schrodinger.application.desmond.fep_scholar

Class ScholarStructureItem

This class adds new function to the base structure_item class that allows to show some atoms and bonds with highlighting.

Instance Methods

[hide private]

generatePictureHighlight(self, atoms, bonds, color, gen_coord)
Generates a QPicture of the structure.

Inherited from ui.qt.structure2d.structure_item: __init__, add_annotator, add_annotator_function_return, boundingRect, clear, clear_annotators, generate_picture, getBondAtLocation, mousePressEvent, paint, set_colormap, set_rect, set_structure, set_text

Inherited from PyQt5.QtWidgets.QGraphicsItem: acceptDrops, acceptHoverEvents, acceptTouchEvents, acceptedMouseButtons, advance, boundingRegion, boundingRegionGranularity, cacheMode, childItems, childrenBoundingRect, clearFocus, clipPath, collidesWithItem, collidesWithPath, collidingItems, commonAncestorItem, contains, contextMenuEvent, cursor, data, deviceTransform, dragEnterEvent, dragLeaveEvent, dragMoveEvent, dropEvent, effectiveOpacity, ensureVisible, filtersChildEvents, flags, focusInEvent, focusItem, focusOutEvent, focusProxy, grabKeyboard, grabMouse, graphicsEffect, group, hasCursor, hasFocus, hide, hoverEnterEvent, hoverLeaveEvent, hoverMoveEvent, inputMethodEvent, inputMethodHints, inputMethodQuery, installSceneEventFilter, isActive, isAncestorOf, isBlockedByModalPanel, isClipped, isEnabled, isObscured, isObscuredBy, isPanel, isSelected, isUnderMouse, isVisible, isVisibleTo, isWidget, isWindow, itemChange, itemTransform, keyPressEvent, keyReleaseEvent, mapFromItem, mapFromParent, mapFromScene, mapRectFromItem, mapRectFromParent, mapRectFromScene, mapRectToItem, mapRectToParent, mapRectToScene, mapToItem, mapToParent, mapToScene, mouseDoubleClickEvent, mouseMoveEvent, mouseReleaseEvent, moveBy, opacity, opaqueArea, panel, panelModality, parentItem, parentObject, parentWidget, pos, prepareGeometryChange, removeSceneEventFilter, resetTransform, rotation, scale, scene, sceneBoundingRect, sceneEvent, sceneEventFilter, scenePos, sceneTransform, scroll, setAcceptDrops, setAcceptHoverEvents, setAcceptTouchEvents, setAcceptedMouseButtons, setActive, setBoundingRegionGranularity, setCacheMode, setCursor, setData, setEnabled, setFiltersChildEvents, setFlag, setFlags, setFocus, setFocusProxy, setGraphicsEffect, setGroup, setInputMethodHints, setOpacity, setPanelModality, setParentItem, setPos, setRotation, setScale, setSelected, setToolTip, setTransform, setTransformOriginPoint, setTransformations, setVisible, setX, setY, setZValue, shape, show, stackBefore, toGraphicsObject, toolTip, topLevelItem, topLevelWidget, transform, transformOriginPoint, transformations, type, ungrabKeyboard, ungrabMouse, unsetCursor, update, updateMicroFocus, wheelEvent, window, x, y, zValue

Inherited from sip.simplewrapper: __new__

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

Class Variables

[hide private]

Inherited from PyQt5.QtWidgets.QGraphicsItem: DeviceCoordinateCache, ItemAcceptsInputMethod, ItemChildAddedChange, ItemChildRemovedChange, ItemClipsChildrenToShape, ItemClipsToShape, ItemContainsChildrenInShape, ItemCoordinateCache, ItemCursorChange, ItemCursorHasChanged, ItemDoesntPropagateOpacityToChildren, ItemEnabledChange, ItemEnabledHasChanged, ItemFlagsChange, ItemFlagsHaveChanged, ItemHasNoContents, ItemIgnoresParentOpacity, ItemIgnoresTransformations, ItemIsFocusable, ItemIsMovable, ItemIsPanel, ItemIsSelectable, ItemMatrixChange, ItemNegativeZStacksBehindParent, ItemOpacityChange, ItemOpacityHasChanged, ItemParentChange, ItemParentHasChanged, ItemPositionChange, ItemPositionHasChanged, ItemRotationChange, ItemRotationHasChanged, ItemScaleChange, ItemScaleHasChanged, ItemSceneChange, ItemSceneHasChanged, ItemScenePositionHasChanged, ItemSelectedChange, ItemSelectedHasChanged, ItemSendsGeometryChanges, ItemSendsScenePositionChanges, ItemStacksBehindParent, ItemToolTipChange, ItemToolTipHasChanged, ItemTransformChange, ItemTransformHasChanged, ItemTransformOriginPointChange, ItemTransformOriginPointHasChanged, ItemUsesExtendedStyleOption, ItemVisibleChange, ItemVisibleHasChanged, ItemZValueChange, ItemZValueHasChanged, NoCache, NonModal, PanelModal, SceneModal, Type, UserType

generatePictureHighlight(self, atoms, bonds, color, gen_coord)

Generates a QPicture of the structure. This should be called after setting the structure and the accompaning annotators.

Parameters:

atoms (list) - list atom indices that should be highlighted.
bonds (list) - list of bond indices that should be highlighted
color (QtGui.QColor) - highlighting color
gen_coord (bool) - argument indicating whether molecule coordinates should be generated.