schrodinger.ui.picking module

class schrodinger.ui.picking.PickAtomToggle(checkbox, pick_function, pick_text='Pick an atom', enable_lasso=False)

Bases: schrodinger.ui.picking._PickToggle

Class meant to replicate Maestro atom pick toggles. Takes an argument ‘checkbox’ that represents the checkbox for the picking toggle.

__init__(checkbox, pick_function, pick_text='Pick an atom', enable_lasso=False)

The following options are supported:

Parameters

• checkbox (QCheckBox instance.) – Checkbox to hook up the class to.

• pick_function (callable) – will be called when an atom is picked. Must be a callable function that accepts one argument (atom number, or ASL, if enable_lasso is True).

• pick_text (str) – Text that will be displayed in Maestro’s status area (default “Pick an atom”).

• enable_lasso (bool) – Whether to allow multiple atoms to be selected simultaneously via lasso.

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

start()

stop()

class schrodinger.ui.picking.PickBondToggle(checkbox, pick_function, pick_text='Pick a bond')

Bases: schrodinger.ui.picking._PickToggle

Class meant to replicate Maestro bond pick toggles.

The argument ‘checkbox’ represents the QCheckBox object for the picking toggle

The following options are supported:

pick_function - will be called when a bond is picked. Must be a callable

function that accepts two arguments (atom numbers)

pick_text - text that will be displayed in Maestro’s status area

(default “Pick a bond”)

__init__(checkbox, pick_function, pick_text='Pick a bond')

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

start()

stop()

class schrodinger.ui.picking.PickMixedToggle(checkbox, pick_atom_function, pick_bond_function, pick_atom_text='Pick an atom', pick_bond_text='Pick a bond', enable_lasso=False)

Bases: schrodinger.ui.picking._PickToggle

Class allowing to pick atom or bond depending on internal state.

__init__(checkbox, pick_atom_function, pick_bond_function, pick_atom_text='Pick an atom', pick_bond_text='Pick a bond', enable_lasso=False)

Initialize picker class.

Parameters

• checkbox (QtWidgets.QCheckBox) – pick toggle

• pick_atom_function (function) – this function is called when atom is picked. Must be a callable function that accepts one arguments (atom number, or ASL if enable_lasso is True).

• pick_bond_function – this function is called when bond is picked. Must be a callable function that accepts two arguments (bond atoms).

• pick_atom_text (str) – atom pick text that will be displayed in Maestro’s status area (default “Pick an atom”).

• pick_bond_text (str) – bond pick text that will be displayed in Maestro’s status area (default “Pick an atom”).

• enable_lasso (param) – Whether to allow multiple atoms to be selected simultaneously via lasso.

property enable_lasso

setPickAtom(state)

Turn pick atom mode on and off. If it’s off bonds will be picked instead.

Parameters

state (bool) – True or False, if True atoms will be picked. Otherwise bonds will be picked.

setPickBond(state)

Convenience function to turn pick atom mode on and off. If its off bonds will be picked instead.

Parameters

state (bool) – True or False, if True bonds will be picked. Otherwise atoms will be picked.

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

start()

stop()

class schrodinger.ui.picking.PickCategoryToggle(checkbox, pick_function, pick_category)

Bases: schrodinger.ui.picking._PickToggle

Class to pick graphics objects using pick categories

__init__(checkbox, pick_function, pick_category)

Parameters

• checkbox (QtWidgets.QCheckBox) – The checkbox instance to control picking

• pick_function (callable) – Module-level function that takes one argument (the pick_id attribute of the picked graphics object). Must be a module-level function because maestro will call it by name, rather than by reference.

• pick_category (str) – The pick_category attribute of the graphics objects to pick. Must be defined in mm_graphicspick.cxx

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

start()

stop()

class schrodinger.ui.picking.PickAslToggle(checkbox, pick_function, picking_mode, pick_text='Pick atoms to define a group', allow_locked_entries=False)

Bases: schrodinger.ui.picking._PickGroupToggleBase

The pick toggle makes use of maestro’s picking_asl_start which allows a custom pick state to be chosen (residue, molecule, chain, etc.) These pick states are defined as constants in maestro.py. The pick function that is passed as an argument must take a string as an argument, this string will be a valid asl statement

__init__(checkbox, pick_function, picking_mode, pick_text='Pick atoms to define a group', allow_locked_entries=False)

See parent class for argument documentation.

Parameters

picking_mode (int) – The mode to set Maestro’s picker feature to. These are defined in schrodinger.maestro.maestro

callPickFunction()

Call the pick function with the current selection

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

reset()

Unpick all atoms and update markers

setPickText(new_text)

Set’s the text that is shown in the workspace banner

Parameters

new_text (str) – The text to show in the banner

start()

stop()

class schrodinger.ui.picking.PickAtomsToggle(checkbox, natoms, pick_function, pick_text='Pick atoms to define a group', allow_locked_entries=False)

Bases: schrodinger.ui.picking._PickGroupToggleBase

This pick toggle allows you to select multiple atoms at once, each individually. Clicking on an already selected atom will unselect it. The pick_function should expect a list of integers (which correspond to atom indices) as an argument

__init__(checkbox, natoms, pick_function, pick_text='Pick atoms to define a group', allow_locked_entries=False)

See parent class for argument documentation.

Parameters

natoms (int or None) – the number of atoms in the group or None to allow any number of picks

property workspace_ct

Get a copy of the workspace structure

(lazily and cached)

reset()

Unpick all atoms and update markers

callPickFunction()

Call the pick function with the current selection

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

setPickText(new_text)

Set’s the text that is shown in the workspace banner

Parameters

new_text (str) – The text to show in the banner

start()

stop()

class schrodinger.ui.picking.PickAtomsLassoToggle(checkbox, pick_function, pick_text='Pick atoms to define a group', allow_locked_entries=False)

Bases: schrodinger.ui.picking.PickAtomsToggle

Class for creating a PickAtomsToggle that allows the user to pick atoms using marquee selection

__init__(checkbox, pick_function, pick_text='Pick atoms to define a group', allow_locked_entries=False)

See parent class for argument documentation.

Parameters

natoms (int or None) – the number of atoms in the group or None to allow any number of picks

callPickFunction()

Call the pick function with the current selection

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

reset()

Unpick all atoms and update markers

setPickText(new_text)

Set’s the text that is shown in the workspace banner

Parameters

new_text (str) – The text to show in the banner

start()

stop()

property workspace_ct

Get a copy of the workspace structure

(lazily and cached)

class schrodinger.ui.picking.PickResiduesToggle(checkbox, pick_function, pick_text='Pick residues', allow_locked_entries=False)

Bases: schrodinger.ui.picking.PickAtomsToggle

Class for creating a PickAtomsToggle that allows the user to pick and unpick residues by clicking on any of their atoms

__init__(checkbox, pick_function, pick_text='Pick residues', allow_locked_entries=False)

See parent class for argument documentation.

Parameters

natoms (int or None) – the number of atoms in the group or None to allow any number of picks

callPickFunction()

Call the pick function with the current selection

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

reset()

Unpick all atoms and update markers

setPickText(new_text)

Set’s the text that is shown in the workspace banner

Parameters

new_text (str) – The text to show in the banner

start()

stop()

property workspace_ct

Get a copy of the workspace structure

(lazily and cached)

class schrodinger.ui.picking.PickPairToggle(checkbox, pick_function, pick_text='Pick 2 atoms to define a pair', allow_locked_entries=False)

Bases: schrodinger.ui.picking.PickAtomsToggle

Class for creating a picker that allows the user to define a pair of atoms by sequentially picking 2 atoms.

__init__(checkbox, pick_function, pick_text='Pick 2 atoms to define a pair', allow_locked_entries=False)

See parent class for argument documentation.

Parameters

natoms (int or None) – the number of atoms in the group or None to allow any number of picks

callPickFunction()

Call the pick function with the current selection

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

reset()

Unpick all atoms and update markers

setPickText(new_text)

Set’s the text that is shown in the workspace banner

Parameters

new_text (str) – The text to show in the banner

start()

stop()

property workspace_ct

Get a copy of the workspace structure

(lazily and cached)

class schrodinger.ui.picking.PickTorsionToggle(checkbox, pick_function, pick_text='Pick 4 atoms to define a torsion', allow_locked_entries=False)

Bases: schrodinger.ui.picking.PickAtomsToggle

Class for creating a picker that allows the user to define a torsion by sequentually picking 4 atoms.

__init__(checkbox, pick_function, pick_text='Pick 4 atoms to define a torsion', allow_locked_entries=False)

See parent class for argument documentation.

Parameters

natoms (int or None) – the number of atoms in the group or None to allow any number of picks

callPickFunction()

Call the pick function with the current selection

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

reset()

Unpick all atoms and update markers

setPickText(new_text)

Set’s the text that is shown in the workspace banner

Parameters

new_text (str) – The text to show in the banner

start()

stop()

property workspace_ct

Get a copy of the workspace structure

(lazily and cached)

class schrodinger.ui.picking.Pick3DObjectToggle(checkbox, pick_function, pick_category, pick_text='Pick an object')

Bases: schrodinger.ui.picking._PickToggle

Class meant to replicate a Maestro pick toggle. This object allows you to pick objects from the schrodinger.graphics3d module. This picker allows you to pick any object assigned to the picking category argument ‘pick_category’

Parameters

• checkbox – The QCheckBox object for the picking toggle

• pick_function – Will be called when a bond is picked. Must be a callable function that accepts two arguments (atom numbers)

• pick_category – The category of objects to pick. Strings must be defined in mm_graphicspick.cxx string_pick_map. This will allow picking of 3D objects with the corresponding pick_category attribute.

• pick_text – text that will be displayed in Maestro’s status area (default “Pick an object”)

__init__(checkbox, pick_function, pick_category, pick_text='Pick an object')

fullCommand(toggled)

Gets called when the checkbutton is toggled. Manages settings of all pick toggles, and then calls the user-specified command (if it exists).

Parameters

toggled (bool) – indicates whether check box is toggled on or off

on()

start()

stop()

class schrodinger.ui.picking.MaestrolessLigandListModel(st, parent=None)

Bases: schrodinger.ui.qt.table_helper.RowBasedListModel

Model for ligand lists that can be used outside of Maestro.

__init__(st, parent=None)

Parameters

• st (schrodinger.structure.Structure) – Structure containing ligands

• parent (QtWidgets.QWidget or None) – The Qt parent widget.

CHECKABLE_COLS = ()

COLUMN = None

class CheckIndexOption(value)

Bases: enum.Flag

An enumeration.

NoOption = 0

IndexIsValid = 1

DoNotUseParent = 2

ParentIsInvalid = 4

Column = None

EDITABLE_COLS = <object object>

HorizontalSortHint = 2

class LayoutChangeHint(value)

Bases: enum.Enum

An enumeration.

NoLayoutChangeHint = 0

VerticalSortHint = 1

HorizontalSortHint = 2

NO_DATA_CHANGED = <object object>

NoLayoutChangeHint = 0

ROW_CLASS = None

ROW_LIST_OFFSET = 0

SHOW_ROW_NUMBERS = False

UNEDITABLE_COLS = <object object>

VerticalSortHint = 1

af2SettingsGetValue()

This function adds support for the settings mixin. It allows to save table cell values in case this table is included in the settings panel. Returns list of rows if table model is of RowBasedTableModel class type.

Returns

list of rows in tbe table’s model.

Return type

list or None

af2SettingsSetValue(value)

This function adds support for the settings mixin. It allows to set table cell values when this table is included in the settings panel.

Parameters

value (list) – settings value, which is a list of row data here.

appendRow(*args, **kwargs)

Add a row to the table. All arguments are passed to ROW_CLASS initialization.

Returns

The row number of the new row

Return type

int

appendRowObject(row)

Add a row to the table.

Parameters

row (ROW_CLASS) – Row object to add to the table.

Returns

The row number of the new row

Return type

int

appendRowObjects(rows)

Add rows to the table.

Parameters

rows (ROW_CLASS) – Row objects to add to the table.

beginInsertColumns(self, parent: QModelIndex, first: int, last: int)

beginInsertRows(self, parent: QModelIndex, first: int, last: int)

beginMoveColumns(self, sourceParent: QModelIndex, sourceFirst: int, sourceLast: int, destinationParent: QModelIndex, destinationColumn: int) → bool

beginMoveRows(self, sourceParent: QModelIndex, sourceFirst: int, sourceLast: int, destinationParent: QModelIndex, destinationRow: int) → bool

beginRemoveColumns(self, parent: QModelIndex, first: int, last: int)

beginRemoveRows(self, parent: QModelIndex, first: int, last: int)

beginResetModel(self)

blockSignals(self, b: bool) → bool

buddy(self, index: QModelIndex) → QModelIndex

canDropMimeData(self, data: QMimeData, action: Qt.DropAction, row: int, column: int, parent: QModelIndex) → bool

canFetchMore(self, parent: QModelIndex) → bool

changePersistentIndex(self, from_: QModelIndex, to: QModelIndex)

changePersistentIndexList(self, from_: Iterable[QModelIndex], to: Iterable[QModelIndex])

checkIndex(self, index: QModelIndex, options: QAbstractItemModel.CheckIndexOption = QAbstractItemModel.CheckIndexOption.NoOption) → bool

childEvent(self, a0: QChildEvent)

children(self) → List[QObject]

clearItemData(self, index: QModelIndex) → bool

columnChanged(col_number)

Call this method when a specific column object has been modified. Will cause the view to redraw that column.

Parameters

col_number (int) – 0-indexed column number in the model.

columnCount(self, parent: QModelIndex = QModelIndex()) → int

columnsAboutToBeInserted

columnsAboutToBeInserted(self, parent: QModelIndex, first: int, last: int) [signal]

columnsAboutToBeMoved

columnsAboutToBeMoved(self, sourceParent: QModelIndex, sourceStart: int, sourceEnd: int, destinationParent: QModelIndex, destinationColumn: int) [signal]

columnsAboutToBeRemoved

columnsAboutToBeRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

columnsInserted

columnsInserted(self, parent: QModelIndex, first: int, last: int) [signal]

columnsMoved

columnsMoved(self, parent: QModelIndex, start: int, end: int, destination: QModelIndex, column: int) [signal]

columnsRemoved

columnsRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

connectNotify(self, signal: QMetaMethod)

createIndex(self, row: int, column: int, object: object = 0) → QModelIndex

customEvent(self, a0: QEvent)

data(index, role=ItemDataRole.DisplayRole)

Provide data for the specified index and role. Classes should not redefine this method. Instead, new methods should be created and decorated with data_method.

See Qt documentation for an explanation of arguments and return value

dataChanged

dataChanged(self, topLeft: QModelIndex, bottomRight: QModelIndex, roles: Iterable[int] = []) [signal]

decodeData(self, row: int, column: int, parent: QModelIndex, stream: QDataStream) → bool

deleteLater(self)

destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)

dropMimeData(self, data: QMimeData, action: Qt.DropAction, row: int, column: int, parent: QModelIndex) → bool

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

encodeData(self, indexes: Iterable[QModelIndex], stream: QDataStream)

endInsertColumns(self)

endInsertRows(self)

endMoveColumns(self)

endMoveRows(self)

endRemoveColumns(self)

endRemoveRows(self)

endResetModel(self)

event(self, a0: QEvent) → bool

eventFilter(self, a0: QObject, a1: QEvent) → bool

fetchMore(self, parent: QModelIndex)

findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

flags(index)

See Qt documentation for an method documentation.

formatFloat(value, role, digits, fmt='')

Format floating point values for display or sorting. If role is Qt.DisplayRole, then value will be returned as a string with the specified formatting. All other role values are assumed to be a sorting role and value will be returned unchanged.

Parameters

• value (float) – The floating point value to format

• role (int) – The Qt data role

• digits (int) – The number of digits to include after the decimal point for Qt.DisplayRole

• fmt (str) – Additional floating point formatting options

Returns

The formatted or unmodified value

Return type

str or float

hasChildren(self, parent: QModelIndex = QModelIndex()) → bool

hasIndex(self, row: int, column: int, parent: QModelIndex = QModelIndex()) → bool

headerData(section, orientation, role=ItemDataRole.DisplayRole)

Provide column headers, and optionally column tooltips and row numbers.

See Qt documentation for an explanation of arguments and return value

headerDataChanged

headerDataChanged(self, orientation: Qt.Orientation, first: int, last: int) [signal]

index(self, row: int, column: int, parent: QModelIndex = QModelIndex()) → QModelIndex

inherits(self, classname: str) → bool

insertColumn(self, column: int, parent: QModelIndex = QModelIndex()) → bool

insertColumns(self, column: int, count: int, parent: QModelIndex = QModelIndex()) → bool

insertRow(self, row: int, parent: QModelIndex = QModelIndex()) → bool

insertRows(self, row: int, count: int, parent: QModelIndex = QModelIndex()) → bool

installEventFilter(self, a0: QObject)

isSignalConnected(self, signal: QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

itemData(self, index: QModelIndex) → Dict[int, Any]

killTimer(self, id: int)

layoutAboutToBeChanged

layoutAboutToBeChanged(self, parents: Iterable[QPersistentModelIndex] = [], hint: QAbstractItemModel.LayoutChangeHint = QAbstractItemModel.NoLayoutChangeHint) [signal]

layoutChanged

layoutChanged(self, parents: Iterable[QPersistentModelIndex] = [], hint: QAbstractItemModel.LayoutChangeHint = QAbstractItemModel.NoLayoutChangeHint) [signal]

loadData(rows)

Load data into the table and replace all existing data.

Parameters

rows (list) – A list of ROW_CLASS objects

match(self, start: QModelIndex, role: int, value: Any, hits: int = 1, flags: Qt.MatchFlag = Qt.MatchFlags(Qt.MatchStartsWith | Qt.MatchWrap)) → List[QModelIndex]

metaObject(self) → QMetaObject

mimeData(self, indexes: Iterable[QModelIndex]) → QMimeData

mimeTypes(self) → List[str]

modelAboutToBeReset

modelAboutToBeReset(self) [signal]

modelReset

modelReset(self) [signal]

modelResetContext()

A context manager for resetting the model. See model_reset_method for a decorator version of this.

moveColumn(self, sourceParent: QModelIndex, sourceColumn: int, destinationParent: QModelIndex, destinationChild: int) → bool

moveColumns(self, sourceParent: QModelIndex, sourceColumn: int, count: int, destinationParent: QModelIndex, destinationChild: int) → bool

moveRow(self, sourceParent: QModelIndex, sourceRow: int, destinationParent: QModelIndex, destinationChild: int) → bool

moveRows(self, sourceParent: QModelIndex, sourceRow: int, count: int, destinationParent: QModelIndex, destinationChild: int) → bool

moveToThread(self, thread: QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, objectName: str) [signal]

parent(self) → QObject

persistentIndexList(self) → List[QModelIndex]

property(self, name: 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, signal: PYQT_SIGNAL) → int

removeColumn(self, column: int, parent: QModelIndex = QModelIndex()) → bool

removeColumns(self, column: int, count: int, parent: QModelIndex = QModelIndex()) → bool

removeEventFilter(self, a0: QObject)

removeRow(self, row: int, parent: QModelIndex = QModelIndex()) → bool

removeRows(self, row: int, count: int, parent: QModelIndex = QModelIndex()) → bool

removeRowsByIndices(indices)

Remove all rows from the model specified by the given QModelIndex items.

removeRowsByRowNumbers(rows)

Remove the given rows from the model, specified by row number, 0-indexed.

replaceRows(new_rows)

Replace the contents of the model with the contents of the given list. The change will be presented to the view as a series of row insertions and deletions rather than as a model reset. This allows the view to properly update table selections and scroll bar position. This method may only be used if:

• the ROW_CLASS objects can be compared using < and ==

• the contents of the model (i.e. self._rows) are sorted in ascending order

• the contents of new_rows are sorted in ascending order

This method is primarily intended for use when the table contains rows based on project table rows. On every project change, the project table can be reread and used to generate new_list and this method can then properly update the model.

Parameters

new_rows (list) – A list of ROW_CLASS objects

reset()

Remove all data from the model

resetInternalData(self)

revert(self)

roleNames(self) → Dict[int, QByteArray]

rowChanged(row_number)

Call this method when a specific row object has been modified. Will cause the view to redraw that row.

Parameters

row_number (int) – 0-indexed row number in the model. Corresponds to the index in the “.rows” iterator.

rowCount(self, parent: QModelIndex = QModelIndex()) → int

property rows

Iterate over all rows in the model. If any data is changed, call rowChanged() method with the row’s 0-indexed number to update the view.

rowsAboutToBeInserted

rowsAboutToBeInserted(self, parent: QModelIndex, first: int, last: int) [signal]

rowsAboutToBeMoved

rowsAboutToBeMoved(self, sourceParent: QModelIndex, sourceStart: int, sourceEnd: int, destinationParent: QModelIndex, destinationRow: int) [signal]

rowsAboutToBeRemoved

rowsAboutToBeRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

rowsInserted

rowsInserted(self, parent: QModelIndex, first: int, last: int) [signal]

rowsMoved

rowsMoved(self, parent: QModelIndex, start: int, end: int, destination: QModelIndex, row: int) [signal]

rowsRemoved

rowsRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

sender(self) → QObject

senderSignalIndex(self) → int

setData(index, value, role=ItemDataRole.EditRole)

Set data for the specified index and role. Whenever possible, sub- classes should redefine _setData rather than this method.

See Qt documentation for an explanation of arguments and return value.

setHeaderData(self, section: int, orientation: Qt.Orientation, value: Any, role: int = Qt.EditRole) → bool

setItemData(self, index: QModelIndex, roles: Dict[int, Any]) → bool

setObjectName(self, name: str)

setParent(self, a0: QObject)

setProperty(self, name: str, value: Any) → bool

sibling(self, row: int, column: int, idx: QModelIndex) → QModelIndex

signalsBlocked(self) → bool

sort(self, column: int, order: Qt.SortOrder = Qt.AscendingOrder)

span(self, index: QModelIndex) → QSize

startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

submit(self) → bool

supportedDragActions(self) → Qt.DropAction

supportedDropActions(self) → Qt.DropAction

thread(self) → QThread

timerEvent(self, a0: QTimerEvent)

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str

class schrodinger.ui.picking.MaestrolessPickLigandDialog(st, parent=None)

Bases: PyQt6.QtWidgets.QDialog

Dialog to allow users to pick ligands outside of Maestro. Used by ifd_gui.py and covalent_docking_gui.py

__init__(st, parent=None)

Parameters

• st (schrodinger.structure.Structure) – Structure containing the ligands

• parent (QtWidgets.QWidget) – The dialog’s parent widget

accept()

Called when the user clicks OK button

Accepted = 1

class DialogCode(value)

Bases: enum.IntEnum

An enumeration.

Rejected = 0

Accepted = 1

DrawChildren = 2

DrawWindowBackground = 1

IgnoreMask = 4

class PaintDeviceMetric(value)

Bases: enum.Enum

An enumeration.

PdmWidth = 1

PdmHeight = 2

PdmWidthMM = 3

PdmHeightMM = 4

PdmNumColors = 5

PdmDepth = 6

PdmDpiX = 7

PdmDpiY = 8

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

PdmDepth = 6

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

PdmDpiX = 7

PdmDpiY = 8

PdmHeight = 2

PdmHeightMM = 4

PdmNumColors = 5

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmWidth = 1

PdmWidthMM = 3

Rejected = 0

class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1

DrawChildren = 2

IgnoreMask = 4

acceptDrops(self) → bool

accepted

accepted(self) [signal]

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, a0: QActionEvent)

actions(self) → List[QAction]

activateWindow(self)

addAction(self, action: QAction)

addActions(self, actions: Iterable[QAction])

adjustSize(self)

autoFillBackground(self) → bool

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

blockSignals(self, b: bool) → bool

changeEvent(self, a0: QEvent)

childAt(self, p: QPoint) → QWidget

childAt(self, ax: int, ay: int) → QWidget

childEvent(self, a0: QChildEvent)

children(self) → List[QObject]

childrenRect(self) → QRect

childrenRegion(self) → QRegion

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(self, a0: QCloseEvent)

colorCount(self) → int

connectNotify(self, signal: QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, a0: QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

create(self, window: PyQt6.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)

createWindowContainer(window: QWindow, parent: typing.Optional[QWidget] = None, flags: Qt.WindowType = Qt.WindowFlags()) → QWidget

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)

deleteLater(self)

depth(self) → int

destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)

destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

devType(self) → int

devicePixelRatio(self) → float

devicePixelRatioF(self) → float

devicePixelRatioFScale() → float

disconnect(a0: QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)

done(self, a0: int)

dragEnterEvent(self, a0: QDragEnterEvent)

dragLeaveEvent(self, a0: QDragLeaveEvent)

dragMoveEvent(self, a0: QDragMoveEvent)

dropEvent(self, a0: QDropEvent)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

effectiveWinId(self) → PyQt6.sip.voidptr

ensurePolished(self)

enterEvent(self, event: QEnterEvent)

event(self, a0: QEvent) → bool

eventFilter(self, a0: QObject, a1: QEvent) → bool

exec(self) → int

find(a0: PyQt6.sip.voidptr) → QWidget

findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

finished

finished(self, result: int) [signal]

focusInEvent(self, a0: QFocusEvent)

focusNextChild(self) → bool

focusNextPrevChild(self, next: bool) → bool

focusOutEvent(self, a0: QFocusEvent)

focusPolicy(self) → Qt.FocusPolicy

focusPreviousChild(self) → bool

focusProxy(self) → QWidget

focusWidget(self) → QWidget

font(self) → QFont

fontInfo(self) → QFontInfo

fontMetrics(self) → QFontMetrics

foregroundRole(self) → QPalette.ColorRole

frameGeometry(self) → QRect

frameSize(self) → QSize

geometry(self) → QRect

grab(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(- 1, - 1))) → QPixmap

grabGesture(self, type: Qt.GestureType, flags: Qt.GestureFlag = Qt.GestureFlags())

grabKeyboard(self)

grabMouse(self)

grabMouse(self, a0: Union[QCursor, Qt.CursorShape]) → None

grabShortcut(self, key: Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int

graphicsEffect(self) → QGraphicsEffect

graphicsProxyWidget(self) → QGraphicsProxyWidget

hasFocus(self) → bool

hasHeightForWidth(self) → bool

hasMouseTracking(self) → bool

hasTabletTracking(self) → bool

height(self) → int

heightForWidth(self, a0: int) → int

heightMM(self) → int

hide(self)

hideEvent(self, a0: QHideEvent)

inherits(self, classname: str) → bool

initPainter(self, painter: QPainter)

inputMethodEvent(self, a0: QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHint

inputMethodQuery(self, a0: Qt.InputMethodQuery) → Any

insertAction(self, before: QAction, action: QAction)

insertActions(self, before: QAction, actions: Iterable[QAction])

installEventFilter(self, a0: QObject)

isActiveWindow(self) → bool

isAncestorOf(self, child: QWidget) → bool

isEnabled(self) → bool

isEnabledTo(self, a0: QWidget) → bool

isFullScreen(self) → bool

isHidden(self) → bool

isLeftToRight(self) → bool

isMaximized(self) → bool

isMinimized(self) → bool

isModal(self) → bool

isRightToLeft(self) → bool

isSignalConnected(self, signal: QMetaMethod) → bool

isSizeGripEnabled(self) → bool

isVisible(self) → bool

isVisibleTo(self, a0: QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

keyPressEvent(self, a0: QKeyEvent)

keyReleaseEvent(self, a0: QKeyEvent)

keyboardGrabber() → QWidget

killTimer(self, id: int)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

leaveEvent(self, a0: QEvent)

locale(self) → QLocale

logicalDpiX(self) → int

logicalDpiY(self) → int

lower(self)

mapFrom(self, a0: QWidget, a1: QPoint) → QPoint

mapFrom(self, a0: QWidget, a1: QPointF) → QPointF

mapFromGlobal(self, a0: QPoint) → QPoint

mapFromGlobal(self, a0: QPointF) → QPointF

mapFromParent(self, a0: QPoint) → QPoint

mapFromParent(self, a0: QPointF) → QPointF

mapTo(self, a0: QWidget, a1: QPoint) → QPoint

mapTo(self, a0: QWidget, a1: QPointF) → QPointF

mapToGlobal(self, a0: QPoint) → QPoint

mapToGlobal(self, a0: QPointF) → QPointF

mapToParent(self, a0: QPoint) → QPoint

mapToParent(self, a0: QPointF) → QPointF

mask(self) → QRegion

maximumHeight(self) → int

maximumSize(self) → QSize

maximumWidth(self) → int

metaObject(self) → QMetaObject

metric(self, a0: QPaintDevice.PaintDeviceMetric) → int

minimumHeight(self) → int

minimumSize(self) → QSize

minimumSizeHint(self) → QSize

minimumWidth(self) → int

mouseDoubleClickEvent(self, a0: QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, a0: QMouseEvent)

mousePressEvent(self, a0: QMouseEvent)

mouseReleaseEvent(self, a0: QMouseEvent)

move(self, a0: QPoint)

move(self, ax: int, ay: int) → None

moveEvent(self, a0: QMoveEvent)

moveToThread(self, thread: QThread)

nativeEvent(self, eventType: QByteArray, message: PyQt6.sip.voidptr) → Tuple[bool, PyQt6.sip.voidptr]

nativeParentWidget(self) → QWidget

nextInFocusChain(self) → QWidget

normalGeometry(self) → QRect

objectName(self) → str

objectNameChanged

objectNameChanged(self, objectName: str) [signal]

open(self)

overrideWindowFlags(self, type: Qt.WindowType)

overrideWindowState(self, state: Qt.WindowState)

paintEngine(self) → QPaintEngine

paintEvent(self, a0: QPaintEvent)

paintingActive(self) → bool

palette(self) → QPalette

parent(self) → QObject

parentWidget(self) → QWidget

physicalDpiX(self) → int

physicalDpiY(self) → int

pos(self) → QPoint

previousInFocusChain(self) → QWidget

property(self, name: 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.

raise_(self)

receivers(self, signal: PYQT_SIGNAL) → int

rect(self) → QRect

reject(self)

rejected

rejected(self) [signal]

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, id: int)

removeAction(self, action: QAction)

removeEventFilter(self, a0: QObject)

render(self, target: QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: QWidget.RenderFlag = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren))

render(self, painter: QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: QWidget.RenderFlag = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren)) → None

repaint(self)

repaint(self, x: int, y: int, w: int, h: int) → None

repaint(self, a0: QRect) → None

repaint(self, a0: QRegion) → None

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

resizeEvent(self, a0: QResizeEvent)

restoreGeometry(self, geometry: QByteArray) → bool

result(self) → int

saveGeometry(self) → QByteArray

screen(self) → QScreen

scroll(self, dx: int, dy: int)

scroll(self, dx: int, dy: int, a2: QRect) → None

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, on: bool)

setAccessibleDescription(self, description: str)

setAccessibleName(self, name: str)

setAttribute(self, attribute: Qt.WidgetAttribute, on: bool = True)

setAutoFillBackground(self, enabled: bool)

setBackgroundRole(self, a0: QPalette.ColorRole)

setBaseSize(self, basew: int, baseh: int)

setBaseSize(self, s: QSize) → None

setContentsMargins(self, left: int, top: int, right: int, bottom: int)

setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)

setCursor(self, a0: Union[QCursor, Qt.CursorShape])

setDisabled(self, a0: bool)

setEnabled(self, a0: bool)

setFixedHeight(self, h: int)

setFixedSize(self, a0: QSize)

setFixedSize(self, w: int, h: int) → None

setFixedWidth(self, w: int)

setFocus(self)

setFocus(self, reason: Qt.FocusReason) → None

setFocusPolicy(self, policy: Qt.FocusPolicy)

setFocusProxy(self, a0: QWidget)

setFont(self, a0: QFont)

setForegroundRole(self, a0: QPalette.ColorRole)

setGeometry(self, a0: QRect)

setGeometry(self, ax: int, ay: int, aw: int, ah: int) → None

setGraphicsEffect(self, effect: QGraphicsEffect)

setHidden(self, hidden: bool)

setInputMethodHints(self, hints: Qt.InputMethodHint)

setLayout(self, a0: QLayout)

setLayoutDirection(self, direction: Qt.LayoutDirection)

setLocale(self, locale: QLocale)

setMask(self, a0: QBitmap)

setMask(self, a0: QRegion) → None

setMaximumHeight(self, maxh: int)

setMaximumSize(self, maxw: int, maxh: int)

setMaximumSize(self, s: QSize) → None

setMaximumWidth(self, maxw: int)

setMinimumHeight(self, minh: int)

setMinimumSize(self, minw: int, minh: int)

setMinimumSize(self, s: QSize) → None

setMinimumWidth(self, minw: int)

setModal(self, modal: bool)

setMouseTracking(self, enable: bool)

setObjectName(self, name: str)

setPalette(self, a0: QPalette)

setParent(self, parent: QWidget)

setParent(self, parent: QWidget, f: Qt.WindowType) → None

setProperty(self, name: str, value: Any) → bool

setResult(self, r: int)

setScreen(self, a0: QScreen)

setShortcutAutoRepeat(self, id: int, enabled: bool = True)

setShortcutEnabled(self, id: int, enabled: bool = True)

setSizeGripEnabled(self, a0: bool)

setSizeIncrement(self, w: int, h: int)

setSizeIncrement(self, s: QSize) → None

setSizePolicy(self, a0: QSizePolicy)

setSizePolicy(self, hor: QSizePolicy.Policy, ver: QSizePolicy.Policy) → None

setStatusTip(self, a0: str)

setStyle(self, a0: QStyle)

setStyleSheet(self, styleSheet: str)

setTabOrder(a0: QWidget, a1: QWidget)

setTabletTracking(self, enable: bool)

setToolTip(self, a0: str)

setToolTipDuration(self, msec: int)

setUpdatesEnabled(self, enable: bool)

setVisible(self, visible: bool)

setWhatsThis(self, a0: str)

setWindowFilePath(self, filePath: str)

setWindowFlag(self, a0: Qt.WindowType, on: bool = True)

setWindowFlags(self, type: Qt.WindowType)

setWindowIcon(self, icon: QIcon)

setWindowIconText(self, a0: str)

setWindowModality(self, windowModality: Qt.WindowModality)

setWindowModified(self, a0: bool)

setWindowOpacity(self, level: float)

setWindowRole(self, a0: str)

setWindowState(self, state: Qt.WindowState)

setWindowTitle(self, a0: str)

sharedPainter(self) → QPainter

show(self)

showEvent(self, a0: QShowEvent)

showFullScreen(self)

showMaximized(self)

showMinimized(self)

showNormal(self)

signalsBlocked(self) → bool

size(self) → QSize

sizeHint(self) → QSize

sizeIncrement(self) → QSize

sizePolicy(self) → QSizePolicy

stackUnder(self, a0: QWidget)

startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

statusTip(self) → str

style(self) → QStyle

styleSheet(self) → str

tabletEvent(self, a0: QTabletEvent)

testAttribute(self, attribute: Qt.WidgetAttribute) → bool

thread(self) → QThread

timerEvent(self, a0: QTimerEvent)

toolTip(self) → str

toolTipDuration(self) → int

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str

underMouse(self) → bool

ungrabGesture(self, type: Qt.GestureType)

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, a0: QRect) → None

update(self, a0: QRegion) → None

update(self, ax: int, ay: int, aw: int, ah: int) → None

updateGeometry(self)

updateMicroFocus(self, query: Qt.InputMethodQuery = Qt.ImQueryAll)

updatesEnabled(self) → bool

visibleRegion(self) → QRegion

whatsThis(self) → str

wheelEvent(self, a0: QWheelEvent)

width(self) → int

widthMM(self) → int

winId(self) → PyQt6.sip.voidptr

window(self) → QWidget

windowFilePath(self) → str

windowFlags(self) → Qt.WindowType

windowHandle(self) → QWindow

windowIcon(self) → QIcon

windowIconChanged

windowIconChanged(self, icon: QIcon) [signal]

windowIconText(self) → str

windowIconTextChanged

windowIconTextChanged(self, iconText: str) [signal]

windowModality(self) → Qt.WindowModality

windowOpacity(self) → float

windowRole(self) → str

windowState(self) → Qt.WindowState

windowTitle(self) → str

windowTitleChanged

windowTitleChanged(self, title: str) [signal]

windowType(self) → Qt.WindowType

x(self) → int

y(self) → int

class schrodinger.ui.picking.ResidueRow(res, markers_color=None)

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

Class representing a residue in the active site. Used by ResiduesModel and SelectResiduesDialog.

__init__(res, markers_color=None)

Parameters

• res (schrodinger.structure.Residue) – Residue to be added as a row.

• markers_color (3-tuple of floats, each between 0.0 and 1.0, or None) – Color to add workspace markers as for this residue. If None, no markers will be added.

findInStructure(st)

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.

show()

Re-show all panel markers when the panel is re-shown. This separate method is needed for QDialog instances.

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.

class schrodinger.ui.picking.PickResidueRow(res, distance=None)

Bases: schrodinger.ui.picking.ResidueRow

Base class for rows to be used in models inheriting _BaseMaestrolessPickModel.

__init__(res, distance=None)

Parameters

• res (schrodinger.structure._Residue) – Residue for this row

• distance (float or None) – Distance of the residue to a ligand or None

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.

findInStructure(st)

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.

show()

Re-show all panel markers when the panel is re-shown. This separate method is needed for QDialog instances.

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.

class schrodinger.ui.picking.PickResiduesChangedMixin

Bases: object

Mixin to provide common signals for dialogs that allow users to pick residues.

residues_centroid_changed

residues_changed

getResiduesList(res_objs)

Return the list of residue strings (e.g. [‘A:217’, ‘A:231b’]) of the selected residues.

Parameters

res_objs (List of ResidueRow) – List of residue objects to get strings for

:return List of residue strings for each row. @rtyp: list of str

getResiduesCenter(res_objs)

Return the (x, y, z) tuple for the center of the selected residues. Will raise ValueError if no residues were picked.

@pram res_objs: Residue objects to get the center of :type res_objs: List of ResidueRow

Returns

Tuple of center x, y, z coordinates

Return type

tuple of (float, float, float)

class schrodinger.ui.picking.PickResidueModel(parent, multi_select=True)

Bases: schrodinger.ui.picking._BaseMaestrolessPickModel

Model for tables to allow picking residues from a structure outside of Maestro.

Column

alias of <unknown>.PickResidueColumns

ROW_CLASS

alias of schrodinger.ui.picking.PickResidueRow

CHECKABLE_COLS = ()

COLUMN = None

class CheckIndexOption(value)

Bases: enum.Flag

An enumeration.

NoOption = 0

IndexIsValid = 1

DoNotUseParent = 2

ParentIsInvalid = 4

EDITABLE_COLS = <object object>

HorizontalSortHint = 2

class LayoutChangeHint(value)

Bases: enum.Enum

An enumeration.

NoLayoutChangeHint = 0

VerticalSortHint = 1

HorizontalSortHint = 2

NO_DATA_CHANGED = <object object>

NoLayoutChangeHint = 0

ROW_LIST_OFFSET = 0

SHOW_ROW_NUMBERS = False

UNEDITABLE_COLS = <object object>

VerticalSortHint = 1

__init__(parent, multi_select=True)

af2SettingsGetValue()

This function adds support for the settings mixin. It allows to save table cell values in case this table is included in the settings panel. Returns list of rows if table model is of RowBasedTableModel class type.

Returns

list of rows in tbe table’s model.

Return type

list or None

af2SettingsSetValue(value)

This function adds support for the settings mixin. It allows to set table cell values when this table is included in the settings panel.

Parameters

value (list) – settings value, which is a list of row data here.

appendRow(*args, **kwargs)

Add a row to the table. All arguments are passed to ROW_CLASS initialization.

Returns

The row number of the new row

Return type

int

appendRowObject(row)

Add a row to the table.

Parameters

row (ROW_CLASS) – Row object to add to the table.

Returns

The row number of the new row

Return type

int

appendRowObjects(rows)

Add rows to the table.

Parameters

rows (ROW_CLASS) – Row objects to add to the table.

beginInsertColumns(self, parent: QModelIndex, first: int, last: int)

beginInsertRows(self, parent: QModelIndex, first: int, last: int)

beginMoveColumns(self, sourceParent: QModelIndex, sourceFirst: int, sourceLast: int, destinationParent: QModelIndex, destinationColumn: int) → bool

beginMoveRows(self, sourceParent: QModelIndex, sourceFirst: int, sourceLast: int, destinationParent: QModelIndex, destinationRow: int) → bool

beginRemoveColumns(self, parent: QModelIndex, first: int, last: int)

beginRemoveRows(self, parent: QModelIndex, first: int, last: int)

beginResetModel(self)

blockSignals(self, b: bool) → bool

buddy(self, index: QModelIndex) → QModelIndex

canDropMimeData(self, data: QMimeData, action: Qt.DropAction, row: int, column: int, parent: QModelIndex) → bool

canFetchMore(self, parent: QModelIndex) → bool

changePersistentIndex(self, from_: QModelIndex, to: QModelIndex)

changePersistentIndexList(self, from_: Iterable[QModelIndex], to: Iterable[QModelIndex])

checkIndex(self, index: QModelIndex, options: QAbstractItemModel.CheckIndexOption = QAbstractItemModel.CheckIndexOption.NoOption) → bool

childEvent(self, a0: QChildEvent)

children(self) → List[QObject]

clearItemData(self, index: QModelIndex) → bool

columnChanged(col_number)

Call this method when a specific column object has been modified. Will cause the view to redraw that column.

Parameters

col_number (int) – 0-indexed column number in the model.

columnCount(self, parent: QModelIndex = QModelIndex()) → int

columnsAboutToBeInserted

columnsAboutToBeInserted(self, parent: QModelIndex, first: int, last: int) [signal]

columnsAboutToBeMoved

columnsAboutToBeMoved(self, sourceParent: QModelIndex, sourceStart: int, sourceEnd: int, destinationParent: QModelIndex, destinationColumn: int) [signal]

columnsAboutToBeRemoved

columnsAboutToBeRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

columnsInserted

columnsInserted(self, parent: QModelIndex, first: int, last: int) [signal]

columnsMoved

columnsMoved(self, parent: QModelIndex, start: int, end: int, destination: QModelIndex, column: int) [signal]

columnsRemoved

columnsRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

connectNotify(self, signal: QMetaMethod)

createIndex(self, row: int, column: int, object: object = 0) → QModelIndex

customEvent(self, a0: QEvent)

data(index, role=ItemDataRole.DisplayRole)

Provide data for the specified index and role. Classes should not redefine this method. Instead, new methods should be created and decorated with data_method.

See Qt documentation for an explanation of arguments and return value

dataChanged

dataChanged(self, topLeft: QModelIndex, bottomRight: QModelIndex, roles: Iterable[int] = []) [signal]

decodeData(self, row: int, column: int, parent: QModelIndex, stream: QDataStream) → bool

deleteLater(self)

destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)

dropMimeData(self, data: QMimeData, action: Qt.DropAction, row: int, column: int, parent: QModelIndex) → bool

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

encodeData(self, indexes: Iterable[QModelIndex], stream: QDataStream)

endInsertColumns(self)

endInsertRows(self)

endMoveColumns(self)

endMoveRows(self)

endRemoveColumns(self)

endRemoveRows(self)

endResetModel(self)

event(self, a0: QEvent) → bool

eventFilter(self, a0: QObject, a1: QEvent) → bool

fetchMore(self, parent: QModelIndex)

findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

flags(index)

See Qt documentation for an method documentation.

formatFloat(value, role, digits, fmt='')

Format floating point values for display or sorting. If role is Qt.DisplayRole, then value will be returned as a string with the specified formatting. All other role values are assumed to be a sorting role and value will be returned unchanged.

Parameters

• value (float) – The floating point value to format

• role (int) – The Qt data role

• digits (int) – The number of digits to include after the decimal point for Qt.DisplayRole

• fmt (str) – Additional floating point formatting options

Returns

The formatted or unmodified value

Return type

str or float

hasChildren(self, parent: QModelIndex = QModelIndex()) → bool

hasIndex(self, row: int, column: int, parent: QModelIndex = QModelIndex()) → bool

headerData(section, orientation, role=ItemDataRole.DisplayRole)

Provide column headers, and optionally column tooltips and row numbers.

See Qt documentation for an explanation of arguments and return value

headerDataChanged

headerDataChanged(self, orientation: Qt.Orientation, first: int, last: int) [signal]

index(self, row: int, column: int, parent: QModelIndex = QModelIndex()) → QModelIndex

inherits(self, classname: str) → bool

insertColumn(self, column: int, parent: QModelIndex = QModelIndex()) → bool

insertColumns(self, column: int, count: int, parent: QModelIndex = QModelIndex()) → bool

insertRow(self, row: int, parent: QModelIndex = QModelIndex()) → bool

insertRows(self, row: int, count: int, parent: QModelIndex = QModelIndex()) → bool

installEventFilter(self, a0: QObject)

isSignalConnected(self, signal: QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

itemData(self, index: QModelIndex) → Dict[int, Any]

killTimer(self, id: int)

layoutAboutToBeChanged

layoutAboutToBeChanged(self, parents: Iterable[QPersistentModelIndex] = [], hint: QAbstractItemModel.LayoutChangeHint = QAbstractItemModel.NoLayoutChangeHint) [signal]

layoutChanged

layoutChanged(self, parents: Iterable[QPersistentModelIndex] = [], hint: QAbstractItemModel.LayoutChangeHint = QAbstractItemModel.NoLayoutChangeHint) [signal]

loadData(rows)

Load data into the table and replace all existing data.

Parameters

rows (list) – A list of ROW_CLASS objects

match(self, start: QModelIndex, role: int, value: Any, hits: int = 1, flags: Qt.MatchFlag = Qt.MatchFlags(Qt.MatchStartsWith | Qt.MatchWrap)) → List[QModelIndex]

metaObject(self) → QMetaObject

mimeData(self, indexes: Iterable[QModelIndex]) → QMimeData

mimeTypes(self) → List[str]

modelAboutToBeReset

modelAboutToBeReset(self) [signal]

modelReset

modelReset(self) [signal]

modelResetContext()

A context manager for resetting the model. See model_reset_method for a decorator version of this.

moveColumn(self, sourceParent: QModelIndex, sourceColumn: int, destinationParent: QModelIndex, destinationChild: int) → bool

moveColumns(self, sourceParent: QModelIndex, sourceColumn: int, count: int, destinationParent: QModelIndex, destinationChild: int) → bool

moveRow(self, sourceParent: QModelIndex, sourceRow: int, destinationParent: QModelIndex, destinationChild: int) → bool

moveRows(self, sourceParent: QModelIndex, sourceRow: int, count: int, destinationParent: QModelIndex, destinationChild: int) → bool

moveToThread(self, thread: QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, objectName: str) [signal]

parent(self) → QObject

persistentIndexList(self) → List[QModelIndex]

property(self, name: 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, signal: PYQT_SIGNAL) → int

removeColumn(self, column: int, parent: QModelIndex = QModelIndex()) → bool

removeColumns(self, column: int, count: int, parent: QModelIndex = QModelIndex()) → bool

removeEventFilter(self, a0: QObject)

removeRow(self, row: int, parent: QModelIndex = QModelIndex()) → bool

removeRows(self, row: int, count: int, parent: QModelIndex = QModelIndex()) → bool

removeRowsByIndices(indices)

Remove all rows from the model specified by the given QModelIndex items.

removeRowsByRowNumbers(rows)

Remove the given rows from the model, specified by row number, 0-indexed.

replaceRows(new_rows)

Replace the contents of the model with the contents of the given list. The change will be presented to the view as a series of row insertions and deletions rather than as a model reset. This allows the view to properly update table selections and scroll bar position. This method may only be used if:

• the ROW_CLASS objects can be compared using < and ==

• the contents of the model (i.e. self._rows) are sorted in ascending order

• the contents of new_rows are sorted in ascending order

This method is primarily intended for use when the table contains rows based on project table rows. On every project change, the project table can be reread and used to generate new_list and this method can then properly update the model.

Parameters

new_rows (list) – A list of ROW_CLASS objects

reset()

Remove all data from the model

resetInternalData(self)

revert(self)

roleNames(self) → Dict[int, QByteArray]

rowChanged(row_number)

Call this method when a specific row object has been modified. Will cause the view to redraw that row.

Parameters

row_number (int) – 0-indexed row number in the model. Corresponds to the index in the “.rows” iterator.

rowCount(self, parent: QModelIndex = QModelIndex()) → int

property rows

Iterate over all rows in the model. If any data is changed, call rowChanged() method with the row’s 0-indexed number to update the view.

rowsAboutToBeInserted

rowsAboutToBeInserted(self, parent: QModelIndex, first: int, last: int) [signal]

rowsAboutToBeMoved

rowsAboutToBeMoved(self, sourceParent: QModelIndex, sourceStart: int, sourceEnd: int, destinationParent: QModelIndex, destinationRow: int) [signal]

rowsAboutToBeRemoved

rowsAboutToBeRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

rowsInserted

rowsInserted(self, parent: QModelIndex, first: int, last: int) [signal]

rowsMoved

rowsMoved(self, parent: QModelIndex, start: int, end: int, destination: QModelIndex, row: int) [signal]

rowsRemoved

rowsRemoved(self, parent: QModelIndex, first: int, last: int) [signal]

sender(self) → QObject

senderSignalIndex(self) → int

setData(index, value, role=ItemDataRole.EditRole)

Set data for the specified index and role. Whenever possible, sub- classes should redefine _setData rather than this method.

See Qt documentation for an explanation of arguments and return value.

setHeaderData(self, section: int, orientation: Qt.Orientation, value: Any, role: int = Qt.EditRole) → bool

setItemData(self, index: QModelIndex, roles: Dict[int, Any]) → bool

setObjectName(self, name: str)

setParent(self, a0: QObject)

setProperty(self, name: str, value: Any) → bool

sibling(self, row: int, column: int, idx: QModelIndex) → QModelIndex

signalsBlocked(self) → bool

sort(self, column: int, order: Qt.SortOrder = Qt.AscendingOrder)

span(self, index: QModelIndex) → QSize

startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

submit(self) → bool

supportedDragActions(self) → Qt.DropAction

supportedDropActions(self) → Qt.DropAction

thread(self) → QThread

timerEvent(self, a0: QTimerEvent)

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str

class schrodinger.ui.picking.MaestrolessPickResidueDialog(st, lig_st=None, find_ws_lig=False, multi_select=True, parent=None)

Bases: schrodinger.ui.picking._BaseMaestrolessPickResDialog

Class for picking residues outside of Maestro.

PickModelClass

alias of schrodinger.ui.picking.PickResidueModel

ALL_RESIDUES = 'All residues'

NEAR_RESIDUES = 'Residues near ligand (within 5A)'

__init__(st, lig_st=None, find_ws_lig=False, multi_select=True, parent=None)

Parameters

• st (schrodinger.structure.Structure) – Structure containing the residues

• lig_st (schrodinger.structure.Structure or None) – Ligand structure to check distances of residues against. Cannot be specified if find_ws_lig is set to True. If not specified and find_ws_lig is False, distance filtering will not be enabled.

• find_ws_lig (bool) – Whether to search self.st for a single ligand. If more than one ligand is identified, none will be used. Cannot be True if a ligand is specified via ligand_st.

• multi_select (bool) – Whether to allow selection of multiple residues, vs a single residue only. Default is True.

• parent (QtWidgets.QWidget) – Parent widget to the dialog

af2SettingsGetValue()

Used with schrodinger.ui.qt.appframework2.settings.SettingsMixin to save the dialog state to JSON.

Returns

List of panel attributes to serialize

Return type

list

Accepted = 1

class DialogCode(value)

Bases: enum.IntEnum

An enumeration.

Rejected = 0

Accepted = 1

DrawChildren = 2

DrawWindowBackground = 1

IgnoreMask = 4

class PaintDeviceMetric(value)

Bases: enum.Enum

An enumeration.

PdmWidth = 1

PdmHeight = 2

PdmWidthMM = 3

PdmHeightMM = 4

PdmNumColors = 5

PdmDepth = 6

PdmDpiX = 7

PdmDpiY = 8

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

PdmDepth = 6

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

PdmDpiX = 7

PdmDpiY = 8

PdmHeight = 2

PdmHeightMM = 4

PdmNumColors = 5

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmWidth = 1

PdmWidthMM = 3

Rejected = 0

class RenderFlag(value)

Bases: enum.Flag

An enumeration.

DrawWindowBackground = 1

DrawChildren = 2

IgnoreMask = 4

accept()

Called when the OK button is clicked on the dialog.

acceptDrops(self) → bool

accepted

accepted(self) [signal]

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, a0: QActionEvent)

actions(self) → List[QAction]

activateWindow(self)

addAction(self, action: QAction)

addActions(self, actions: Iterable[QAction])

adjustSize(self)

af2SettingsSetValue(value)

Used with schrodinger.ui.qt.appframework2.settings.SettingsMixin to reload the dialog state from JSON.

Parameters

value (list) – Values to set for the panel

autoFillBackground(self) → bool

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

blockSignals(self, b: bool) → bool

changeEvent(self, a0: QEvent)

childAt(self, p: QPoint) → QWidget

childAt(self, ax: int, ay: int) → QWidget

childEvent(self, a0: QChildEvent)

children(self) → List[QObject]

childrenRect(self) → QRect

childrenRegion(self) → QRegion

clear()

Unpick all rows in the model.

clearFocus(self)

clearMask(self)

close(self) → bool

closeEvent(self, a0: QCloseEvent)

colorCount(self) → int

connectNotify(self, signal: QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, a0: QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

create(self, window: PyQt6.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)

createWindowContainer(window: QWindow, parent: typing.Optional[QWidget] = None, flags: Qt.WindowType = Qt.WindowFlags()) → QWidget

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, pos: QPoint) [signal]

customEvent(self, a0: QEvent)

deleteLater(self)

depth(self) → int

destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)

destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

devType(self) → int

devicePixelRatio(self) → float

devicePixelRatioF(self) → float

devicePixelRatioFScale() → float

disconnect(a0: QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, signal: QMetaMethod)

display()

Show the panel

done(self, a0: int)

dragEnterEvent(self, a0: QDragEnterEvent)

dragLeaveEvent(self, a0: QDragLeaveEvent)

dragMoveEvent(self, a0: QDragMoveEvent)

dropEvent(self, a0: QDropEvent)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

effectiveWinId(self) → PyQt6.sip.voidptr

ensurePolished(self)

enterEvent(self, event: QEnterEvent)

event(self, a0: QEvent) → bool

eventFilter(self, a0: QObject, a1: QEvent) → bool

exec(self) → int

find(a0: PyQt6.sip.voidptr) → QWidget

findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

finished

finished(self, result: int) [signal]

focusInEvent(self, a0: QFocusEvent)

focusNextChild(self) → bool

focusNextPrevChild(self, next: bool) → bool

focusOutEvent(self, a0: QFocusEvent)

focusPolicy(self) → Qt.FocusPolicy

focusPreviousChild(self) → bool

focusProxy(self) → QWidget

focusWidget(self) → QWidget

font(self) → QFont

fontInfo(self) → QFontInfo

fontMetrics(self) → QFontMetrics

foregroundRole(self) → QPalette.ColorRole

frameGeometry(self) → QRect

frameSize(self) → QSize

geometry(self) → QRect

getResiduesAndDistances()

Return a list of 2-tuples containing the residues and their distance from a ligand, if specified.

Returns

Tuple of each residue in the structure and the residue distance from the specified ligand, or None if no ligand is specified.

Return type

list of (schrodinger.structure._Residue, float) or (schrodinger.structure._Residue, None)

getResiduesCenter(res_objs)

Return the (x, y, z) tuple for the center of the selected residues. Will raise ValueError if no residues were picked.

@pram res_objs: Residue objects to get the center of :type res_objs: List of ResidueRow

Returns

Tuple of center x, y, z coordinates

Return type

tuple of (float, float, float)

getResiduesList(res_objs)

Return the list of residue strings (e.g. [‘A:217’, ‘A:231b’]) of the selected residues.

Parameters

res_objs (List of ResidueRow) – List of residue objects to get strings for

:return List of residue strings for each row. @rtyp: list of str

grab(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(- 1, - 1))) → QPixmap

grabGesture(self, type: Qt.GestureType, flags: Qt.GestureFlag = Qt.GestureFlags())

grabKeyboard(self)

grabMouse(self)

grabMouse(self, a0: Union[QCursor, Qt.CursorShape]) → None

grabShortcut(self, key: Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int

graphicsEffect(self) → QGraphicsEffect

graphicsProxyWidget(self) → QGraphicsProxyWidget

hasFocus(self) → bool

hasHeightForWidth(self) → bool

hasMouseTracking(self) → bool

hasTabletTracking(self) → bool

height(self) → int

heightForWidth(self, a0: int) → int

heightMM(self) → int

hide(self)

hideEvent(self, a0: QHideEvent)

inherits(self, classname: str) → bool

initPainter(self, painter: QPainter)

inputMethodEvent(self, a0: QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHint

inputMethodQuery(self, a0: Qt.InputMethodQuery) → Any

insertAction(self, before: QAction, action: QAction)

insertActions(self, before: QAction, actions: Iterable[QAction])

installEventFilter(self, a0: QObject)

isActiveWindow(self) → bool

isAncestorOf(self, child: QWidget) → bool

isEnabled(self) → bool

isEnabledTo(self, a0: QWidget) → bool

isFullScreen(self) → bool

isHidden(self) → bool

isLeftToRight(self) → bool

isMaximized(self) → bool

isMinimized(self) → bool

isModal(self) → bool

isRightToLeft(self) → bool

isSignalConnected(self, signal: QMetaMethod) → bool

isSizeGripEnabled(self) → bool

isVisible(self) → bool

isVisibleTo(self, a0: QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

keyPressEvent(self, a0: QKeyEvent)

keyReleaseEvent(self, a0: QKeyEvent)

keyboardGrabber() → QWidget

killTimer(self, id: int)

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

leaveEvent(self, a0: QEvent)

locale(self) → QLocale

logicalDpiX(self) → int

logicalDpiY(self) → int

lower(self)

mapFrom(self, a0: QWidget, a1: QPoint) → QPoint

mapFrom(self, a0: QWidget, a1: QPointF) → QPointF

mapFromGlobal(self, a0: QPoint) → QPoint

mapFromGlobal(self, a0: QPointF) → QPointF

mapFromParent(self, a0: QPoint) → QPoint

mapFromParent(self, a0: QPointF) → QPointF

mapTo(self, a0: QWidget, a1: QPoint) → QPoint

mapTo(self, a0: QWidget, a1: QPointF) → QPointF

mapToGlobal(self, a0: QPoint) → QPoint

mapToGlobal(self, a0: QPointF) → QPointF

mapToParent(self, a0: QPoint) → QPoint

mapToParent(self, a0: QPointF) → QPointF

mask(self) → QRegion

maximumHeight(self) → int

maximumSize(self) → QSize

maximumWidth(self) → int

metaObject(self) → QMetaObject

metric(self, a0: QPaintDevice.PaintDeviceMetric) → int

minimumHeight(self) → int

minimumSize(self) → QSize

minimumSizeHint(self) → QSize

minimumWidth(self) → int

mouseDoubleClickEvent(self, a0: QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, a0: QMouseEvent)

mousePressEvent(self, a0: QMouseEvent)

mouseReleaseEvent(self, a0: QMouseEvent)

move(self, a0: QPoint)

move(self, ax: int, ay: int) → None

moveEvent(self, a0: QMoveEvent)

moveToThread(self, thread: QThread)

nativeEvent(self, eventType: QByteArray, message: PyQt6.sip.voidptr) → Tuple[bool, PyQt6.sip.voidptr]

nativeParentWidget(self) → QWidget

nextInFocusChain(self) → QWidget

normalGeometry(self) → QRect

objectName(self) → str

objectNameChanged

objectNameChanged(self, objectName: str) [signal]

open(self)

overrideWindowFlags(self, type: Qt.WindowType)

overrideWindowState(self, state: Qt.WindowState)

paintEngine(self) → QPaintEngine

paintEvent(self, a0: QPaintEvent)

paintingActive(self) → bool

palette(self) → QPalette

parent(self) → QObject

parentWidget(self) → QWidget

physicalDpiX(self) → int

physicalDpiY(self) → int

pos(self) → QPoint

previousInFocusChain(self) → QWidget

property(self, name: 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.

raise_(self)

receivers(self, signal: PYQT_SIGNAL) → int

rect(self) → QRect

reject(self)

rejected

rejected(self) [signal]

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, id: int)

removeAction(self, action: QAction)

removeEventFilter(self, a0: QObject)

render(self, target: QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: QWidget.RenderFlag = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren))

render(self, painter: QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: QWidget.RenderFlag = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren)) → None

repaint(self)

repaint(self, x: int, y: int, w: int, h: int) → None

repaint(self, a0: QRect) → None

repaint(self, a0: QRegion) → None

residues_centroid_changed

residues_changed

resize(self, a0: QSize)

resize(self, w: int, h: int) → None

resizeEvent(self, a0: QResizeEvent)

restoreGeometry(self, geometry: QByteArray) → bool

result(self) → int

saveGeometry(self) → QByteArray

screen(self) → QScreen

scroll(self, dx: int, dy: int)

scroll(self, dx: int, dy: int, a2: QRect) → None

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, on: bool)

setAccessibleDescription(self, description: str)

setAccessibleName(self, name: str)

setAttribute(self, attribute: Qt.WidgetAttribute, on: bool = True)

setAutoFillBackground(self, enabled: bool)

setBackgroundRole(self, a0: QPalette.ColorRole)

setBaseSize(self, basew: int, baseh: int)

setBaseSize(self, s: QSize) → None

setContentsMargins(self, left: int, top: int, right: int, bottom: int)

setContentsMargins(self, margins: QMargins) → None

setContextMenuPolicy(self, policy: Qt.ContextMenuPolicy)

setCursor(self, a0: Union[QCursor, Qt.CursorShape])

setDisabled(self, a0: bool)

setEnabled(self, a0: bool)

setFixedHeight(self, h: int)

setFixedSize(self, a0: QSize)

setFixedSize(self, w: int, h: int) → None

setFixedWidth(self, w: int)

setFocus(self)

setFocus(self, reason: Qt.FocusReason) → None

setFocusPolicy(self, policy: Qt.FocusPolicy)

setFocusProxy(self, a0: QWidget)

setFont(self, a0: QFont)

setForegroundRole(self, a0: QPalette.ColorRole)

setGeometry(self, a0: QRect)

setGeometry(self, ax: int, ay: int, aw: int, ah: int) → None

setGraphicsEffect(self, effect: QGraphicsEffect)

setHidden(self, hidden: bool)

setInputMethodHints(self, hints: Qt.InputMethodHint)

setLayout(self, a0: QLayout)

setLayoutDirection(self, direction: Qt.LayoutDirection)

setLocale(self, locale: QLocale)

setMask(self, a0: QBitmap)

setMask(self, a0: QRegion) → None

setMaximumHeight(self, maxh: int)

setMaximumSize(self, maxw: int, maxh: int)

setMaximumSize(self, s: QSize) → None

setMaximumWidth(self, maxw: int)

setMinimumHeight(self, minh: int)

setMinimumSize(self, minw: int, minh: int)

setMinimumSize(self, s: QSize) → None

setMinimumWidth(self, minw: int)

setModal(self, modal: bool)

setMouseTracking(self, enable: bool)

setObjectName(self, name: str)

setPalette(self, a0: QPalette)

setParent(self, parent: QWidget)

setParent(self, parent: QWidget, f: Qt.WindowType) → None

setProperty(self, name: str, value: Any) → bool

setResult(self, r: int)

setScreen(self, a0: QScreen)

setShortcutAutoRepeat(self, id: int, enabled: bool = True)

setShortcutEnabled(self, id: int, enabled: bool = True)

setSizeGripEnabled(self, a0: bool)

setSizeIncrement(self, w: int, h: int)

setSizeIncrement(self, s: QSize) → None

setSizePolicy(self, a0: QSizePolicy)

setSizePolicy(self, hor: QSizePolicy.Policy, ver: QSizePolicy.Policy) → None

setStatusTip(self, a0: str)

setStyle(self, a0: QStyle)

setStyleSheet(self, styleSheet: str)

setTabOrder(a0: QWidget, a1: QWidget)

setTabletTracking(self, enable: bool)

setToolTip(self, a0: str)

setToolTipDuration(self, msec: int)

setUpdatesEnabled(self, enable: bool)

setVisible(self, visible: bool)

setWhatsThis(self, a0: str)

setWindowFilePath(self, filePath: str)

setWindowFlag(self, a0: Qt.WindowType, on: bool = True)

setWindowFlags(self, type: Qt.WindowType)

setWindowIcon(self, icon: QIcon)

setWindowIconText(self, a0: str)

setWindowModality(self, windowModality: Qt.WindowModality)

setWindowModified(self, a0: bool)

setWindowOpacity(self, level: float)

setWindowRole(self, a0: str)

setWindowState(self, state: Qt.WindowState)

setWindowTitle(self, a0: str)

sharedPainter(self) → QPainter

show(self)

showEvent(self, a0: QShowEvent)

showFullScreen(self)

showMaximized(self)

showMinimized(self)

showNormal(self)

signalsBlocked(self) → bool

size(self) → QSize

sizeHint(self) → QSize

sizeIncrement(self) → QSize

sizePolicy(self) → QSizePolicy

stackUnder(self, a0: QWidget)

startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

statusTip(self) → str

style(self) → QStyle

styleSheet(self) → str

tabletEvent(self, a0: QTabletEvent)

testAttribute(self, attribute: Qt.WidgetAttribute) → bool

thread(self) → QThread

timerEvent(self, a0: QTimerEvent)

toolTip(self) → str

toolTipDuration(self) → int

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str

underMouse(self) → bool

ungrabGesture(self, type: Qt.GestureType)

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, a0: QRect) → None

update(self, a0: QRegion) → None

update(self, ax: int, ay: int, aw: int, ah: int) → None

updateGeometry(self)

updateMicroFocus(self, query: Qt.InputMethodQuery = Qt.ImQueryAll)

updatesEnabled(self) → bool

visibleRegion(self) → QRegion

whatsThis(self) → str

wheelEvent(self, a0: QWheelEvent)

width(self) → int

widthMM(self) → int

winId(self) → PyQt6.sip.voidptr

window(self) → QWidget

windowFilePath(self) → str

windowFlags(self) → Qt.WindowType

windowHandle(self) → QWindow

windowIcon(self) → QIcon

windowIconChanged

windowIconChanged(self, icon: QIcon) [signal]

windowIconText(self) → str

windowIconTextChanged

windowIconTextChanged(self, iconText: str) [signal]

windowModality(self) → Qt.WindowModality

windowOpacity(self) → float

windowRole(self) → str

windowState(self) → Qt.WindowState

windowTitle(self) → str

windowTitleChanged

windowTitleChanged(self, title: str) [signal]

windowType(self) → Qt.WindowType

x(self) → int

y(self) → int

onShowComboIndexChanged()

Called when the index of the Show combo box is changed. Updates the available residues based on the selected option.

updateNumPickedResiduesLabel()

Update the label for number of picked residues.