Package schrodinger :: Package application :: Package desmond :: Module fep_gui :: Class _ProMut

Class _ProMut

       object --+                
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sip.simplewrapper --+            
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          sip.wrapper --+        
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     PyQt4.QtCore.QObject --+    
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           object --+       |    
                    |       |    
    sip.simplewrapper --+   |    
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 PyQt4.QtGui.QPaintDevice --+    
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          PyQt4.QtGui.QWidget --+
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                               _ProMut

Main code of the Protein Residue Mutation GUI

Nested Classes

[hide private]

_Site

Inherited from PyQt4.QtGui.QWidget: RenderFlag, RenderFlags

Inherited from PyQt4.QtGui.QPaintDevice: PaintDeviceMetric

Instance Methods

[hide private]

__init__(self, master, win, mode='desmond')
x.__init__(...) initializes x; see help(type(x)) for signature

viewClicked(self, index)

resetClicked(self, index)

deleteButtonClicked(self)

_paint_res(self, mut_site, should_color=True)

_show(self)

_reset_mutation_cmd(self)

_disect_struc_impl(self, protein_atom=None, ligand_atom=None)

_disect_struc(self, protein_atom=None, ligand_atom=None)

_mark_res(self, residue, res_marker)

prepickLigCallback(self)

pickLigCallback(self, i_atom)
Called when the user picks a ligand atom.

prepickResidueCallback(self)

pickResidueCallback(self, i_atom)

_handle_focusin(self)

generateCombintations(self, sites)
Generates all combintations for all sites.

populateButtonClicked(self)

_mutate_impl(self, m)

_mutate(self, m)

_gen_mutant_impl(self, i_row)

_gen_mutant(self, i_row)

_show_mutant_impl(self, i_row)

_show_mutant(self, i_row)

_reset_mutant_impl(self, i_row)

_reset_mutant(self, i_row)

selectionChangedCallback(self, ignored1, ignored2)

reset(self)

getFragList(self)

_peel_off_ligand(self, this_ct)
Returned object is a two-element list: The first element is a CT containing only non-ligand molecules, the second element is a CT containing only the ligand molecule.

_getStructs(self, frag_list=[])
Protein residue mutation - get the structures

getStructures(self, fraglist=[])
Protein residue mutation: Returns a list of CTs and number of selected rows.

Inherited from PyQt4.QtGui.QWidget: acceptDrops, accessibleDescription, accessibleName, actionEvent, actions, activateWindow, addAction, addActions, adjustSize, autoFillBackground, backgroundRole, baseSize, changeEvent, childAt, childrenRect, childrenRegion, clearFocus, clearMask, close, closeEvent, contentsMargins, contentsRect, contextMenuEvent, contextMenuPolicy, create, cursor, customContextMenuRequested, destroy, devType, dragEnterEvent, dragLeaveEvent, dragMoveEvent, dropEvent, effectiveWinId, enabledChange, ensurePolished, enterEvent, event, find, focusInEvent, focusNextChild, focusNextPrevChild, focusOutEvent, focusPolicy, focusPreviousChild, focusProxy, focusWidget, font, fontChange, fontInfo, fontMetrics, foregroundRole, frameGeometry, frameSize, geometry, getContentsMargins, grabGesture, grabKeyboard, grabMouse, grabShortcut, graphicsEffect, graphicsProxyWidget, handle, hasFocus, hasMouseTracking, height, heightForWidth, hide, hideEvent, inputContext, inputMethodEvent, inputMethodHints, inputMethodQuery, insertAction, insertActions, isActiveWindow, isAncestorOf, isEnabled, isEnabledTo, isEnabledToTLW, isFullScreen, isHidden, isLeftToRight, isMaximized, isMinimized, isModal, isRightToLeft, isTopLevel, isVisible, isVisibleTo, isWindow, isWindowModified, keyPressEvent, keyReleaseEvent, keyboardGrabber, languageChange, layout, layoutDirection, leaveEvent, locale, lower, mapFrom, mapFromGlobal, mapFromParent, mapTo, mapToGlobal, mapToParent, mask, maximumHeight, maximumSize, maximumWidth, metric, minimumHeight, minimumSize, minimumSizeHint, minimumWidth, mouseDoubleClickEvent, mouseGrabber, mouseMoveEvent, mousePressEvent, mouseReleaseEvent, move, moveEvent, nativeParentWidget, nextInFocusChain, normalGeometry, overrideWindowFlags, overrideWindowState, paintEngine, paintEvent, palette, paletteChange, parentWidget, pos, previousInFocusChain, raise_, rect, releaseKeyboard, releaseMouse, releaseShortcut, removeAction, render, repaint, resetInputContext, resize, resizeEvent, 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, setInputContext, setInputMethodHints, setLayout, setLayoutDirection, setLocale, setMask, setMaximumHeight, setMaximumSize, setMaximumWidth, setMinimumHeight, setMinimumSize, setMinimumWidth, setMouseTracking, setPalette, setParent, setShortcutAutoRepeat, setShortcutEnabled, setShown, setSizeIncrement, setSizePolicy, setStatusTip, setStyle, setStyleSheet, setTabOrder, setToolTip, setUpdatesEnabled, setVisible, setWhatsThis, setWindowFilePath, setWindowFlags, setWindowIcon, setWindowIconText, setWindowModality, setWindowModified, setWindowOpacity, setWindowRole, setWindowState, setWindowTitle, show, showEvent, showFullScreen, showMaximized, showMinimized, showNormal, size, sizeHint, sizeIncrement, sizePolicy, stackUnder, statusTip, style, styleSheet, tabletEvent, testAttribute, toolTip, topLevelWidget, underMouse, ungrabGesture, unsetCursor, unsetLayoutDirection, unsetLocale, update, updateGeometry, updateMicroFocus, updatesEnabled, visibleRegion, whatsThis, wheelEvent, width, winId, window, windowActivationChange, windowFilePath, windowFlags, windowIcon, windowIconText, windowModality, windowOpacity, windowRole, windowState, windowTitle, windowType, x, x11Info, x11PictureHandle, y

Inherited from PyQt4.QtCore.QObject: __getattr__, blockSignals, childEvent, children, connect, connectNotify, customEvent, deleteLater, destroyed, disconnect, disconnectNotify, dumpObjectInfo, dumpObjectTree, dynamicPropertyNames, emit, eventFilter, findChild, findChildren, inherits, installEventFilter, isWidgetType, killTimer, metaObject, moveToThread, objectName, parent, property, pyqtConfigure, receivers, removeEventFilter, sender, setObjectName, setProperty, signalsBlocked, startTimer, thread, timerEvent, tr, trUtf8

Inherited from PyQt4.QtGui.QPaintDevice: colorCount, depth, heightMM, logicalDpiX, logicalDpiY, numColors, paintingActive, physicalDpiX, physicalDpiY, widthMM

Inherited from sip.simplewrapper: __new__

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

Class Variables

[hide private]

AA_NAME = []

AA_MAP = {}

AA_NAME_KNOWN = ['GLH', 'HIP', 'ILE', 'GLN', 'TPO', 'LYS', 'SR...

FRAG_LIB_NAME = 'diverse_fragments'

ATOM_MARKER = 'i_fep_subst'

RES_MARKER = 'i_fep_residue'

LIG_MARKER = 'i_fep_ligand'

PRO_MARKER = 'i_fep_protein'

Inherited from PyQt4.QtGui.QWidget: DrawChildren, DrawWindowBackground, IgnoreMask

Inherited from PyQt4.QtCore.QObject: staticMetaObject

Inherited from PyQt4.QtGui.QPaintDevice: PdmDepth, PdmDpiX, PdmDpiY, PdmHeight, PdmHeightMM, PdmNumColors, PdmPhysicalDpiX, PdmPhysicalDpiY, PdmWidth, PdmWidthMM

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, master, win, mode=`'desmond'`)
(Constructor)

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

Overrides: object.__init__: (inherited documentation)

generateCombintations(self, sites)

Generates all combintations for all sites. Returns a list of (mut-list, mut-name) tuples.

_peel_off_ligand(self, this_ct)

Returned object is a two-element list: The first element is a CT containing only non-ligand molecules, the second element is a CT containing only the ligand molecule. If 'this_ct' contains only the ligand molecule, the first element of the returned list will be None. If 'this_ct' does not contain the ligand molecule, the second element of the returned list will be None.

Class Variable Details

[hide private]

AA_NAME_KNOWN

Value:

['GLH',
 'HIP',
 'ILE',
 'GLN',
 'TPO',
 'LYS',
 'SRO',
 'THR',
...

Class _ProMut

__init__(self, master, win, mode='desmond') (Constructor)

generateCombintations(self, sites)

_peel_off_ligand(self, this_ct)

AA_NAME_KNOWN

init(self, master, win, mode=`'desmond'`)
(Constructor)