schrodinger.ui.qt.pdb_dialog module¶

Contains class that is used to display “Get Pdb Dialog”.

schrodinger.ui.qt.pdb_dialog.validate_pdb_id(pdb_id)[source]¶: Return True if given string is a valid PDB ID: 4 characters beginning with a digit, and characters 2-4 should be alphanumeric.

schrodinger.ui.qt.pdb_dialog.extract_chain(filename, chain_name)[source]¶

Extract the specific chain from the given protein structure file. Raises KeyError if chain is not present.

Parameters

filename (str) – Name of the protein file.
chain_name (str) – Chain to be extracted.

:return : Structure of the extracted chain :rtype: schrodinger.structure.Structure

schrodinger.ui.qt.pdb_dialog.create_biounits(filename)[source]¶: Generate biological assemblies, and write a single Maestro file with multiple structures. Maestro is used instead of PDB mainly because PDB format doesn’t support custom title properties. Assembly number will be added to the title of each output structure.

class schrodinger.ui.qt.pdb_dialog.PDBDialog(import_pdbs=False)[source]¶

Bases: schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin, PyQt5.QtWidgets.QDialog

A QDialog to download Pdb file from pdb_id given by user.

__init__(import_pdbs=False)[source]¶

geometry(self) → QRect¶

setupFetchingOptions()[source]¶: Set up fetching options menu.

onBiologicalUnitToggled(checked)[source]¶

Respond to toggling of ‘Biological unit’ checkbox.

Parameters: checked (bool) – whether ‘Biological unit’ checkbox is checked or not

onRetrieveFromLocalToggled(checked)[source]¶

Respond to toggling of ‘Local Installation Only’ menu item.

Parameters: checked (bool) – whether ‘Local Installation Only’ menu item is checked or not

getHelp()[source]¶: Show help documentation of functionality of dialog.

updateDownloadButton()[source]¶: Disable the Download button if there is no PDB ID, else enable it.

manageDownloadFile()[source]¶

execRemoteQueryDialog() → bool[source]¶

Launches the relevant remote query dialog if applicable.

Returns: if the remote dialog is accepted

getPDB()[source]¶

Download the pdb file(s) with optional diffraction data. Return 0 for successful download else 1

Returns: List of files written on success, or None on failure.
Return type: list(str) or None

downloadFile()[source]¶: Download the pdb file(s) of given PDB ID(s) by user. If diffraction data is requested tries to download diffraction data files and EM maps. If EM maps are found their surfaces are added to corresponding PDB entries in the Project Table.

cancel()[source]¶: Reject the Pdb dialog.

exec()[source]¶: Shows the dialog as a modal dialog, blocking until the user closes it.

Accepted = 1¶

class DialogCode¶: Bases: int

DrawChildren = 2¶

DrawWindowBackground = 1¶

IgnoreMask = 4¶

class PaintDeviceMetric¶: Bases: int

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¶: Bases: int

class RenderFlags¶

class RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) → None

class RenderFlags(QWidget.RenderFlags) → None

Bases: sip.simplewrapper

__init__(*args, **kwargs)¶

accept(self)¶

acceptDrops(self) → bool¶

accepted¶: accepted(self) [signal]

accessibleDescription(self) → str¶

accessibleName(self) → str¶

actionEvent(self, QActionEvent)¶

actions(self) → List[QAction]¶

activateWindow(self)¶

addAction(self, QAction)¶

addActions(self, Iterable[QAction])¶

adjustSize(self)¶

autoFillBackground(self) → bool¶

backgroundRole(self) → QPalette.ColorRole¶

baseSize(self) → QSize¶

blockSignals(self, bool) → bool¶

changeEvent(self, QEvent)¶

childAt(self, QPoint) → QWidget¶
PDBDialog.childAt(self, int, int) -> QWidget

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

childrenRect(self) → QRect¶

childrenRegion(self) → QRegion¶

clearFocus(self)¶

clearMask(self)¶

close(self) → bool¶

closeEvent(self, QCloseEvent)¶

colorCount(self) → int¶

connectNotify(self, QMetaMethod)¶

contentsMargins(self) → QMargins¶

contentsRect(self) → QRect¶

contextMenuEvent(self, QContextMenuEvent)¶

contextMenuPolicy(self) → Qt.ContextMenuPolicy¶

create(self, window: PyQt5.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)¶

createWindowContainer(QWindow, parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = 0) → QWidget¶

cursor(self) → QCursor¶

customContextMenuRequested¶: customContextMenuRequested(self, QPoint) [signal]

customEvent(self, QEvent)¶

deleteLater(self)¶

depth(self) → int¶

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

destroyed¶: destroyed(self, object: QObject = None) [signal]

devType(self) → int¶

devicePixelRatio(self) → int¶

devicePixelRatioF(self) → float¶

devicePixelRatioFScale() → float¶

disconnect(QMetaObject.Connection) → bool¶
disconnect(self) → None

disconnectNotify(self, QMetaMethod)¶

done(self, int)¶

dragEnterEvent(self, QDragEnterEvent)¶

dragLeaveEvent(self, QDragLeaveEvent)¶

dragMoveEvent(self, QDragMoveEvent)¶

dropEvent(self, QDropEvent)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

effectiveWinId(self) → PyQt5.sip.voidptr¶

ensurePolished(self)¶

enterEvent(self, QEvent)¶

error(*args, **kwargs)¶: Shows a popup error message box. For parameter documentation see messagebox.MessageBox.

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

exec_(self) → int¶

find(PyQt5.sip.voidptr) → QWidget¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶
findChild(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶
findChildren(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

finished¶: finished(self, int) [signal]

focusInEvent(self, QFocusEvent)¶

focusNextChild(self) → bool¶

focusNextPrevChild(self, bool) → bool¶

focusOutEvent(self, 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¶

forgetMessageBoxResponse(key)¶

Forgets any previously saved response that was stored via a save_response_key.

Parameters: key – the key for the response to forget

frameGeometry(self) → QRect¶

frameSize(self) → QSize¶

getContentsMargins(self) → Tuple[int, int, int, int]¶

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

grabGesture(self, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())¶

grabKeyboard(self)¶

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

grabShortcut(self, 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, int) → int¶

heightMM(self) → int¶

hide(self)¶

hideEvent(self, QHideEvent)¶

info(*args, **kwargs)¶: Shows a popup information message box. For parameter documentation see messagebox.MessageBox.

inherits(self, str) → bool¶

initPainter(self, QPainter)¶

inputMethodEvent(self, QInputMethodEvent)¶

inputMethodHints(self) → Qt.InputMethodHints¶

inputMethodQuery(self, Qt.InputMethodQuery) → Any¶

PDBDialog.insertAction(self, QAction, QAction)

insertActions(self, QAction, Iterable[QAction])¶

installEventFilter(self, QObject)¶

isActiveWindow(self) → bool¶

isAncestorOf(self, QWidget) → bool¶

isEnabled(self) → bool¶

isEnabledTo(self, 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, QMetaMethod) → bool¶

isSizeGripEnabled(self) → bool¶

isVisible(self) → bool¶

isVisibleTo(self, QWidget) → bool¶

isWidgetType(self) → bool¶

isWindow(self) → bool¶

isWindowModified(self) → bool¶

isWindowType(self) → bool¶

keyPressEvent(self, QKeyEvent)¶

keyReleaseEvent(self, QKeyEvent)¶

keyboardGrabber() → QWidget¶

killTimer(self, int)¶

layout(self) → QLayout¶

layoutDirection(self) → Qt.LayoutDirection¶

leaveEvent(self, QEvent)¶

locale(self) → QLocale¶

logicalDpiX(self) → int¶

logicalDpiY(self) → int¶

lower(self)¶

mapFrom(self, QWidget, QPoint) → QPoint¶

mapFromGlobal(self, QPoint) → QPoint¶

mapFromParent(self, QPoint) → QPoint¶

mapTo(self, QWidget, QPoint) → QPoint¶

mapToGlobal(self, QPoint) → QPoint¶

mapToParent(self, QPoint) → QPoint¶

mask(self) → QRegion¶

maximumHeight(self) → int¶

maximumSize(self) → QSize¶

maximumWidth(self) → int¶

metaObject(self) → QMetaObject¶

metric(self, QPaintDevice.PaintDeviceMetric) → int¶

minimumHeight(self) → int¶

minimumSize(self) → QSize¶

minimumSizeHint(self) → QSize¶

minimumWidth(self) → int¶

mouseDoubleClickEvent(self, QMouseEvent)¶

mouseGrabber() → QWidget¶

mouseMoveEvent(self, QMouseEvent)¶

mousePressEvent(self, QMouseEvent)¶

mouseReleaseEvent(self, QMouseEvent)¶

move(self, QPoint)¶
PDBDialog.move(self, int, int) -> None

moveEvent(self, QMoveEvent)¶

moveToThread(self, QThread)¶

nativeEvent(self, Union[QByteArray, bytes, bytearray], sip.voidptr) → Tuple[bool, int]¶

nativeParentWidget(self) → QWidget¶

nextInFocusChain(self) → QWidget¶

normalGeometry(self) → QRect¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

open(self)¶

overrideWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])¶

overrideWindowState(self, Union[Qt.WindowStates, Qt.WindowState])¶

paintEngine(self) → QPaintEngine¶

paintEvent(self, 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, 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.

question(*args, **kwargs)¶: Shows a popup question message box. For parameter documentation see messagebox.QuestionMessageBox.

raise_(self)¶

receivers(self, PYQT_SIGNAL) → int¶

rect(self) → QRect¶

reject(self)¶

rejected¶: rejected(self) [signal]

releaseKeyboard(self)¶

releaseMouse(self)¶

releaseShortcut(self, int)¶

removeAction(self, QAction)¶

removeEventFilter(self, QObject)¶

render(self, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.RenderFlag.DrawWindowBackground | QWidget.RenderFlag.DrawChildren))¶
render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.RenderFlag.DrawWindowBackground | QWidget.RenderFlag.DrawChildren)) → None

repaint(self)¶
PDBDialog.repaint(self, int, int, int, int) -> None
repaint(self, QRect) → None
repaint(self, QRegion) → None

resize(self, QSize)¶
PDBDialog.resize(self, int, int) -> None

resizeEvent(self, QResizeEvent)¶

restoreGeometry(self, Union[QByteArray, bytes, bytearray]) → bool¶

result(self) → int¶

saveGeometry(self) → QByteArray¶

PDBDialog.scroll(self, int, int)
PDBDialog.scroll(self, int, int, QRect) -> None

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setAcceptDrops(self, bool)¶

setAccessibleDescription(self, str)¶

setAccessibleName(self, str)¶

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

setAutoFillBackground(self, bool)¶

setBackgroundRole(self, QPalette.ColorRole)¶

PDBDialog.setBaseSize(self, int, int)
setBaseSize(self, QSize) → None¶

PDBDialog.setContentsMargins(self, int, int, int, int)
setContentsMargins(self, QMargins) → None¶

setContextMenuPolicy(self, Qt.ContextMenuPolicy)¶

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

setDisabled(self, bool)¶

setEnabled(self, bool)¶

setFixedHeight(self, int)¶

setFixedSize(self, QSize)¶
PDBDialog.setFixedSize(self, int, int) -> None

setFixedWidth(self, int)¶

setFocus(self)¶
setFocus(self, Qt.FocusReason) → None

setFocusPolicy(self, Qt.FocusPolicy)¶

setFocusProxy(self, QWidget)¶

setFont(self, QFont)¶

setForegroundRole(self, QPalette.ColorRole)¶

setGeometry(self, QRect)¶
PDBDialog.setGeometry(self, int, int, int, int) -> None

setGraphicsEffect(self, QGraphicsEffect)¶

setHidden(self, bool)¶

setInputMethodHints(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])¶

setLayout(self, QLayout)¶

setLayoutDirection(self, Qt.LayoutDirection)¶

setLocale(self, QLocale)¶

setMask(self, QBitmap)¶
setMask(self, QRegion) → None

setMaximumHeight(self, int)¶

PDBDialog.setMaximumSize(self, int, int)
setMaximumSize(self, QSize) → None¶

setMaximumWidth(self, int)¶

setMinimumHeight(self, int)¶

PDBDialog.setMinimumSize(self, int, int)
setMinimumSize(self, QSize) → None¶

setMinimumWidth(self, int)¶

setModal(self, bool)¶

setMouseTracking(self, bool)¶

setObjectName(self, str)¶

setPalette(self, QPalette)¶

setParent(self, QWidget)¶
setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType]) → None

setProperty(self, str, Any) → bool¶

setResult(self, int)¶

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

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

setSizeGripEnabled(self, bool)¶

PDBDialog.setSizeIncrement(self, int, int)
setSizeIncrement(self, QSize) → None¶

setSizePolicy(self, QSizePolicy)¶
setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy) → None

setStatusTip(self, str)¶

setStyle(self, QStyle)¶

setStyleSheet(self, str)¶

PDBDialog.setTabOrder(QWidget, QWidget)

setTabletTracking(self, bool)¶

setToolTip(self, str)¶

setToolTipDuration(self, int)¶

setUpdatesEnabled(self, bool)¶

setVisible(self, bool)¶

setWhatsThis(self, str)¶

setWindowFilePath(self, str)¶

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

setWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])¶

setWindowIcon(self, QIcon)¶

setWindowIconText(self, str)¶

setWindowModality(self, Qt.WindowModality)¶

setWindowModified(self, bool)¶

setWindowOpacity(self, float)¶

setWindowRole(self, str)¶

setWindowState(self, Union[Qt.WindowStates, Qt.WindowState])¶

setWindowTitle(self, str)¶

sharedPainter(self) → QPainter¶

show(self)¶

showEvent(self, QShowEvent)¶

showFullScreen(self)¶

showMaximized(self)¶

showMessageBox(*args, **kwargs)¶: Shows a popup message box. For parameter documentation see messagebox.MessageBox.

showMinimized(self)¶

showNormal(self)¶

signalsBlocked(self) → bool¶

size(self) → QSize¶

sizeHint(self) → QSize¶

sizeIncrement(self) → QSize¶

sizePolicy(self) → QSizePolicy¶

stackUnder(self, QWidget)¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

statusTip(self) → str¶

style(self) → QStyle¶

styleSheet(self) → str¶

tabletEvent(self, QTabletEvent)¶

testAttribute(self, Qt.WidgetAttribute) → bool¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

toolTip(self) → str¶

toolTipDuration(self) → int¶

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

underMouse(self) → bool¶

ungrabGesture(self, Qt.GestureType)¶

unsetCursor(self)¶

unsetLayoutDirection(self)¶

unsetLocale(self)¶

update(self)¶
update(self, QRect) → None
update(self, QRegion) → None
PDBDialog.update(self, int, int, int, int) -> None

updateGeometry(self)¶

updateMicroFocus(self)¶

updatesEnabled(self) → bool¶

visibleRegion(self) → QRegion¶

warning(*args, **kwargs)¶: Shows a popup warning message box. For parameter documentation see messagebox.MessageBox.

whatsThis(self) → str¶

wheelEvent(self, QWheelEvent)¶

width(self) → int¶

widthMM(self) → int¶

winId(self) → PyQt5.sip.voidptr¶

window(self) → QWidget¶

windowFilePath(self) → str¶

windowFlags(self) → Qt.WindowFlags¶

windowHandle(self) → QWindow¶

windowIcon(self) → QIcon¶

windowIconChanged¶: windowIconChanged(self, QIcon) [signal]

windowIconText(self) → str¶

windowIconTextChanged¶: windowIconTextChanged(self, str) [signal]

windowModality(self) → Qt.WindowModality¶

windowOpacity(self) → float¶

windowRole(self) → str¶

windowState(self) → Qt.WindowStates¶

windowTitle(self) → str¶

windowTitleChanged¶: windowTitleChanged(self, str) [signal]

windowType(self) → Qt.WindowType¶

x(self) → int¶

y(self) → int¶

schrodinger.ui.qt.pdb_dialog.getPdbDialog()[source]¶: Called by maestro to bring up the dialog box. Returns string of downloaded filenames, separated by semi-colon. On cancel, returns empty string.