Package schrodinger :: Package application :: Package bioluminate :: Module bwidgets :: Class SequenceFileDialog

Class SequenceFileDialog

       object --+                            
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sip.simplewrapper --+                        
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          sip.wrapper --+                    
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     PyQt5.QtCore.QObject --+                
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           object --+       |                
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    sip.simplewrapper --+   |                
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 PyQt5.QtGui.QPaintDevice --+                
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      PyQt5.QtWidgets.QWidget --+            
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          PyQt5.QtWidgets.QDialog --+        
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          PyQt5.QtWidgets.QFileDialog --+    
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                           object --+   |    
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  ui.qt.filedialog.CustomSideBarMixin --+    
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              ui.qt.filedialog.FileDialog --+
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                                           SequenceFileDialog

Custom class to handle opening files related to sequences.

Nested Classes

[hide private]

Inherited from PyQt5.QtWidgets.QFileDialog: AcceptMode, DialogLabel, FileMode, Option, Options, ViewMode

Inherited from PyQt5.QtWidgets.QDialog: DialogCode

Inherited from PyQt5.QtWidgets.QWidget: RenderFlag, RenderFlags

Inherited from PyQt5.QtGui.QPaintDevice: PaintDeviceMetric

Instance Methods

[hide private]

__init__(self, parent=None, add_options=True, **kwargs)
x.__init__(...) initializes x; see help(type(x)) for signature

addOptions(self)
Adds three widgets on the bottom of the dialog window that allow users to optionally:

str or None

getOpenFileName(self, multiple=False)
Convenience function that returns a single filename as selected by the user

Inherited from PyQt5.QtWidgets.QFileDialog: accept, acceptMode, changeEvent, currentChanged, currentUrlChanged, defaultSuffix, directory, directoryEntered, directoryUrl, directoryUrlEntered, done, fileMode, fileSelected, filesSelected, filter, filterSelected, getExistingDirectoryUrl, getOpenFileUrl, getOpenFileUrls, getSaveFileUrl, history, iconProvider, itemDelegate, labelText, mimeTypeFilters, nameFilters, open, options, proxyModel, restoreState, saveState, selectFile, selectMimeTypeFilter, selectNameFilter, selectUrl, selectedFiles, selectedNameFilter, selectedUrls, setAcceptMode, setDefaultSuffix, setDirectory, setDirectoryUrl, setFileMode, setFilter, setHistory, setIconProvider, setItemDelegate, setLabelText, setMimeTypeFilters, setNameFilter, setNameFilters, setOption, setOptions, setProxyModel, setSidebarUrls, setSupportedSchemes, setViewMode, setVisible, sidebarUrls, supportedSchemes, testOption, urlSelected, urlsSelected, viewMode

Inherited from PyQt5.QtWidgets.QDialog: accepted, closeEvent, contextMenuEvent, eventFilter, exec_, finished, isSizeGripEnabled, keyPressEvent, minimumSizeHint, reject, rejected, resizeEvent, result, setModal, setResult, setSizeGripEnabled, showEvent, sizeHint

Inherited from PyQt5.QtWidgets.QWidget: acceptDrops, accessibleDescription, accessibleName, actionEvent, actions, activateWindow, addAction, addActions, adjustSize, autoFillBackground, backgroundRole, baseSize, childAt, childrenRect, childrenRegion, clearFocus, clearMask, close, contentsMargins, contentsRect, contextMenuPolicy, create, createWindowContainer, cursor, customContextMenuRequested, destroy, devType, dragEnterEvent, dragLeaveEvent, dragMoveEvent, dropEvent, effectiveWinId, ensurePolished, enterEvent, event, find, focusInEvent, focusNextChild, focusNextPrevChild, focusOutEvent, focusPolicy, focusPreviousChild, focusProxy, focusWidget, font, fontInfo, fontMetrics, foregroundRole, frameGeometry, frameSize, geometry, getContentsMargins, grab, grabGesture, grabKeyboard, grabMouse, grabShortcut, graphicsEffect, graphicsProxyWidget, hasFocus, hasHeightForWidth, hasMouseTracking, height, heightForWidth, hide, hideEvent, initPainter, inputMethodEvent, inputMethodHints, inputMethodQuery, insertAction, insertActions, isActiveWindow, isAncestorOf, isEnabled, isEnabledTo, isFullScreen, isHidden, isLeftToRight, isMaximized, isMinimized, isModal, isRightToLeft, isVisible, isVisibleTo, isWindow, isWindowModified, keyReleaseEvent, keyboardGrabber, layout, layoutDirection, leaveEvent, locale, lower, mapFrom, mapFromGlobal, mapFromParent, mapTo, mapToGlobal, mapToParent, mask, maximumHeight, maximumSize, maximumWidth, metric, minimumHeight, minimumSize, minimumWidth, mouseDoubleClickEvent, mouseGrabber, mouseMoveEvent, mousePressEvent, mouseReleaseEvent, move, moveEvent, nativeEvent, nativeParentWidget, nextInFocusChain, normalGeometry, overrideWindowFlags, overrideWindowState, paintEngine, paintEvent, palette, parentWidget, pos, previousInFocusChain, raise_, rect, releaseKeyboard, releaseMouse, releaseShortcut, removeAction, render, repaint, resize, restoreGeometry, saveGeometry, scroll, setAcceptDrops, setAccessibleDescription, setAccessibleName, setAttribute, setAutoFillBackground, setBackgroundRole, setBaseSize, setContentsMargins, setContextMenuPolicy, setCursor, setDisabled, setEnabled, setFixedHeight, setFixedSize, setFixedWidth, setFocus, setFocusPolicy, setFocusProxy, setFont, setForegroundRole, setGeometry, setGraphicsEffect, setHidden, setInputMethodHints, setLayout, setLayoutDirection, setLocale, setMask, setMaximumHeight, setMaximumSize, setMaximumWidth, setMinimumHeight, setMinimumSize, setMinimumWidth, setMouseTracking, setPalette, setParent, setShortcutAutoRepeat, setShortcutEnabled, setSizeIncrement, setSizePolicy, setStatusTip, setStyle, setStyleSheet, setTabOrder, setToolTip, setToolTipDuration, setUpdatesEnabled, setWhatsThis, setWindowFilePath, setWindowFlags, setWindowIcon, setWindowIconText, setWindowModality, setWindowModified, setWindowOpacity, setWindowRole, setWindowState, setWindowTitle, sharedPainter, show, showFullScreen, showMaximized, showMinimized, showNormal, size, sizeIncrement, sizePolicy, stackUnder, statusTip, style, styleSheet, tabletEvent, testAttribute, toolTip, toolTipDuration, underMouse, ungrabGesture, unsetCursor, unsetLayoutDirection, unsetLocale, update, updateGeometry, updateMicroFocus, updatesEnabled, visibleRegion, whatsThis, wheelEvent, width, winId, window, windowFilePath, windowFlags, windowHandle, windowIcon, windowIconChanged, windowIconText, windowIconTextChanged, windowModality, windowOpacity, windowRole, windowState, windowTitle, windowTitleChanged, windowType, x, y

Inherited from PyQt5.QtCore.QObject: __getattr__, blockSignals, childEvent, children, connectNotify, customEvent, deleteLater, destroyed, disconnect, disconnectNotify, dumpObjectInfo, dumpObjectTree, dynamicPropertyNames, findChild, findChildren, inherits, installEventFilter, isSignalConnected, isWidgetType, isWindowType, killTimer, metaObject, moveToThread, objectName, objectNameChanged, parent, property, pyqtConfigure, receivers, removeEventFilter, sender, senderSignalIndex, setObjectName, setProperty, signalsBlocked, startTimer, thread, timerEvent, tr

Inherited from PyQt5.QtGui.QPaintDevice: colorCount, depth, devicePixelRatio, devicePixelRatioF, devicePixelRatioFScale, heightMM, logicalDpiX, logicalDpiY, paintingActive, physicalDpiX, physicalDpiY, widthMM

Inherited from sip.simplewrapper: __new__

Inherited from ui.qt.filedialog.CustomSideBarMixin (private): _setup_sidebar, _updateItemNames

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods

[hide private]

get_open_file_names(parent=None, add_options=True, multiple=True, **kwargs)

get_open_file_name(parent=None, add_options=True, **kwargs)

Inherited from ui.qt.filedialog.FileDialog: getExistingDirectory, getOpenFileNames, getSaveFileName

Class Variables

[hide private]

CAPTION = 'Import Sequences'

DEFAULT_FILTERS = 'FASTA (*.fasta *.fst *.fas *.seq);;Maestro ...
The default MSV filters.

REFERENCE_FILTERS = 'Common (*.fasta *.fst *.fas *.seq *.mae *...
Filters for reference sequences in homology model building.

STRUCTURE_FILTERS = 'Structure files (*.mae *.maegz *.mae.gz *...
Filters that have structures associated with them.

Inherited from PyQt5.QtWidgets.QFileDialog: Accept, AcceptOpen, AcceptSave, AnyFile, Detail, Directory, DirectoryOnly, DontConfirmOverwrite, DontResolveSymlinks, DontUseCustomDirectoryIcons, DontUseNativeDialog, DontUseSheet, ExistingFile, ExistingFiles, FileName, FileType, HideNameFilterDetails, List, LookIn, ReadOnly, Reject, ShowDirsOnly

Inherited from PyQt5.QtWidgets.QDialog: Accepted, Rejected

Inherited from PyQt5.QtWidgets.QWidget: DrawChildren, DrawWindowBackground, IgnoreMask

Inherited from PyQt5.QtCore.QObject: staticMetaObject

Inherited from PyQt5.QtGui.QPaintDevice: PdmDepth, PdmDevicePixelRatio, PdmDevicePixelRatioScaled, PdmDpiX, PdmDpiY, PdmHeight, PdmHeightMM, PdmNumColors, PdmPhysicalDpiX, PdmPhysicalDpiY, PdmWidth, PdmWidthMM

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, parent=None, add_options=True, **kwargs)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

parent - the widget over which this dialog should be shown. If not given, the Dialog will be placed by PyQt.
caption - the name that appears in the titlebar of this dialog. If not given the title will be the default PyQt caption.
directory - the initial directory displayed in this dialog, default is the current directory.
filter - the list of filters that can be applied to this directory the format is "filetype1 (*.ex1);; filetype2 (*.ex2, *.ex3)". examples:
- "image files (*.png *.jpg *.bmp)"
- "images (*.png *.xpm *.jpg);;text files (*.txt);;all files (*)"
Default is all files.
custom_sidebar - True if the Schrodinger sidebar should be used, False if the default PyQt sidebar should be used.
sidebar_links - Use to create extra links in the left-hand sidebar of the dialog. the keys of the dictionary are a unique identifier for each link (note that 'home' and 'working' are already used), and the values are tuples of the form (path, name) where path and name are str, path indicates the path the sidebar link points to, and name is the name displayed for the link.

Overrides: object.__init__

(inherited documentation)

addOptions(self)

Adds three widgets on the bottom of the dialog window that allow users to optionally:

Align to query sequence
Replace matching sequences
Incorporate PDB files into Maestro

getOpenFileName(self, multiple=False)

Convenience function that returns a single filename as selected by the user

The base class base_file_dialog documents the keyword arguments for this class.

Returns: str or None: full pathname of the file selected by the user, or None if Cancel was pressed
Overrides: PyQt5.QtWidgets.QFileDialog.getOpenFileName

Class Variable Details

[hide private]

DEFAULT_FILTERS

The default MSV filters.

Value:

'FASTA (*.fasta *.fst *.fas *.seq);;Maestro (*.mae *.maegz *.mae.gz );
;PDB (*.pdb *.ent);;SWISSPROT (*.sw *.sp *.swiss *.swissprot);;GCG (*.
gcg *.msf);;EMBL (*.embl *.emb);;PIR (*.pir);;All Files (*.*)'

REFERENCE_FILTERS

Filters for reference sequences in homology model building.

Value:

'Common (*.fasta *.fst *.fas *.seq *.mae *.maegz *.mae.gz *.pdb *.ent 
*.txt);;FASTA (*.fasta *.fst *.fas *.seq);;PDB (*.pdb *.ent);;Maestro 
(*.mae *.maegz *.mae.gz );;All Files (*.*)'

STRUCTURE_FILTERS

Filters that have structures associated with them.

Value:

'Structure files (*.mae *.maegz *.mae.gz *.pdb *.ent);;Maestro (*.mae 
*.maegz *.mae.gz );;PDB (*.pdb *.ent)'

Class SequenceFileDialog

__init__(self, parent=None, add_options=True, **kwargs) (Constructor)

addOptions(self)

getOpenFileName(self, multiple=False)

DEFAULT_FILTERS

REFERENCE_FILTERS

STRUCTURE_FILTERS

init(self, parent=None, add_options=True, **kwargs)
(Constructor)