for marker icons

NONE

Used by autodoc_mock_imports.

LOCK

Used by autodoc_mock_imports.

SPRING

Used by autodoc_mock_imports.

EYE

Used by autodoc_mock_imports.

EQUALS

Used by autodoc_mock_imports.

FRAGMARK

Used by autodoc_mock_imports.

CHECKMARK

Used by autodoc_mock_imports.

DIAMOND

Used by autodoc_mock_imports.

RSI

Used by autodoc_mock_imports.

TRANSROT

Used by autodoc_mock_imports.

TORSIONROTATE

Used by autodoc_mock_imports.

CHECK

Used by autodoc_mock_imports.

SCISSORS

Used by autodoc_mock_imports.

BREAK

Used by autodoc_mock_imports.

DDRIVE

Used by autodoc_mock_imports.

LONEPAIR

Used by autodoc_mock_imports.

SMAGGLASS

Used by autodoc_mock_imports.

GMAGGLASS

Used by autodoc_mock_imports.

MAGGLASS

Used by autodoc_mock_imports.

WMAGGLASS

Used by autodoc_mock_imports.

IMAGGLASS

Used by autodoc_mock_imports.

VMAGGLASS

Used by autodoc_mock_imports.

EMAGGLASS

Used by autodoc_mock_imports.

ARROWDOWN

Used by autodoc_mock_imports.

SCANATOM

Used by autodoc_mock_imports.

SCANDIST

Used by autodoc_mock_imports.

SCANANGLE

Used by autodoc_mock_imports.

__init__

Initialize self. See help(type(self)) for accurate signature.

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).
hide()

Hide the markers

show(asl=None)

Show the markers. If a new ASL is shown, 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.

class schrodinger.maestro.markers.AtomMarker(atom, marker_color=None, icon=<sphinx.ext.autodoc.importer._MockObject object>, alt_color=None, highlight=False)

Bases: schrodinger.maestro.markers._BaseMarker

Class for marking a single atom.

SETTINGS_VARS = {'alt_color', 'color', 'highlight', 'icon'}
__init__(atom, marker_color=None, icon=<sphinx.ext.autodoc.importer._MockObject object>, 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.
applySettings(settings)

Apply the specified marker settings

Parameters:settings (dict) – A dictionary of marker settings. The keys of this dictionary must appear in SETTINGS_VARS. Note that not all keys need to be specified.
classmethod defaultSettings()

Get the default marker settings

Returns:A dictionary of marker settings. The keys of this dictionary will be SETTING_VARS.
Return type:dict
getSettings()

Get the current marker settings.

Returns:A dictionary of the marker settings. The keys of this dictionary will be SETTING_VARS.
Return type:dict
hide()

Hide this marker.

setAltColor(alt_color)

Change the text color

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

Change the marker and icon color

Parameters: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.
setHighlight(highlight)

Change whether the marker is highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Parameters:highlight (bool) – Whether the marker should be highlighted.
setIcon(icon)

Change the marker icon

Parameters:icon (int) – The icon to draw next to the marker. Should be one the Icons.* constants. If not given, no icon will be drawn.
setVisible(show)

If “show” is True, show the marker, otherwise hide it.

show()

Show this marker.

update()

Update the marker in response to the workspace contents changing. If any marked atom is not in the workspace, the marker will be deleted.

class schrodinger.maestro.markers.PairMarker(atom1, atom2, marker_color=None, icon=<sphinx.ext.autodoc.importer._MockObject object>, text='', alt_color=None, highlight=False)

Bases: schrodinger.maestro.markers._BaseMarker

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

__init__(atom1, atom2, marker_color=None, icon=<sphinx.ext.autodoc.importer._MockObject object>, 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.

SETTINGS_VARS = {'alt_color', 'color', 'highlight', 'icon', 'text'}
applySettings(settings)

Apply the specified marker settings

Parameters:settings (dict) – A dictionary of marker settings. The keys of this dictionary must appear in SETTINGS_VARS. Note that not all keys need to be specified.
classmethod defaultSettings()

Get the default marker settings

Returns:A dictionary of marker settings. The keys of this dictionary will be SETTING_VARS.
Return type:dict
getSettings()

Get the current marker settings.

Returns:A dictionary of the marker settings. The keys of this dictionary will be SETTING_VARS.
Return type:dict
hide()

Hide this marker.

setAltColor(alt_color)

Change the text color

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

Change the marker and icon color

Parameters: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.
setHighlight(highlight)

Change whether the marker is highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Parameters:highlight (bool) – Whether the marker should be highlighted.
setIcon(icon)

Change the marker icon

Parameters:icon (int) – The icon to draw next to the marker. Should be one the Icons.* constants. If not given, no icon will be drawn.
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.
setVisible(show)

If “show” is True, show the marker, otherwise hide it.

show()

Show this marker.

update()

Update the marker in response to the workspace contents changing. If any marked atom is not in the workspace, the marker will be deleted.

class schrodinger.maestro.markers.TripleMarker(atom1, atom2, atom3, marker_color=None, icon=<sphinx.ext.autodoc.importer._MockObject object>, text='', alt_color=None, highlight=False)

Bases: schrodinger.maestro.markers._BaseMarker

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

__init__(atom1, atom2, atom3, marker_color=None, icon=<sphinx.ext.autodoc.importer._MockObject object>, 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.

SETTINGS_VARS = {'alt_color', 'color', 'highlight', 'icon', 'text'}
applySettings(settings)

Apply the specified marker settings

Parameters:settings (dict) – A dictionary of marker settings. The keys of this dictionary must appear in SETTINGS_VARS. Note that not all keys need to be specified.
classmethod defaultSettings()

Get the default marker settings

Returns:A dictionary of marker settings. The keys of this dictionary will be SETTING_VARS.
Return type:dict
getSettings()

Get the current marker settings.

Returns:A dictionary of the marker settings. The keys of this dictionary will be SETTING_VARS.
Return type:dict
hide()

Hide this marker.

setAltColor(alt_color)

Change the text color

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

Change the marker and icon color

Parameters: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.
setHighlight(highlight)

Change whether the marker is highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Parameters:highlight (bool) – Whether the marker should be highlighted.
setIcon(icon)

Change the marker icon

Parameters:icon (int) – The icon to draw next to the marker. Should be one the Icons.* constants. If not given, no icon will be drawn.
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.
setVisible(show)

If “show” is True, show the marker, otherwise hide it.

show()

Show this marker.

update()

Update the marker in response to the workspace contents changing. If any marked atom is not in the workspace, the marker will be deleted.

class schrodinger.maestro.markers.QuadMarker(atom1, atom2, atom3, atom4, marker_color=None, icon=<sphinx.ext.autodoc.importer._MockObject object>, text='', alt_color=None, highlight=False)

Bases: schrodinger.maestro.markers._BaseMarker

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

__init__(atom1, atom2, atom3, atom4, marker_color=None, icon=<sphinx.ext.autodoc.importer._MockObject object>, 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.

SETTINGS_VARS = {'alt_color', 'color', 'highlight', 'icon', 'text'}
applySettings(settings)

Apply the specified marker settings

Parameters:settings (dict) – A dictionary of marker settings. The keys of this dictionary must appear in SETTINGS_VARS. Note that not all keys need to be specified.
classmethod defaultSettings()

Get the default marker settings

Returns:A dictionary of marker settings. The keys of this dictionary will be SETTING_VARS.
Return type:dict
getSettings()

Get the current marker settings.

Returns:A dictionary of the marker settings. The keys of this dictionary will be SETTING_VARS.
Return type:dict
hide()

Hide this marker.

setAltColor(alt_color)

Change the text color

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

Change the marker and icon color

Parameters: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.
setHighlight(highlight)

Change whether the marker is highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Parameters:highlight (bool) – Whether the marker should be highlighted.
setIcon(icon)

Change the marker icon

Parameters:icon (int) – The icon to draw next to the marker. Should be one the Icons.* constants. If not given, no icon will be drawn.
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.
setVisible(show)

If “show” is True, show the marker, otherwise hide it.

show()

Show this marker.

update()

Update the marker in response to the workspace contents changing. If any marked atom is not in the workspace, the marker will be deleted.

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

Bases: schrodinger.maestro.markers._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.

SETTINGS_VARS = {'alt_color', 'color', 'highlight', 'icon', 'text'}
applySettings(settings)

Apply the specified marker settings

Parameters:settings (dict) – A dictionary of marker settings. The keys of this dictionary must appear in SETTINGS_VARS. Note that not all keys need to be specified.
classmethod defaultSettings()

Get the default marker settings

Returns:A dictionary of marker settings. The keys of this dictionary will be SETTING_VARS.
Return type:dict
getSettings()

Get the current marker settings.

Returns:A dictionary of the marker settings. The keys of this dictionary will be SETTING_VARS.
Return type:dict
hide()

Hide this marker.

setAltColor(alt_color)

Change the text color

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

Change the marker and icon color

Parameters: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.
setHighlight(highlight)

Change whether the marker is highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Parameters:highlight (bool) – Whether the marker should be highlighted.
setIcon(icon)

Change the marker icon

Parameters:icon (int) – The icon to draw next to the marker. Should be one the Icons.* constants. If not given, no icon will be drawn.
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.
setVisible(show)

If “show” is True, show the marker, otherwise hide it.

show()

Show this marker.

exception schrodinger.maestro.markers.NotInWorkspaceError

Bases: Exception

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

__init__

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.