└── DockingPie1 ├── lib └── docking_program_main │ ├── config │ ├── version.txt │ ├── RxDock │ │ ├── pharma.const │ │ ├── Cavity │ │ └── standard_prm_file │ ├── info_sdsorter.txt │ ├── info_spyrmsd.txt │ ├── info_adfr.txt │ ├── info_smina.txt │ ├── info_openbabel.txt │ ├── consensus_info.txt │ ├── info_vina.txt │ └── info_rxdock.txt │ ├── docking_program_gui │ ├── aqua │ │ ├── __init__.py │ │ ├── images │ │ │ ├── spinup.png │ │ │ ├── vline.png │ │ │ ├── dropdown.png │ │ │ ├── sizegrip.png │ │ │ ├── spindown.png │ │ │ ├── up_arrow.png │ │ │ ├── branch-end.png │ │ │ ├── branch-more.png │ │ │ ├── branch-open.png │ │ │ ├── down_arrow.png │ │ │ ├── dropdown_on.png │ │ │ ├── left_arrow.png │ │ │ ├── right_arrow.png │ │ │ ├── branch-closed.png │ │ │ ├── checkbox_checked.png │ │ │ ├── sizegrip_hover.png │ │ │ ├── spindown_pressed.png │ │ │ ├── spinup_disabled.png │ │ │ ├── spinup_pressed.png │ │ │ ├── up_arrow_pressed.png │ │ │ ├── branch-open_hover.png │ │ │ ├── down_arrow_pressed.png │ │ │ ├── dropdown_disabled.png │ │ │ ├── left_arrow_pressed.png │ │ │ ├── scrollbar_up_arrow.png │ │ │ ├── spindown_disabled.png │ │ │ ├── branch-closed_hover.png │ │ │ ├── left_arrow_disabled.png │ │ │ ├── radiobutton_checked.png │ │ │ ├── right_arrow_disabled.png │ │ │ ├── right_arrow_pressed.png │ │ │ ├── scrollbar_down_arrow.png │ │ │ ├── scrollbar_left_arrow.png │ │ │ ├── scrollbar_right_arrow.png │ │ │ ├── checkbox_indeterminate.png │ │ │ ├── checkbox_checked_disabled.png │ │ │ ├── scrollbar_up_arrow_pressed.png │ │ │ ├── radiobutton_checked_disabled.png │ │ │ ├── scrollbar_down_arrow_pressed.png │ │ │ ├── scrollbar_left_arrow_pressed.png │ │ │ ├── scrollbar_up_arrow_disabled.png │ │ │ ├── checkbox_indeterminate_disabled.png │ │ │ ├── scrollbar_down_arrow_disabled.png │ │ │ ├── scrollbar_left_arrow_disabled.png │ │ │ ├── scrollbar_right_arrow_disabled.png │ │ │ └── scrollbar_right_arrow_pressed.png │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-37.pyc │ │ │ └── qsshelper.cpython-37.pyc │ │ └── qsshelper.py │ └── __pycache__ │ │ ├── tabs.cpython-37.pyc │ │ ├── tabs.cpython-38.pyc │ │ ├── dialogs.cpython-37.pyc │ │ ├── dialogs.cpython-38.pyc │ │ ├── frames.cpython-37.pyc │ │ ├── frames.cpython-38.pyc │ │ ├── new_window.cpython-37.pyc │ │ ├── main_window.cpython-37.pyc │ │ ├── main_window.cpython-38.pyc │ │ ├── new_windows.cpython-37.pyc │ │ └── new_windows.cpython-38.pyc │ ├── plots │ ├── pyqtgraph │ │ ├── util │ │ │ ├── __init__.py │ │ │ ├── colorama │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── win32.cpython-37.pyc │ │ │ │ │ ├── win32.cpython-38.pyc │ │ │ │ │ ├── winterm.cpython-37.pyc │ │ │ │ │ ├── winterm.cpython-38.pyc │ │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ │ └── __init__.cpython-38.pyc │ │ │ │ └── LICENSE.txt │ │ │ ├── __pycache__ │ │ │ │ ├── cprint.cpython-37.pyc │ │ │ │ ├── cprint.cpython-38.pyc │ │ │ │ ├── mutex.cpython-37.pyc │ │ │ │ ├── mutex.cpython-38.pyc │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── lru_cache.cpython-37.pyc │ │ │ │ └── lru_cache.cpython-38.pyc │ │ │ ├── get_resolution.py │ │ │ ├── tests │ │ │ │ └── test_lru_cache.py │ │ │ └── garbage_collector.py │ │ ├── widgets │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── ComboBox.cpython-37.pyc │ │ │ │ ├── ComboBox.cpython-38.pyc │ │ │ │ ├── GroupBox.cpython-37.pyc │ │ │ │ ├── GroupBox.cpython-38.pyc │ │ │ │ ├── SpinBox.cpython-37.pyc │ │ │ │ ├── SpinBox.cpython-38.pyc │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── BusyCursor.cpython-37.pyc │ │ │ │ ├── BusyCursor.cpython-38.pyc │ │ │ │ ├── CheckTable.cpython-37.pyc │ │ │ │ ├── CheckTable.cpython-38.pyc │ │ │ │ ├── ColorButton.cpython-37.pyc │ │ │ │ ├── ColorButton.cpython-38.pyc │ │ │ │ ├── FileDialog.cpython-37.pyc │ │ │ │ ├── FileDialog.cpython-38.pyc │ │ │ │ ├── PathButton.cpython-37.pyc │ │ │ │ ├── PathButton.cpython-38.pyc │ │ │ │ ├── PlotWidget.cpython-37.pyc │ │ │ │ ├── PlotWidget.cpython-38.pyc │ │ │ │ ├── TableWidget.cpython-37.pyc │ │ │ │ ├── TableWidget.cpython-38.pyc │ │ │ │ ├── TreeWidget.cpython-37.pyc │ │ │ │ ├── TreeWidget.cpython-38.pyc │ │ │ │ ├── ValueLabel.cpython-37.pyc │ │ │ │ ├── ValueLabel.cpython-38.pyc │ │ │ │ ├── GraphicsView.cpython-37.pyc │ │ │ │ ├── GraphicsView.cpython-38.pyc │ │ │ │ ├── LayoutWidget.cpython-37.pyc │ │ │ │ ├── LayoutWidget.cpython-38.pyc │ │ │ │ ├── VerticalLabel.cpython-37.pyc │ │ │ │ ├── VerticalLabel.cpython-38.pyc │ │ │ │ ├── ColorMapWidget.cpython-37.pyc │ │ │ │ ├── ColorMapWidget.cpython-38.pyc │ │ │ │ ├── DataFilterWidget.cpython-37.pyc │ │ │ │ ├── DataFilterWidget.cpython-38.pyc │ │ │ │ ├── DataTreeWidget.cpython-37.pyc │ │ │ │ ├── DataTreeWidget.cpython-38.pyc │ │ │ │ ├── DiffTreeWidget.cpython-37.pyc │ │ │ │ ├── DiffTreeWidget.cpython-38.pyc │ │ │ │ ├── FeedbackButton.cpython-37.pyc │ │ │ │ ├── FeedbackButton.cpython-38.pyc │ │ │ │ ├── GradientWidget.cpython-37.pyc │ │ │ │ ├── GradientWidget.cpython-38.pyc │ │ │ │ ├── JoystickButton.cpython-37.pyc │ │ │ │ ├── JoystickButton.cpython-38.pyc │ │ │ │ ├── MultiPlotWidget.cpython-37.pyc │ │ │ │ ├── MultiPlotWidget.cpython-38.pyc │ │ │ │ ├── ProgressDialog.cpython-37.pyc │ │ │ │ ├── ProgressDialog.cpython-38.pyc │ │ │ │ ├── HistogramLUTWidget.cpython-37.pyc │ │ │ │ ├── HistogramLUTWidget.cpython-38.pyc │ │ │ │ ├── RemoteGraphicsView.cpython-37.pyc │ │ │ │ ├── RemoteGraphicsView.cpython-38.pyc │ │ │ │ ├── ScatterPlotWidget.cpython-37.pyc │ │ │ │ ├── ScatterPlotWidget.cpython-38.pyc │ │ │ │ ├── GraphicsLayoutWidget.cpython-37.pyc │ │ │ │ └── GraphicsLayoutWidget.cpython-38.pyc │ │ │ ├── FileDialog.py │ │ │ ├── HistogramLUTWidget.py │ │ │ ├── tests │ │ │ │ ├── test_histogramlutwidget.py │ │ │ │ ├── test_combobox.py │ │ │ │ └── test_spinbox.py │ │ │ ├── BusyCursor.py │ │ │ ├── MatplotlibWidget.py │ │ │ └── PathButton.py │ │ ├── opengl │ │ │ ├── items │ │ │ │ ├── __init__.py │ │ │ │ ├── GLBarGraphItem.py │ │ │ │ └── GLAxisItem.py │ │ │ ├── glInfo.py │ │ │ └── __init__.py │ │ ├── exporters │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_image.py │ │ │ │ └── test_csv.py │ │ │ ├── __pycache__ │ │ │ │ ├── Exporter.cpython-37.pyc │ │ │ │ ├── Exporter.cpython-38.pyc │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── CSVExporter.cpython-37.pyc │ │ │ │ ├── CSVExporter.cpython-38.pyc │ │ │ │ ├── Matplotlib.cpython-37.pyc │ │ │ │ ├── Matplotlib.cpython-38.pyc │ │ │ │ ├── SVGExporter.cpython-37.pyc │ │ │ │ ├── SVGExporter.cpython-38.pyc │ │ │ │ ├── HDF5Exporter.cpython-37.pyc │ │ │ │ ├── HDF5Exporter.cpython-38.pyc │ │ │ │ ├── ImageExporter.cpython-37.pyc │ │ │ │ ├── ImageExporter.cpython-38.pyc │ │ │ │ ├── PrintExporter.cpython-37.pyc │ │ │ │ └── PrintExporter.cpython-38.pyc │ │ │ └── __init__.py │ │ ├── metaarray │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── MetaArray.cpython-37.pyc │ │ │ │ ├── MetaArray.cpython-38.pyc │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ └── __init__.cpython-38.pyc │ │ │ ├── license.txt │ │ │ └── readMeta.m │ │ ├── console │ │ │ ├── __init__.py │ │ │ └── CmdInput.py │ │ ├── GraphicsScene │ │ │ ├── __init__.py │ │ │ └── __pycache__ │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── mouseEvents.cpython-37.pyc │ │ │ │ ├── mouseEvents.cpython-38.pyc │ │ │ │ ├── GraphicsScene.cpython-37.pyc │ │ │ │ └── GraphicsScene.cpython-38.pyc │ │ ├── graphicsItems │ │ │ ├── PlotItem │ │ │ │ ├── __init__.py │ │ │ │ └── __pycache__ │ │ │ │ │ ├── PlotItem.cpython-37.pyc │ │ │ │ │ ├── PlotItem.cpython-38.pyc │ │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ │ ├── plotConfigTemplate_pyqt5.cpython-37.pyc │ │ │ │ │ └── plotConfigTemplate_pyqt5.cpython-38.pyc │ │ │ ├── ViewBox │ │ │ │ ├── __init__.py │ │ │ │ └── __pycache__ │ │ │ │ │ ├── ViewBox.cpython-37.pyc │ │ │ │ │ ├── ViewBox.cpython-38.pyc │ │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ │ ├── ViewBoxMenu.cpython-37.pyc │ │ │ │ │ ├── ViewBoxMenu.cpython-38.pyc │ │ │ │ │ ├── axisCtrlTemplate_pyqt5.cpython-37.pyc │ │ │ │ │ └── axisCtrlTemplate_pyqt5.cpython-38.pyc │ │ │ ├── __pycache__ │ │ │ │ ├── ROI.cpython-37.pyc │ │ │ │ ├── ROI.cpython-38.pyc │ │ │ │ ├── ArrowItem.cpython-37.pyc │ │ │ │ ├── ArrowItem.cpython-38.pyc │ │ │ │ ├── AxisItem.cpython-37.pyc │ │ │ │ ├── AxisItem.cpython-38.pyc │ │ │ │ ├── ButtonItem.cpython-37.pyc │ │ │ │ ├── ButtonItem.cpython-38.pyc │ │ │ │ ├── CurvePoint.cpython-37.pyc │ │ │ │ ├── CurvePoint.cpython-38.pyc │ │ │ │ ├── GraphItem.cpython-37.pyc │ │ │ │ ├── GraphItem.cpython-38.pyc │ │ │ │ ├── GridItem.cpython-37.pyc │ │ │ │ ├── GridItem.cpython-38.pyc │ │ │ │ ├── ImageItem.cpython-37.pyc │ │ │ │ ├── ImageItem.cpython-38.pyc │ │ │ │ ├── ItemGroup.cpython-37.pyc │ │ │ │ ├── ItemGroup.cpython-38.pyc │ │ │ │ ├── LabelItem.cpython-37.pyc │ │ │ │ ├── LabelItem.cpython-38.pyc │ │ │ │ ├── LegendItem.cpython-37.pyc │ │ │ │ ├── LegendItem.cpython-38.pyc │ │ │ │ ├── ScaleBar.cpython-37.pyc │ │ │ │ ├── ScaleBar.cpython-38.pyc │ │ │ │ ├── TextItem.cpython-37.pyc │ │ │ │ ├── TextItem.cpython-38.pyc │ │ │ │ ├── VTickGroup.cpython-37.pyc │ │ │ │ ├── VTickGroup.cpython-38.pyc │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── BarGraphItem.cpython-37.pyc │ │ │ │ ├── BarGraphItem.cpython-38.pyc │ │ │ │ ├── DateAxisItem.cpython-37.pyc │ │ │ │ ├── DateAxisItem.cpython-38.pyc │ │ │ │ ├── ErrorBarItem.cpython-37.pyc │ │ │ │ ├── ErrorBarItem.cpython-38.pyc │ │ │ │ ├── GraphicsItem.cpython-37.pyc │ │ │ │ ├── GraphicsItem.cpython-38.pyc │ │ │ │ ├── InfiniteLine.cpython-37.pyc │ │ │ │ ├── InfiniteLine.cpython-38.pyc │ │ │ │ ├── IsocurveItem.cpython-37.pyc │ │ │ │ ├── IsocurveItem.cpython-38.pyc │ │ │ │ ├── PlotDataItem.cpython-37.pyc │ │ │ │ ├── PlotDataItem.cpython-38.pyc │ │ │ │ ├── FillBetweenItem.cpython-37.pyc │ │ │ │ ├── FillBetweenItem.cpython-38.pyc │ │ │ │ ├── GradientLegend.cpython-37.pyc │ │ │ │ ├── GradientLegend.cpython-38.pyc │ │ │ │ ├── GraphicsLayout.cpython-37.pyc │ │ │ │ ├── GraphicsLayout.cpython-38.pyc │ │ │ │ ├── GraphicsObject.cpython-37.pyc │ │ │ │ ├── GraphicsObject.cpython-38.pyc │ │ │ │ ├── GraphicsWidget.cpython-37.pyc │ │ │ │ ├── GraphicsWidget.cpython-38.pyc │ │ │ │ ├── MultiPlotItem.cpython-37.pyc │ │ │ │ ├── MultiPlotItem.cpython-38.pyc │ │ │ │ ├── PlotCurveItem.cpython-37.pyc │ │ │ │ ├── PlotCurveItem.cpython-38.pyc │ │ │ │ ├── ScatterPlotItem.cpython-37.pyc │ │ │ │ ├── ScatterPlotItem.cpython-38.pyc │ │ │ │ ├── UIGraphicsItem.cpython-37.pyc │ │ │ │ ├── UIGraphicsItem.cpython-38.pyc │ │ │ │ ├── HistogramLUTItem.cpython-37.pyc │ │ │ │ ├── HistogramLUTItem.cpython-38.pyc │ │ │ │ ├── LinearRegionItem.cpython-37.pyc │ │ │ │ ├── LinearRegionItem.cpython-38.pyc │ │ │ │ ├── GradientEditorItem.cpython-37.pyc │ │ │ │ ├── GradientEditorItem.cpython-38.pyc │ │ │ │ ├── GraphicsWidgetAnchor.cpython-37.pyc │ │ │ │ └── GraphicsWidgetAnchor.cpython-38.pyc │ │ │ ├── tests │ │ │ │ ├── test_TextItem.py │ │ │ │ ├── test_GraphicsItem.py │ │ │ │ ├── test_ErrorBarItem.py │ │ │ │ └── test_PlotCurveItem.py │ │ │ ├── ItemGroup.py │ │ │ ├── __init__.py │ │ │ ├── ButtonItem.py │ │ │ └── GraphicsObject.py │ │ ├── dockarea │ │ │ ├── __init__.py │ │ │ └── tests │ │ │ │ └── test_dock.py │ │ ├── canvas │ │ │ ├── __init__.py │ │ │ └── TransformGuiTemplate.ui │ │ ├── pixmaps │ │ │ ├── auto.png │ │ │ ├── ctrl.png │ │ │ ├── lock.png │ │ │ ├── default.png │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── pixmapData_3.cpython-37.pyc │ │ │ │ └── pixmapData_3.cpython-38.pyc │ │ │ ├── compile.py │ │ │ └── __init__.py │ │ ├── flowchart │ │ │ ├── __init__.py │ │ │ ├── library │ │ │ │ └── __init__.py │ │ │ └── FlowchartGraphicsView.py │ │ ├── __pycache__ │ │ │ ├── Qt.cpython-37.pyc │ │ │ ├── Qt.cpython-38.pyc │ │ │ ├── Point.cpython-37.pyc │ │ │ ├── Point.cpython-38.pyc │ │ │ ├── Vector.cpython-37.pyc │ │ │ ├── Vector.cpython-38.pyc │ │ │ ├── debug.cpython-37.pyc │ │ │ ├── debug.cpython-38.pyc │ │ │ ├── ptime.cpython-37.pyc │ │ │ ├── ptime.cpython-38.pyc │ │ │ ├── reload.cpython-37.pyc │ │ │ ├── reload.cpython-38.pyc │ │ │ ├── __init__.cpython-37.pyc │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── colormap.cpython-37.pyc │ │ │ ├── colormap.cpython-38.pyc │ │ │ ├── functions.cpython-37.pyc │ │ │ ├── functions.cpython-38.pyc │ │ │ ├── python2_3.cpython-37.pyc │ │ │ ├── python2_3.cpython-38.pyc │ │ │ ├── SignalProxy.cpython-37.pyc │ │ │ ├── SignalProxy.cpython-38.pyc │ │ │ ├── Transform3D.cpython-37.pyc │ │ │ ├── Transform3D.cpython-38.pyc │ │ │ ├── WidgetGroup.cpython-37.pyc │ │ │ ├── WidgetGroup.cpython-38.pyc │ │ │ ├── SRTTransform.cpython-37.pyc │ │ │ ├── SRTTransform.cpython-38.pyc │ │ │ ├── SRTTransform3D.cpython-37.pyc │ │ │ ├── SRTTransform3D.cpython-38.pyc │ │ │ ├── pgcollections.cpython-37.pyc │ │ │ ├── pgcollections.cpython-38.pyc │ │ │ ├── ThreadsafeTimer.cpython-37.pyc │ │ │ ├── ThreadsafeTimer.cpython-38.pyc │ │ │ ├── graphicsWindows.cpython-37.pyc │ │ │ └── graphicsWindows.cpython-38.pyc │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_qt.py │ │ │ ├── test_configparser.py │ │ │ ├── uictest.ui │ │ │ └── test_srttransform3d.py │ │ ├── imageview │ │ │ ├── __pycache__ │ │ │ │ ├── ImageView.cpython-37.pyc │ │ │ │ ├── ImageView.cpython-38.pyc │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── ImageViewTemplate_pyqt5.cpython-37.pyc │ │ │ │ └── ImageViewTemplate_pyqt5.cpython-38.pyc │ │ │ ├── __init__.py │ │ │ └── tests │ │ │ │ └── test_imageview.py │ │ ├── multiprocess │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── processes.cpython-37.pyc │ │ │ │ ├── processes.cpython-38.pyc │ │ │ │ ├── remoteproxy.cpython-37.pyc │ │ │ │ ├── remoteproxy.cpython-38.pyc │ │ │ │ ├── parallelizer.cpython-37.pyc │ │ │ │ └── parallelizer.cpython-38.pyc │ │ │ ├── __init__.py │ │ │ └── bootstrap.py │ │ ├── parametertree │ │ │ ├── __pycache__ │ │ │ │ ├── Parameter.cpython-37.pyc │ │ │ │ ├── Parameter.cpython-38.pyc │ │ │ │ ├── __init__.cpython-37.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── SystemSolver.cpython-37.pyc │ │ │ │ ├── SystemSolver.cpython-38.pyc │ │ │ │ ├── ParameterItem.cpython-37.pyc │ │ │ │ ├── ParameterItem.cpython-38.pyc │ │ │ │ ├── ParameterSystem.cpython-37.pyc │ │ │ │ ├── ParameterSystem.cpython-38.pyc │ │ │ │ ├── ParameterTree.cpython-37.pyc │ │ │ │ ├── ParameterTree.cpython-38.pyc │ │ │ │ ├── parameterTypes.cpython-37.pyc │ │ │ │ └── parameterTypes.cpython-38.pyc │ │ │ └── __init__.py │ │ ├── python2_3.py │ │ ├── LICENSE.txt │ │ ├── ptime.py │ │ ├── units.py │ │ ├── ThreadsafeTimer.py │ │ ├── PlotData.py │ │ ├── frozenSupport.py │ │ └── Transform3D.py │ └── __pycache__ │ │ ├── plots_window.cpython-37.pyc │ │ └── plots_window.cpython-38.pyc │ ├── __pycache__ │ ├── files.cpython-37.pyc │ ├── __init__.cpython-37.pyc │ ├── __init__.cpython-38.pyc │ ├── pymod_vars.cpython-37.pyc │ └── pymol_interactions.cpython-37.pyc │ ├── tables │ └── __pycache__ │ │ ├── tables.cpython-37.pyc │ │ └── tables.cpython-38.pyc │ ├── Functions │ ├── __pycache__ │ │ ├── threads.cpython-37.pyc │ │ ├── threads.cpython-38.pyc │ │ ├── exceptions.cpython-37.pyc │ │ ├── exceptions.cpython-38.pyc │ │ ├── installer.cpython-37.pyc │ │ ├── installer.cpython-38.pyc │ │ ├── adfr_functions.cpython-37.pyc │ │ ├── adfr_functions.cpython-38.pyc │ │ ├── dockings_thread.cpython-37.pyc │ │ ├── dockings_thread.cpython-38.pyc │ │ ├── handle_widgets.cpython-37.pyc │ │ ├── handle_widgets.cpython-38.pyc │ │ ├── smina_functions.cpython-37.pyc │ │ ├── smina_functions.cpython-38.pyc │ │ ├── vina_functions.cpython-37.pyc │ │ ├── vina_functions.cpython-38.pyc │ │ ├── general_functions.cpython-37.pyc │ │ ├── general_functions.cpython-38.pyc │ │ ├── rxdock_functions.cpython-37.pyc │ │ ├── rxdock_functions.cpython-38.pyc │ │ ├── consensus_protocol.cpython-37.pyc │ │ ├── consensus_protocol.cpython-38.pyc │ │ ├── general_docking_func.cpython-37.pyc │ │ ├── general_docking_func.cpython-38.pyc │ │ ├── pymol_interactions.cpython-37.pyc │ │ └── pymol_interactions.cpython-38.pyc │ └── exceptions.py │ └── __init__.py └── __pycache__ ├── __init__.cpython-37.pyc └── __init__.cpython-38.pyc /DockingPie1/lib/docking_program_main/config/version.txt: -------------------------------------------------------------------------------- 1 | Files_v1.2.1 2 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/docking_program_gui/aqua/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/util/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/widgets/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/opengl/items/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/util/colorama/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/exporters/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/RxDock/pharma.const: -------------------------------------------------------------------------------- 1 | 187.474 169.935 19.454 0.0 Any 2 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/metaarray/__init__.py: -------------------------------------------------------------------------------- 1 | from .MetaArray import * 2 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/console/__init__.py: -------------------------------------------------------------------------------- 1 | from .Console import ConsoleWidget -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/GraphicsScene/__init__.py: -------------------------------------------------------------------------------- 1 | from .GraphicsScene import * 2 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/graphicsItems/PlotItem/__init__.py: -------------------------------------------------------------------------------- 1 | from .PlotItem import PlotItem 2 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/graphicsItems/ViewBox/__init__.py: -------------------------------------------------------------------------------- 1 | from .ViewBox import ViewBox 2 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/dockarea/__init__.py: -------------------------------------------------------------------------------- 1 | from .DockArea import DockArea 2 | from .Dock import Dock -------------------------------------------------------------------------------- /DockingPie1/__pycache__/__init__.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paiardin/DockingPie/HEAD/DockingPie1/__pycache__/__init__.cpython-37.pyc -------------------------------------------------------------------------------- /DockingPie1/__pycache__/__init__.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paiardin/DockingPie/HEAD/DockingPie1/__pycache__/__init__.cpython-38.pyc -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/canvas/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from .Canvas import * 3 | from .CanvasItem import * 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ParameterTree 3 | from .ParameterItem import ParameterItem 4 | from .ParameterSystem import ParameterSystem, SystemSolver 5 | from . import parameterTypes as types -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/exporters/__init__.py: -------------------------------------------------------------------------------- 1 | from .Exporter import Exporter 2 | from .ImageExporter import * 3 | from .SVGExporter import * 4 | from .Matplotlib import * 5 | from .CSVExporter import * 6 | from .PrintExporter import * 7 | from .HDF5Exporter import * 8 | 9 | def listExporters(): 10 | return Exporter.Exporters[:] 11 | 12 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/imageview/tests/test_imageview.py: -------------------------------------------------------------------------------- 1 | import pyqtgraph as pg 2 | import numpy as np 3 | 4 | app = pg.mkQApp() 5 | 6 | def test_nan_image(): 7 | img = np.ones((10,10)) 8 | img[0,0] = np.nan 9 | v = pg.image(img) 10 | v.imageItem.getHistogram() 11 | app.processEvents() 12 | v.window().close() 13 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/info_sdsorter.txt: -------------------------------------------------------------------------------- 1 | sdsorter 2 | 3 | sdsorter is a tool for manipulating molecular data within an sdf file 4 | based on the contents of the sd tags. 5 | 6 | [1] https://sourceforge.net/projects/sdsorter/ 7 | 8 | 9 | sdsorter in DockingPie 10 | 11 | The binaries for macOS are directly provided in DockingPie source code. 12 | By clicking the "Install" button, sdsorter will be made executable. 13 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/info_spyrmsd.txt: -------------------------------------------------------------------------------- 1 | sPyRMSD [1] 2 | 3 | sPyRMSD is a is a Python tool for symmetry-corrected RMSD calculations. 4 | 5 | [1] Meli, R., Biggin, P.C. spyrmsd: symmetry-corrected RMSD calculations in Python. J Cheminform 12, 49 (2020). https://doi.org/10.1186/s13321-020-00455-2 6 | 7 | 8 | sPyRMSD in DockingPie 9 | By clicking the "Install" button, sPyRMSD conda-forge release will be installed in the PyMOL Conda Environment. 10 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/exporters/tests/test_image.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | import pyqtgraph as pg 3 | from pyqtgraph.exporters import ImageExporter 4 | 5 | app = pg.mkQApp() 6 | 7 | 8 | def test_ImageExporter_filename_dialog(): 9 | """Tests ImageExporter code path that opens a file dialog. Regression test 10 | for pull request 1133.""" 11 | p = pg.plot() 12 | exp = ImageExporter(p.getPlotItem()) 13 | exp.export() 14 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/graphicsItems/tests/test_TextItem.py: -------------------------------------------------------------------------------- 1 | import pytest 2 | import pyqtgraph as pg 3 | 4 | app = pg.mkQApp() 5 | 6 | 7 | def test_TextItem_setAngle(): 8 | plt = pg.plot() 9 | plt.setXRange(-10, 10) 10 | plt.setYRange(-20, 20) 11 | item = pg.TextItem(text="test") 12 | plt.addItem(item) 13 | 14 | t1 = item.transform() 15 | 16 | item.setAngle(30) 17 | app.processEvents() 18 | 19 | t2 = item.transform() 20 | 21 | assert t1 != t2 22 | assert not t1.isRotating() 23 | assert t2.isRotating() 24 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/widgets/FileDialog.py: -------------------------------------------------------------------------------- 1 | from ..Qt import QtGui, QtCore 2 | import sys 3 | 4 | __all__ = ['FileDialog'] 5 | 6 | class FileDialog(QtGui.QFileDialog): 7 | ## Compatibility fix for OSX: 8 | ## For some reason the native dialog doesn't show up when you set AcceptMode to AcceptSave on OS X, so we don't use the native dialog 9 | 10 | def __init__(self, *args): 11 | QtGui.QFileDialog.__init__(self, *args) 12 | 13 | if sys.platform == 'darwin': 14 | self.setOption(QtGui.QFileDialog.DontUseNativeDialog) -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/util/get_resolution.py: -------------------------------------------------------------------------------- 1 | from .. import mkQApp 2 | 3 | def test_screenInformation(): 4 | qApp = mkQApp() 5 | desktop = qApp.desktop() 6 | resolution = desktop.screenGeometry() 7 | availableResolution = desktop.availableGeometry() 8 | print("Screen resolution: {}x{}".format(resolution.width(), resolution.height())) 9 | print("Available geometry: {}x{}".format(availableResolution.width(), availableResolution.height())) 10 | print("Number of Screens: {}".format(desktop.screenCount())) 11 | return None 12 | 13 | 14 | if __name__ == "__main__": 15 | test_screenInformation() -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/info_adfr.txt: -------------------------------------------------------------------------------- 1 | ADFR [1,2] 2 | 3 | "AutoDockFR (or ADFR in short) is a protein-ligand docking program developed in the Sanner laboratory at Scripps Research under the AutoDock umbrella." 4 | 5 | [1] https://ccsb.scripps.edu/adfr/ 6 | [2] Ravindranath PA, Forli S, Goodsell DS, Olson AJ, Sanner MF. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility. PLoS Comput Biol. 2015;11(12):e1004586. Published 2015 Dec 2. doi:10.1371/journal.pcbi.1004586 7 | 8 | 9 | ADFR in DockingPie 10 | By clicking the "Install" button, ADFR will be installed in Config directory with an Academic Installation 11 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/info_smina.txt: -------------------------------------------------------------------------------- 1 | Smina [1] 2 | 3 | A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. 4 | 5 | [1] Koes, David Ryan et al. “Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise.” 6 | Journal of chemical information and modeling vol. 53,8 (2013): 1893-904. doi:10.1021/ci300604z 7 | 8 | 9 | Smina in DockingPie 10 | 11 | The binaries for macOS and Linux are directly provided in DockingPie source code. 12 | By clicking the "Install" button, Smina will be made executable. 13 | 14 | Smina is not available for Windows 15 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/info_openbabel.txt: -------------------------------------------------------------------------------- 1 | Openbabel 2 | 3 | Open Babel is a chemical toolbox designed to speak the many languages of chemical data. 4 | It's an open, collaborative project allowing anyone to search, convert, analyze, 5 | or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas [1]. 6 | 7 | [1] O'Boyle, N.M., Banck, M., James, C.A. et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011). https://doi.org/10.1186/1758-2946-3-33 8 | 9 | 10 | Openbabel in DockingPie 11 | By clicking the "Install" button, Openbabel conda-forge release will be installed in the PyMOL Conda Environment. 12 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/opengl/glInfo.py: -------------------------------------------------------------------------------- 1 | from ..Qt import QtCore, QtGui, QtOpenGL 2 | from OpenGL.GL import * 3 | app = QtGui.QApplication([]) 4 | 5 | class GLTest(QtOpenGL.QGLWidget): 6 | def __init__(self): 7 | QtOpenGL.QGLWidget.__init__(self) 8 | self.makeCurrent() 9 | print("GL version:" + glGetString(GL_VERSION).decode("utf-8")) 10 | print("MAX_TEXTURE_SIZE: %d" % glGetIntegerv(GL_MAX_TEXTURE_SIZE)) 11 | print("MAX_3D_TEXTURE_SIZE: %d" % glGetIntegerv(GL_MAX_3D_TEXTURE_SIZE)) 12 | print("Extensions: " + glGetString(GL_EXTENSIONS).decode("utf-8").replace(" ", "\n")) 13 | 14 | GLTest() 15 | 16 | 17 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/python2_3.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | """ 3 | Helper functions that smooth out the differences between python 2 and 3. 4 | """ 5 | import sys 6 | 7 | def asUnicode(x): 8 | if sys.version_info[0] == 2: 9 | if isinstance(x, unicode): 10 | return x 11 | elif isinstance(x, str): 12 | return x.decode('UTF-8') 13 | else: 14 | return unicode(x) 15 | else: 16 | return str(x) 17 | 18 | 19 | if sys.version_info[0] == 3: 20 | basestring = str 21 | xrange = range 22 | else: 23 | import __builtin__ 24 | basestring = __builtin__.basestring 25 | xrange = __builtin__.xrange 26 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/graphicsItems/ItemGroup.py: -------------------------------------------------------------------------------- 1 | from ..Qt import QtGui, QtCore 2 | from .GraphicsObject import GraphicsObject 3 | 4 | __all__ = ['ItemGroup'] 5 | class ItemGroup(GraphicsObject): 6 | """ 7 | Replacement for QGraphicsItemGroup 8 | """ 9 | 10 | def __init__(self, *args): 11 | GraphicsObject.__init__(self, *args) 12 | if hasattr(self, "ItemHasNoContents"): 13 | self.setFlag(self.ItemHasNoContents) 14 | 15 | def boundingRect(self): 16 | return QtCore.QRectF() 17 | 18 | def paint(self, *args): 19 | pass 20 | 21 | def addItem(self, item): 22 | item.setParentItem(self) 23 | 24 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/consensus_info.txt: -------------------------------------------------------------------------------- 1 | WHAT IS A CONSENSUS SCORING ANALYSIS? 2 | 3 | A rescoring method 4 | 5 | 6 | WHICH ARE THE PURPOSES OF THIS METHOD? 7 | 8 | To combine the results of different scoring functions. 9 | Such combination of Scoring Function is aimed to have a much more accurate ranking of the predicted bio-active molecules. 10 | 11 | 12 | WHICH ARE THE STEPS TO PERFORM SUCH ANALYSIS? 13 | 14 | - Run Dockings on the same system with different Docking programs 15 | - Compare the poses of a Docking Run with the poses of the other Docking Run 16 | - Compute the RMSD for each comparison 17 | - Define a threshold of RMSD under which the two compared poses are defined as being 'in consensus' 18 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/graphicsItems/__init__.py: -------------------------------------------------------------------------------- 1 | ### just import everything from sub-modules 2 | 3 | #import os 4 | 5 | #d = os.path.split(__file__)[0] 6 | #files = [] 7 | #for f in os.listdir(d): 8 | #if os.path.isdir(os.path.join(d, f)): 9 | #files.append(f) 10 | #elif f[-3:] == '.py' and f != '__init__.py': 11 | #files.append(f[:-3]) 12 | 13 | #for modName in files: 14 | #mod = __import__(modName, globals(), locals(), fromlist=['*']) 15 | #if hasattr(mod, '__all__'): 16 | #names = mod.__all__ 17 | #else: 18 | #names = [n for n in dir(mod) if n[0] != '_'] 19 | #for k in names: 20 | ##print modName, k 21 | #globals()[k] = getattr(mod, k) 22 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/info_vina.txt: -------------------------------------------------------------------------------- 1 | AutoDock Vina [1,2] 2 | 3 | "AutoDock Vina is an open-source program for doing molecular docking. 4 | It was originally designed and implemented by Dr. Oleg Trott 5 | in the Molecular Graphics Lab (now CCSB) at The Scripps Research Institute [1]" 6 | 7 | [1] https://vina.scripps.edu/ 8 | [2] O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461 9 | 10 | 11 | AutoDock Vina in DockingPie 12 | 13 | The binaries for macOS, Linux and Windows are directly provided in DockingPie source code. 14 | By clicking the "Install" button, Vina will be made executable. 15 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/pixmaps/compile.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | import numpy as np 3 | from PyQt4 import QtGui 4 | import os, pickle, sys 5 | 6 | path = os.path.abspath(os.path.split(__file__)[0]) 7 | pixmaps = {} 8 | for f in os.listdir(path): 9 | if not f.endswith('.png'): 10 | continue 11 | print(f) 12 | img = QtGui.QImage(os.path.join(path, f)) 13 | ptr = img.bits() 14 | ptr.setsize(img.byteCount()) 15 | arr = np.asarray(ptr).reshape(img.height(), img.width(), 4).transpose(1,0,2) 16 | pixmaps[f] = pickle.dumps(arr) 17 | ver = sys.version_info[0] 18 | with open(os.path.join(path, 'pixmapData_%d.py' % (ver, )), 'w') as fh: 19 | fh.write("import numpy as np; pixmapData=%s" % (repr(pixmaps), )) 20 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/RxDock/Cavity: -------------------------------------------------------------------------------- 1 | RBT_PARAMETER_FILE_V1.00 2 | TITLE gart_DUD 3 | 4 | RECEPTOR_FILE inputreceptor.mol2 5 | RECEPTOR_FLEX 3.0 6 | RECEPTOR_SEGMENT_NAME 7 | 8 | ################################################################## 9 | ### CAVITY DEFINITION: REFERENCE LIGAND METHOD 10 | ################################################################## 11 | 12 | SECTION MAPPER 13 | SITE_MAPPER algorithm 14 | REF_MOL referenceligand.sdf 15 | RADIUS 2.0 16 | SMALL_SPHERE 1.0 17 | MIN_VOLUME 100 18 | MAX_CAVITIES 1 19 | VOL_INCR 0.0 20 | GRIDSTEP 0.5 21 | END_SECTION 22 | 23 | ################################# 24 | #CAVITY RESTRAINT PENALTY 25 | ################################# 26 | SECTION CAVITY 27 | SCORING_FUNCTION RbtCavityGridSF 28 | WEIGHT 1.0 29 | END_SECTION 30 | 31 | 32 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/dockarea/tests/test_dock.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | #import sip 3 | #sip.setapi('QString', 1) 4 | 5 | import pyqtgraph as pg 6 | pg.mkQApp() 7 | 8 | import pyqtgraph.dockarea as da 9 | 10 | def test_dock(): 11 | name = pg.asUnicode("évènts_zàhéér") 12 | dock = da.Dock(name=name) 13 | # make sure unicode names work correctly 14 | assert dock.name() == name 15 | # no surprises in return type. 16 | assert type(dock.name()) == type(name) 17 | 18 | def test_closable_dock(): 19 | name = "Test close dock" 20 | dock = da.Dock(name=name, closable=True) 21 | 22 | assert dock.label.closeButton != None 23 | 24 | def test_hide_title_dock(): 25 | name = "Test hide title dock" 26 | dock = da.Dock(name=name, hideTitle=True) 27 | 28 | assert dock.labelHidden == True 29 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/info_rxdock.txt: -------------------------------------------------------------------------------- 1 | RxDock [1,2] 2 | 3 | "RxDock is a fast and versatile open-source docking program that can be used to dock small molecules against proteins and nucleic acids [1]. 4 | RxDock started in 2019 as a fork of rDock [2]" 5 | 6 | [1] https://www.rxdock.org/ 7 | [2] Ruiz-Carmona, S., Alvarez-Garcia, D., Foloppe, N., Garmendia-Doval, A. B., Juhos S., et al. (2014) rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids. PLoS Comput Biol 10(4): e1003571. doi:10.1371/journal.pcbi.1003571 8 | 9 | 10 | RxDock in DockingPie 11 | By clicking the "Install" button, RxDock bioconda release will be installed in the PyMOL Conda Environment. 12 | 13 | RxDock is not available for Windows 14 | 15 | Acknowledgments: the authors are grateful to Vedran Miletić for assistance with RxDock. 16 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/tests/test_qt.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | import pyqtgraph as pg 3 | import gc, os 4 | import pytest 5 | 6 | 7 | app = pg.mkQApp() 8 | 9 | def test_isQObjectAlive(): 10 | o1 = pg.QtCore.QObject() 11 | o2 = pg.QtCore.QObject() 12 | o2.setParent(o1) 13 | del o1 14 | assert not pg.Qt.isQObjectAlive(o2) 15 | 16 | @pytest.mark.skipif(pg.Qt.QT_LIB == 'PySide', reason='pysideuic does not appear to be ' 17 | 'packaged with conda') 18 | @pytest.mark.skipif(pg.Qt.QT_LIB == "PySide2" and "pg.Qt.QtVersion.startswith('5.14')", reason="new PySide2 doesn't have loadUi functionality") 19 | def test_loadUiType(): 20 | path = os.path.dirname(__file__) 21 | formClass, baseClass = pg.Qt.loadUiType(os.path.join(path, 'uictest.ui')) 22 | w = baseClass() 23 | ui = formClass() 24 | ui.setupUi(w) 25 | w.show() 26 | app.processEvents() 27 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/pixmaps/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Allows easy loading of pixmaps used in UI elements. 3 | Provides support for frozen environments as well. 4 | """ 5 | 6 | import os, sys, pickle 7 | from ..functions import makeQImage 8 | from ..Qt import QtGui 9 | from ..python2_3 import basestring 10 | if sys.version_info[0] == 2: 11 | from . import pixmapData_2 as pixmapData 12 | else: 13 | from . import pixmapData_3 as pixmapData 14 | 15 | 16 | def getPixmap(name): 17 | """ 18 | Return a QPixmap corresponding to the image file with the given name. 19 | (eg. getPixmap('auto') loads pyqtgraph/pixmaps/auto.png) 20 | """ 21 | key = name+'.png' 22 | data = pixmapData.pixmapData[key] 23 | if isinstance(data, basestring) or isinstance(data, bytes): 24 | pixmapData.pixmapData[key] = pickle.loads(data) 25 | arr = pixmapData.pixmapData[key] 26 | return QtGui.QPixmap(makeQImage(arr, alpha=True)) 27 | 28 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/flowchart/library/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from ...pgcollections import OrderedDict 3 | import os, types 4 | from ...debug import printExc 5 | from ..NodeLibrary import NodeLibrary, isNodeClass 6 | from ... import reload as reload 7 | 8 | 9 | # Build default library 10 | LIBRARY = NodeLibrary() 11 | 12 | # For backward compatibility, expose the default library's properties here: 13 | NODE_LIST = LIBRARY.nodeList 14 | NODE_TREE = LIBRARY.nodeTree 15 | registerNodeType = LIBRARY.addNodeType 16 | getNodeTree = LIBRARY.getNodeTree 17 | getNodeType = LIBRARY.getNodeType 18 | 19 | # Add all nodes to the default library 20 | from . import Data, Display, Filters, Operators 21 | for mod in [Data, Display, Filters, Operators]: 22 | nodes = [getattr(mod, name) for name in dir(mod) if isNodeClass(getattr(mod, name))] 23 | for node in nodes: 24 | LIBRARY.addNodeType(node, [(mod.__name__.split('.')[-1],)]) 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/graphicsItems/tests/test_GraphicsItem.py: -------------------------------------------------------------------------------- 1 | import gc 2 | import weakref 3 | try: 4 | import faulthandler 5 | faulthandler.enable() 6 | except ImportError: 7 | pass 8 | 9 | import pyqtgraph as pg 10 | pg.mkQApp() 11 | 12 | def test_getViewWidget(): 13 | view = pg.PlotWidget() 14 | vref = weakref.ref(view) 15 | item = pg.InfiniteLine() 16 | view.addItem(item) 17 | assert item.getViewWidget() is view 18 | del view 19 | gc.collect() 20 | assert vref() is None 21 | assert item.getViewWidget() is None 22 | 23 | def test_getViewWidget_deleted(): 24 | view = pg.PlotWidget() 25 | item = pg.InfiniteLine() 26 | view.addItem(item) 27 | assert item.getViewWidget() is view 28 | 29 | # Arrange to have Qt automatically delete the view widget 30 | obj = pg.QtGui.QWidget() 31 | view.setParent(obj) 32 | del obj 33 | gc.collect() 34 | 35 | assert not pg.Qt.isQObjectAlive(view) 36 | assert item.getViewWidget() is None 37 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/tests/test_configparser.py: -------------------------------------------------------------------------------- 1 | from pyqtgraph import configfile 2 | import numpy as np 3 | import tempfile, os 4 | 5 | def test_longArrays(): 6 | """ 7 | Test config saving and loading of long arrays. 8 | """ 9 | tmp = tempfile.mktemp(".cfg") 10 | 11 | arr = np.arange(20) 12 | configfile.writeConfigFile({'arr':arr}, tmp) 13 | config = configfile.readConfigFile(tmp) 14 | 15 | assert all(config['arr'] == arr) 16 | 17 | os.remove(tmp) 18 | 19 | def test_multipleParameters(): 20 | """ 21 | Test config saving and loading of multiple parameters. 22 | """ 23 | tmp = tempfile.mktemp(".cfg") 24 | 25 | par1 = [1,2,3] 26 | par2 = "Test" 27 | par3 = {'a':3,'b':'c'} 28 | 29 | configfile.writeConfigFile({'par1':par1, 'par2':par2, 'par3':par3}, tmp) 30 | config = configfile.readConfigFile(tmp) 31 | 32 | assert config['par1'] == par1 33 | assert config['par2'] == par2 34 | assert config['par3'] == par3 35 | 36 | os.remove(tmp) 37 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/multiprocess/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Multiprocessing utility library 3 | (parallelization done the way I like it) 4 | 5 | Luke Campagnola 6 | 2012.06.10 7 | 8 | This library provides: 9 | 10 | - simple mechanism for starting a new python interpreter process that can be controlled from the original process 11 | (this allows, for example, displaying and manipulating plots in a remote process 12 | while the parent process is free to do other work) 13 | - proxy system that allows objects hosted in the remote process to be used as if they were local 14 | - Qt signal connection between processes 15 | - very simple in-line parallelization (fork only; does not work on windows) for number-crunching 16 | 17 | TODO: 18 | allow remote processes to serve as rendering engines that pass pixmaps back to the parent process for display 19 | (RemoteGraphicsView class) 20 | """ 21 | 22 | from .processes import * 23 | from .parallelizer import Parallelize, CanceledError 24 | from .remoteproxy import proxy, ClosedError, NoResultError 25 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/docking_program_gui/aqua/qsshelper.py: -------------------------------------------------------------------------------- 1 | import os 2 | import re 3 | 4 | 5 | class QSSHelper: 6 | def __init__(self): 7 | pass 8 | 9 | @staticmethod 10 | def open_qss(path): 11 | """ 12 | opens a Qt stylesheet with a path relative to the project 13 | 14 | Note: it changes the urls in the Qt stylesheet (in memory), and makes these urls relative to the project 15 | Warning: the urls in the Qt stylesheet should have the forward slash ('/') as the pathname separator 16 | """ 17 | with open(path) as f: 18 | qss = f.read() 19 | pattern = r'url\((.*?)\);' 20 | for url in sorted(set(re.findall(pattern, qss)), key=len, reverse=True): 21 | directory, basename = os.path.split(path) 22 | new_url = os.path.join(directory, *url.split('/')) 23 | new_url = os.path.normpath(new_url) 24 | new_url = new_url.replace(os.path.sep, '/') 25 | qss = qss.replace(url, new_url) 26 | return qss 27 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/widgets/HistogramLUTWidget.py: -------------------------------------------------------------------------------- 1 | """ 2 | Widget displaying an image histogram along with gradient editor. Can be used to adjust the appearance of images. 3 | This is a wrapper around HistogramLUTItem 4 | """ 5 | 6 | from ..Qt import QtGui, QtCore 7 | from .GraphicsView import GraphicsView 8 | from ..graphicsItems.HistogramLUTItem import HistogramLUTItem 9 | 10 | __all__ = ['HistogramLUTWidget'] 11 | 12 | 13 | class HistogramLUTWidget(GraphicsView): 14 | 15 | def __init__(self, parent=None, *args, **kargs): 16 | background = kargs.pop('background', 'default') 17 | GraphicsView.__init__(self, parent, useOpenGL=False, background=background) 18 | self.item = HistogramLUTItem(*args, **kargs) 19 | self.setCentralItem(self.item) 20 | self.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Expanding) 21 | self.setMinimumWidth(95) 22 | 23 | 24 | def sizeHint(self): 25 | return QtCore.QSize(115, 200) 26 | 27 | 28 | 29 | def __getattr__(self, attr): 30 | return getattr(self.item, attr) 31 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/widgets/tests/test_histogramlutwidget.py: -------------------------------------------------------------------------------- 1 | """ 2 | HistogramLUTWidget test: 3 | 4 | Tests the creation of a HistogramLUTWidget. 5 | """ 6 | 7 | import pyqtgraph as pg 8 | from pyqtgraph.Qt import QtGui 9 | import numpy as np 10 | 11 | def testHistogramLUTWidget(): 12 | pg.mkQApp() 13 | 14 | win = QtGui.QMainWindow() 15 | win.show() 16 | 17 | cw = QtGui.QWidget() 18 | win.setCentralWidget(cw) 19 | 20 | l = QtGui.QGridLayout() 21 | cw.setLayout(l) 22 | l.setSpacing(0) 23 | 24 | v = pg.GraphicsView() 25 | vb = pg.ViewBox() 26 | vb.setAspectLocked() 27 | v.setCentralItem(vb) 28 | l.addWidget(v, 0, 0, 3, 1) 29 | 30 | w = pg.HistogramLUTWidget(background='w') 31 | l.addWidget(w, 0, 1) 32 | 33 | data = pg.gaussianFilter(np.random.normal(size=(256, 256, 3)), (20, 20, 0)) 34 | for i in range(32): 35 | for j in range(32): 36 | data[i*8, j*8] += .1 37 | img = pg.ImageItem(data) 38 | vb.addItem(img) 39 | vb.autoRange() 40 | 41 | w.setImageItem(img) 42 | 43 | QtGui.QApplication.processEvents() 44 | 45 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/graphicsItems/tests/test_ErrorBarItem.py: -------------------------------------------------------------------------------- 1 | import pyqtgraph as pg 2 | import numpy as np 3 | 4 | app = pg.mkQApp() 5 | 6 | 7 | def test_ErrorBarItem_defer_data(): 8 | plot = pg.PlotWidget() 9 | plot.show() 10 | 11 | # plot some data away from the origin to set the view rect 12 | x = np.arange(5) + 10 13 | curve = pg.PlotCurveItem(x=x, y=x) 14 | plot.addItem(curve) 15 | app.processEvents() 16 | r_no_ebi = plot.viewRect() 17 | 18 | # ErrorBarItem with no data shouldn't affect the view rect 19 | err = pg.ErrorBarItem() 20 | plot.addItem(err) 21 | app.processEvents() 22 | r_empty_ebi = plot.viewRect() 23 | 24 | assert r_no_ebi == r_empty_ebi 25 | 26 | err.setData(x=x, y=x, bottom=x, top=x) 27 | app.processEvents() 28 | r_ebi = plot.viewRect() 29 | 30 | assert r_empty_ebi != r_ebi 31 | 32 | # unset data, ErrorBarItem disappears and view rect goes back to original 33 | err.setData(x=None, y=None) 34 | app.processEvents() 35 | r_clear_ebi = plot.viewRect() 36 | 37 | assert r_clear_ebi == r_no_ebi 38 | 39 | plot.close() 40 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/metaarray/license.txt: -------------------------------------------------------------------------------- 1 | Copyright (c) 2010 Luke Campagnola ('luke.campagnola@%s.com' % 'gmail') 2 | The MIT License 3 | Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: 4 | 5 | The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 6 | 7 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 8 | 9 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/opengl/items/GLBarGraphItem.py: -------------------------------------------------------------------------------- 1 | from .GLMeshItem import GLMeshItem 2 | from ..MeshData import MeshData 3 | import numpy as np 4 | 5 | class GLBarGraphItem(GLMeshItem): 6 | def __init__(self, pos, size): 7 | """ 8 | pos is (...,3) array of the bar positions (the corner of each bar) 9 | size is (...,3) array of the sizes of each bar 10 | """ 11 | nCubes = np.prod(pos.shape[:-1]) 12 | cubeVerts = np.mgrid[0:2,0:2,0:2].reshape(3,8).transpose().reshape(1,8,3) 13 | cubeFaces = np.array([ 14 | [0,1,2], [3,2,1], 15 | [4,5,6], [7,6,5], 16 | [0,1,4], [5,4,1], 17 | [2,3,6], [7,6,3], 18 | [0,2,4], [6,4,2], 19 | [1,3,5], [7,5,3]]).reshape(1,12,3) 20 | size = size.reshape((nCubes, 1, 3)) 21 | pos = pos.reshape((nCubes, 1, 3)) 22 | verts = cubeVerts * size + pos 23 | faces = cubeFaces + (np.arange(nCubes) * 8).reshape(nCubes,1,1) 24 | md = MeshData(verts.reshape(nCubes*8,3), faces.reshape(nCubes*12,3)) 25 | 26 | GLMeshItem.__init__(self, meshdata=md, shader='shaded', smooth=False) 27 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/config/RxDock/standard_prm_file: -------------------------------------------------------------------------------- 1 | RBT PARAMETER_FILE_V1.00 2 | TITLE HSP90-PU3-lig-cavity, solvent flex=5 3 | 4 | RECEPTOR_FILE inputreceptor.mol2 5 | RECEPTOR_SEGMENT_NAME PROT 6 | RECEPTOR_FLEX 3.0 7 | 8 | SECTION SOLVENT 9 | FILE inputreceptorwater.pdb 10 | TRANS_MODE TETHERED 11 | ROT_MODE TETHERED 12 | MAX_TRANS 1.0 13 | MAX_ROT 30.0 14 | OCCUPANCY 0.5 15 | END_SECTION 16 | 17 | SECTION_LIGAND 18 | TRANS_MODE FREE 19 | ROT_MODE FREE 20 | DIHEDRAL_MODE FREE 21 | MAX_TRANS 1.0 22 | MAX_ROT 30.0 23 | MAX_DIHEDRAL 30.0 24 | END_SECTION 25 | 26 | SECTION MAPPER 27 | SITE_MAPPER RbtLigandSiteMapper 28 | REF_MOL referenceligand.sd 29 | RADIUS 5.0 30 | SMALL_SPHERE 1.0 31 | MIN_VOLUME 100 32 | MAX_CAVITIES 1 33 | VOL_INCR 0.0 34 | GRIDSTEP 0.5 35 | END_SECTION 36 | 37 | SECTION CAVITY 38 | SCORING_FUNCTION RbtCavityGridSF 39 | WEIGHT 1.0 40 | END_SECTION 41 | 42 | SECTION PHARMA 43 | SCORING_FUNCTION RbtPharmaSF 44 | WEIGHT 1.0 45 | CONSTRAINTS_FILE mandatory.const 46 | OPTIONAL FILE optional.const 47 | NOPT 3 48 | WRITE_ERRORS TRUE 49 | END_SECTION 50 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/LICENSE.txt: -------------------------------------------------------------------------------- 1 | Copyright (c) 2012 University of North Carolina at Chapel Hill 2 | Luke Campagnola ('luke.campagnola@%s.com' % 'gmail') 3 | 4 | The MIT License 5 | Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: 6 | 7 | The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 8 | 9 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 10 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/ptime.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | """ 3 | ptime.py - Precision time function made os-independent (should have been taken care of by python) 4 | Copyright 2010 Luke Campagnola 5 | Distributed under MIT/X11 license. See license.txt for more information. 6 | """ 7 | 8 | 9 | import sys 10 | 11 | if sys.version_info[0] < 3: 12 | from time import clock 13 | from time import time as system_time 14 | else: 15 | from time import perf_counter as clock 16 | from time import time as system_time 17 | 18 | START_TIME = None 19 | time = None 20 | 21 | def winTime(): 22 | """Return the current time in seconds with high precision (windows version, use Manager.time() to stay platform independent).""" 23 | return clock() - START_TIME 24 | #return systime.time() 25 | 26 | def unixTime(): 27 | """Return the current time in seconds with high precision (unix version, use Manager.time() to stay platform independent).""" 28 | return system_time() 29 | 30 | if sys.platform.startswith('win'): 31 | cstart = clock() ### Required to start the clock in windows 32 | START_TIME = system_time() - cstart 33 | 34 | time = winTime 35 | else: 36 | time = unixTime 37 | 38 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/widgets/tests/test_combobox.py: -------------------------------------------------------------------------------- 1 | import pyqtgraph as pg 2 | pg.mkQApp() 3 | 4 | def test_combobox(): 5 | cb = pg.ComboBox() 6 | items = {'a': 1, 'b': 2, 'c': 3} 7 | cb.setItems(items) 8 | cb.setValue(2) 9 | assert str(cb.currentText()) == 'b' 10 | assert cb.value() == 2 11 | 12 | # Clear item list; value should be None 13 | cb.clear() 14 | assert cb.value() == None 15 | 16 | # Reset item list; value should be set automatically 17 | cb.setItems(items) 18 | assert cb.value() == 2 19 | 20 | # Clear item list; repopulate with same names and new values 21 | items = {'a': 4, 'b': 5, 'c': 6} 22 | cb.clear() 23 | cb.setItems(items) 24 | assert cb.value() == 5 25 | 26 | # Set list instead of dict 27 | cb.setItems(list(items.keys())) 28 | assert str(cb.currentText()) == 'b' 29 | 30 | cb.setValue('c') 31 | assert cb.value() == str(cb.currentText()) 32 | assert cb.value() == 'c' 33 | 34 | cb.setItemValue('c', 7) 35 | assert cb.value() == 7 36 | 37 | 38 | if __name__ == '__main__': 39 | cb = pg.ComboBox() 40 | cb.show() 41 | cb.setItems({'': None, 'a': 1, 'b': 2, 'c': 3}) 42 | def fn(ind): 43 | print("New value: %s" % cb.value()) 44 | cb.currentIndexChanged.connect(fn) -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/widgets/BusyCursor.py: -------------------------------------------------------------------------------- 1 | from ..Qt import QtGui, QtCore, QT_LIB 2 | 3 | __all__ = ['BusyCursor'] 4 | 5 | class BusyCursor(object): 6 | """Class for displaying a busy mouse cursor during long operations. 7 | Usage:: 8 | 9 | with pyqtgraph.BusyCursor(): 10 | doLongOperation() 11 | 12 | May be nested. If called from a non-gui thread, then the cursor will not be affected. 13 | """ 14 | active = [] 15 | 16 | def __enter__(self): 17 | app = QtCore.QCoreApplication.instance() 18 | isGuiThread = (app is not None) and (QtCore.QThread.currentThread() == app.thread()) 19 | if isGuiThread and QtGui.QApplication.instance() is not None: 20 | if QT_LIB == 'PySide': 21 | # pass CursorShape rather than QCursor for PySide 22 | # see https://bugreports.qt.io/browse/PYSIDE-243 23 | QtGui.QApplication.setOverrideCursor(QtCore.Qt.WaitCursor) 24 | else: 25 | QtGui.QApplication.setOverrideCursor(QtGui.QCursor(QtCore.Qt.WaitCursor)) 26 | BusyCursor.active.append(self) 27 | self._active = True 28 | else: 29 | self._active = False 30 | 31 | def __exit__(self, *args): 32 | if self._active: 33 | BusyCursor.active.pop(-1) 34 | QtGui.QApplication.restoreOverrideCursor() 35 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/tests/uictest.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | Form 4 | 5 | 6 | 7 | 0 8 | 0 9 | 400 10 | 300 11 | 12 | 13 | 14 | Form 15 | 16 | 17 | 18 | 19 | 10 20 | 10 21 | 120 22 | 80 23 | 24 | 25 | 26 | 27 | 28 | 29 | 10 30 | 110 31 | 120 32 | 80 33 | 34 | 35 | 36 | 37 | 38 | 39 | PlotWidget 40 | QWidget 41 |
pyqtgraph
42 | 1 43 | 44 | 45 | ImageView 46 | QWidget 47 |
pyqtgraph
48 | 1 49 | 50 | 51 | 52 | 53 | 54 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/console/CmdInput.py: -------------------------------------------------------------------------------- 1 | from ..Qt import QtCore, QtGui 2 | from ..python2_3 import asUnicode 3 | 4 | class CmdInput(QtGui.QLineEdit): 5 | 6 | sigExecuteCmd = QtCore.Signal(object) 7 | 8 | def __init__(self, parent): 9 | QtGui.QLineEdit.__init__(self, parent) 10 | self.history = [""] 11 | self.ptr = 0 12 | 13 | def keyPressEvent(self, ev): 14 | if ev.key() == QtCore.Qt.Key_Up: 15 | if self.ptr < len(self.history) - 1: 16 | self.setHistory(self.ptr+1) 17 | ev.accept() 18 | return 19 | elif ev.key() == QtCore.Qt.Key_Down: 20 | if self.ptr > 0: 21 | self.setHistory(self.ptr-1) 22 | ev.accept() 23 | return 24 | elif ev.key() == QtCore.Qt.Key_Return: 25 | self.execCmd() 26 | else: 27 | QtGui.QLineEdit.keyPressEvent(self, ev) 28 | self.history[0] = asUnicode(self.text()) 29 | 30 | def execCmd(self): 31 | cmd = asUnicode(self.text()) 32 | if len(self.history) == 1 or cmd != self.history[1]: 33 | self.history.insert(1, cmd) 34 | self.history[0] = "" 35 | self.setHistory(0) 36 | self.sigExecuteCmd.emit(cmd) 37 | 38 | def setHistory(self, num): 39 | self.ptr = num 40 | self.setText(self.history[self.ptr]) 41 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/util/tests/test_lru_cache.py: -------------------------------------------------------------------------------- 1 | from pyqtgraph.util.lru_cache import LRUCache 2 | 3 | def testLRU(): 4 | lru = LRUCache(2, 1) 5 | # check twice 6 | checkLru(lru) 7 | checkLru(lru) 8 | 9 | def checkLru(lru): 10 | lru[1] = 1 11 | lru[2] = 2 12 | lru[3] = 3 13 | 14 | assert len(lru) == 2 15 | assert set([2, 3]) == set(lru.keys()) 16 | assert set([2, 3]) == set(lru.values()) 17 | 18 | lru[2] = 2 19 | assert set([2, 3]) == set(lru.values()) 20 | 21 | lru[1] = 1 22 | set([2, 1]) == set(lru.values()) 23 | 24 | #Iterates from the used in the last access to others based on access time. 25 | assert [(2, 2), (1, 1)] == list(lru.items(accessTime=True)) 26 | lru[2] = 2 27 | assert [(1, 1), (2, 2)] == list(lru.items(accessTime=True)) 28 | 29 | del lru[2] 30 | assert [(1, 1), ] == list(lru.items(accessTime=True)) 31 | 32 | lru[2] = 2 33 | assert [(1, 1), (2, 2)] == list(lru.items(accessTime=True)) 34 | 35 | _a = lru[1] 36 | assert [(2, 2), (1, 1)] == list(lru.items(accessTime=True)) 37 | 38 | _a = lru[2] 39 | assert [(1, 1), (2, 2)] == list(lru.items(accessTime=True)) 40 | 41 | assert lru.get(2) == 2 42 | assert lru.get(3) == None 43 | assert [(1, 1), (2, 2)] == list(lru.items(accessTime=True)) 44 | 45 | lru.clear() 46 | assert [] == list(lru.items()) 47 | 48 | 49 | if __name__ == '__main__': 50 | testLRU() 51 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/graphicsItems/tests/test_PlotCurveItem.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import pyqtgraph as pg 3 | from pyqtgraph.tests import assertImageApproved 4 | 5 | 6 | def test_PlotCurveItem(): 7 | p = pg.GraphicsWindow() 8 | p.ci.layout.setContentsMargins(4, 4, 4, 4) # default margins vary by platform 9 | v = p.addViewBox() 10 | p.resize(200, 150) 11 | data = np.array([1,4,2,3,np.inf,5,7,6,-np.inf,8,10,9,np.nan,-1,-2,0]) 12 | c = pg.PlotCurveItem(data) 13 | v.addItem(c) 14 | v.autoRange() 15 | 16 | # Check auto-range works. Some platform differences may be expected.. 17 | checkRange = np.array([[-1.1457564053237301, 16.145756405323731], [-3.076811473165955, 11.076811473165955]]) 18 | assert np.allclose(v.viewRange(), checkRange) 19 | 20 | assertImageApproved(p, 'plotcurveitem/connectall', "Plot curve with all points connected.") 21 | 22 | c.setData(data, connect='pairs') 23 | assertImageApproved(p, 'plotcurveitem/connectpairs', "Plot curve with pairs connected.") 24 | 25 | c.setData(data, connect='finite') 26 | assertImageApproved(p, 'plotcurveitem/connectfinite', "Plot curve with finite points connected.") 27 | 28 | c.setData(data, connect=np.array([1,1,1,0,1,1,0,0,1,0,0,0,1,1,0,0])) 29 | assertImageApproved(p, 'plotcurveitem/connectarray', "Plot curve with connection array.") 30 | 31 | p.close() 32 | 33 | 34 | if __name__ == '__main__': 35 | test_PlotCurveItem() 36 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/tests/test_srttransform3d.py: -------------------------------------------------------------------------------- 1 | import pyqtgraph as pg 2 | from pyqtgraph.Qt import QtCore, QtGui 3 | import numpy as np 4 | from numpy.testing import assert_array_almost_equal, assert_almost_equal 5 | 6 | testPoints = np.array([ 7 | [0, 0, 0], 8 | [1, 0, 0], 9 | [0, 1, 0], 10 | [0, 0, 1], 11 | [-1, -1, 0], 12 | [0, -1, -1]]) 13 | 14 | 15 | def testMatrix(): 16 | """ 17 | SRTTransform3D => Transform3D => SRTTransform3D 18 | """ 19 | tr = pg.SRTTransform3D() 20 | tr.setRotate(45, (0, 0, 1)) 21 | tr.setScale(0.2, 0.4, 1) 22 | tr.setTranslate(10, 20, 40) 23 | assert tr.getRotation() == (45, QtGui.QVector3D(0, 0, 1)) 24 | assert tr.getScale() == QtGui.QVector3D(0.2, 0.4, 1) 25 | assert tr.getTranslation() == QtGui.QVector3D(10, 20, 40) 26 | 27 | tr2 = pg.Transform3D(tr) 28 | assert np.all(tr.matrix() == tr2.matrix()) 29 | 30 | # This is the most important test: 31 | # The transition from Transform3D to SRTTransform3D is a tricky one. 32 | tr3 = pg.SRTTransform3D(tr2) 33 | assert_array_almost_equal(tr.matrix(), tr3.matrix()) 34 | assert_almost_equal(tr3.getRotation()[0], tr.getRotation()[0]) 35 | assert_array_almost_equal(tr3.getRotation()[1], tr.getRotation()[1]) 36 | assert_array_almost_equal(tr3.getScale(), tr.getScale()) 37 | assert_array_almost_equal(tr3.getTranslation(), tr.getTranslation()) 38 | 39 | 40 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/flowchart/FlowchartGraphicsView.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from ..Qt import QtGui, QtCore 3 | from ..widgets.GraphicsView import GraphicsView 4 | from ..GraphicsScene import GraphicsScene 5 | from ..graphicsItems.ViewBox import ViewBox 6 | 7 | 8 | class FlowchartGraphicsView(GraphicsView): 9 | 10 | sigHoverOver = QtCore.Signal(object) 11 | sigClicked = QtCore.Signal(object) 12 | 13 | def __init__(self, widget, *args): 14 | GraphicsView.__init__(self, *args, useOpenGL=False) 15 | self._vb = FlowchartViewBox(widget, lockAspect=True, invertY=True) 16 | self.setCentralItem(self._vb) 17 | self.setRenderHint(QtGui.QPainter.Antialiasing, True) 18 | 19 | def viewBox(self): 20 | return self._vb 21 | 22 | 23 | class FlowchartViewBox(ViewBox): 24 | 25 | def __init__(self, widget, *args, **kwargs): 26 | ViewBox.__init__(self, *args, **kwargs) 27 | self.widget = widget 28 | 29 | def getMenu(self, ev): 30 | ## called by ViewBox to create a new context menu 31 | self._fc_menu = QtGui.QMenu() 32 | self._subMenus = self.getContextMenus(ev) 33 | for menu in self._subMenus: 34 | self._fc_menu.addMenu(menu) 35 | return self._fc_menu 36 | 37 | def getContextMenus(self, ev): 38 | ## called by scene to add menus on to someone else's context menu 39 | menu = self.widget.buildMenu(ev.scenePos()) 40 | menu.setTitle("Add node") 41 | return [menu, ViewBox.getMenu(self, ev)] 42 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/util/colorama/LICENSE.txt: -------------------------------------------------------------------------------- 1 | Copyright (c) 2010 Jonathan Hartley 2 | All rights reserved. 3 | 4 | Redistribution and use in source and binary forms, with or without 5 | modification, are permitted provided that the following conditions are met: 6 | 7 | * Redistributions of source code must retain the above copyright notice, this 8 | list of conditions and the following disclaimer. 9 | 10 | * Redistributions in binary form must reproduce the above copyright notice, 11 | this list of conditions and the following disclaimer in the documentation 12 | and/or other materials provided with the distribution. 13 | 14 | * Neither the name of the copyright holders, nor those of its contributors 15 | may be used to endorse or promote products derived from this software without 16 | specific prior written permission. 17 | 18 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 19 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 20 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 21 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 22 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 23 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 24 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 25 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 26 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 27 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 28 | 29 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/units.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | ## Very simple unit support: 3 | ## - creates variable names like 'mV' and 'kHz' 4 | ## - the value assigned to the variable corresponds to the scale prefix 5 | ## (mV = 0.001) 6 | ## - the actual units are purely cosmetic for making code clearer: 7 | ## 8 | ## x = 20*pA is identical to x = 20*1e-12 9 | 10 | ## No unicode variable names (μ,Ω) allowed until python 3 11 | 12 | SI_PREFIXES = 'yzafpnum kMGTPEZY' 13 | UNITS = 'm,s,g,W,J,V,A,F,T,Hz,Ohm,S,N,C,px,b,B'.split(',') 14 | allUnits = {} 15 | 16 | def addUnit(p, n): 17 | g = globals() 18 | v = 1000**n 19 | for u in UNITS: 20 | g[p+u] = v 21 | allUnits[p+u] = v 22 | 23 | for p in SI_PREFIXES: 24 | if p == ' ': 25 | p = '' 26 | n = 0 27 | elif p == 'u': 28 | n = -2 29 | else: 30 | n = SI_PREFIXES.index(p) - 8 31 | 32 | addUnit(p, n) 33 | 34 | cm = 0.01 35 | 36 | 37 | 38 | 39 | 40 | 41 | def evalUnits(unitStr): 42 | """ 43 | Evaluate a unit string into ([numerators,...], [denominators,...]) 44 | Examples: 45 | N m/s^2 => ([N, m], [s, s]) 46 | A*s / V => ([A, s], [V,]) 47 | """ 48 | pass 49 | 50 | def formatUnits(units): 51 | """ 52 | Format a unit specification ([numerators,...], [denominators,...]) 53 | into a string (this is the inverse of evalUnits) 54 | """ 55 | pass 56 | 57 | def simplify(units): 58 | """ 59 | Cancel units that appear in both numerator and denominator, then attempt to replace 60 | groups of units with single units where possible (ie, J/s => W) 61 | """ 62 | pass 63 | 64 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/opengl/__init__.py: -------------------------------------------------------------------------------- 1 | from .GLViewWidget import GLViewWidget 2 | 3 | ## dynamic imports cause too many problems. 4 | #from .. import importAll 5 | #importAll('items', globals(), locals()) 6 | 7 | from .items.GLGridItem import * 8 | from .items.GLBarGraphItem import * 9 | from .items.GLScatterPlotItem import * 10 | from .items.GLMeshItem import * 11 | from .items.GLLinePlotItem import * 12 | from .items.GLAxisItem import * 13 | from .items.GLImageItem import * 14 | from .items.GLSurfacePlotItem import * 15 | from .items.GLBoxItem import * 16 | from .items.GLVolumeItem import * 17 | 18 | from .MeshData import MeshData 19 | ## for backward compatibility: 20 | #MeshData.MeshData = MeshData ## breaks autodoc. 21 | 22 | from . import shaders 23 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/ThreadsafeTimer.py: -------------------------------------------------------------------------------- 1 | from .Qt import QtCore, QtGui 2 | 3 | class ThreadsafeTimer(QtCore.QObject): 4 | """ 5 | Thread-safe replacement for QTimer. 6 | """ 7 | 8 | timeout = QtCore.Signal() 9 | sigTimerStopRequested = QtCore.Signal() 10 | sigTimerStartRequested = QtCore.Signal(object) 11 | 12 | def __init__(self): 13 | QtCore.QObject.__init__(self) 14 | self.timer = QtCore.QTimer() 15 | self.timer.timeout.connect(self.timerFinished) 16 | self.timer.moveToThread(QtCore.QCoreApplication.instance().thread()) 17 | self.moveToThread(QtCore.QCoreApplication.instance().thread()) 18 | self.sigTimerStopRequested.connect(self.stop, QtCore.Qt.QueuedConnection) 19 | self.sigTimerStartRequested.connect(self.start, QtCore.Qt.QueuedConnection) 20 | 21 | 22 | def start(self, timeout): 23 | isGuiThread = QtCore.QThread.currentThread() == QtCore.QCoreApplication.instance().thread() 24 | if isGuiThread: 25 | #print "start timer", self, "from gui thread" 26 | self.timer.start(timeout) 27 | else: 28 | #print "start timer", self, "from remote thread" 29 | self.sigTimerStartRequested.emit(timeout) 30 | 31 | def stop(self): 32 | isGuiThread = QtCore.QThread.currentThread() == QtCore.QCoreApplication.instance().thread() 33 | if isGuiThread: 34 | #print "stop timer", self, "from gui thread" 35 | self.timer.stop() 36 | else: 37 | #print "stop timer", self, "from remote thread" 38 | self.sigTimerStopRequested.emit() 39 | 40 | def timerFinished(self): 41 | self.timeout.emit() -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/widgets/tests/test_spinbox.py: -------------------------------------------------------------------------------- 1 | import pyqtgraph as pg 2 | pg.mkQApp() 3 | 4 | 5 | def test_spinbox_formatting(): 6 | sb = pg.SpinBox() 7 | assert sb.opts['decimals'] == 6 8 | assert sb.opts['int'] is False 9 | 10 | # table of test conditions: 11 | # value, text, options 12 | conds = [ 13 | (0, '0', dict(suffix='', siPrefix=False, dec=False, int=False)), 14 | (100, '100', dict()), 15 | (1000000, '1e+06', dict()), 16 | (1000, '1e+03', dict(decimals=2)), 17 | (1000000, '1e+06', dict(int=True, decimals=6)), 18 | (12345678955, '12345678955', dict(int=True, decimals=100)), 19 | (1.45e-9, '1.45e-09 A', dict(int=False, decimals=6, suffix='A', siPrefix=False)), 20 | (1.45e-9, '1.45 nA', dict(int=False, decimals=6, suffix='A', siPrefix=True)), 21 | (1.45, '1.45 PSI', dict(int=False, decimals=6, suffix='PSI', siPrefix=True)), 22 | (1.45e-3, '1.45 mPSI', dict(int=False, decimals=6, suffix='PSI', siPrefix=True)), 23 | (-2500.3427, '$-2500.34', dict(int=False, format='${value:0.02f}')), 24 | ] 25 | 26 | for (value, text, opts) in conds: 27 | sb.setOpts(**opts) 28 | sb.setValue(value) 29 | assert sb.value() == value 30 | assert pg.asUnicode(sb.text()) == text 31 | 32 | # test setting value 33 | if not opts.get('int', False): 34 | suf = sb.opts['suffix'] 35 | sb.lineEdit().setText('0.1' + suf) 36 | sb.editingFinishedEvent() 37 | assert sb.value() == 0.1 38 | if suf != '': 39 | sb.lineEdit().setText('0.1 m' + suf) 40 | sb.editingFinishedEvent() 41 | assert sb.value() == 0.1e-3 42 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/widgets/MatplotlibWidget.py: -------------------------------------------------------------------------------- 1 | from ..Qt import QtGui, QtCore, QT_LIB 2 | import matplotlib 3 | 4 | if QT_LIB != 'PyQt5': 5 | if QT_LIB == 'PySide': 6 | matplotlib.rcParams['backend.qt4']='PySide' 7 | 8 | from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas 9 | try: 10 | from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar 11 | except ImportError: 12 | from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar 13 | else: 14 | from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas 15 | from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar 16 | 17 | from matplotlib.figure import Figure 18 | 19 | class MatplotlibWidget(QtGui.QWidget): 20 | """ 21 | Implements a Matplotlib figure inside a QWidget. 22 | Use getFigure() and redraw() to interact with matplotlib. 23 | 24 | Example:: 25 | 26 | mw = MatplotlibWidget() 27 | subplot = mw.getFigure().add_subplot(111) 28 | subplot.plot(x,y) 29 | mw.draw() 30 | """ 31 | 32 | def __init__(self, size=(5.0, 4.0), dpi=100): 33 | QtGui.QWidget.__init__(self) 34 | self.fig = Figure(size, dpi=dpi) 35 | self.canvas = FigureCanvas(self.fig) 36 | self.canvas.setParent(self) 37 | self.toolbar = NavigationToolbar(self.canvas, self) 38 | 39 | self.vbox = QtGui.QVBoxLayout() 40 | self.vbox.addWidget(self.toolbar) 41 | self.vbox.addWidget(self.canvas) 42 | 43 | self.setLayout(self.vbox) 44 | 45 | def getFigure(self): 46 | return self.fig 47 | 48 | def draw(self): 49 | self.canvas.draw() 50 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/PlotData.py: -------------------------------------------------------------------------------- 1 | 2 | 3 | class PlotData(object): 4 | """ 5 | Class used for managing plot data 6 | - allows data sharing between multiple graphics items (curve, scatter, graph..) 7 | - each item may define the columns it needs 8 | - column groupings ('pos' or x, y, z) 9 | - efficiently appendable 10 | - log, fft transformations 11 | - color mode conversion (float/byte/qcolor) 12 | - pen/brush conversion 13 | - per-field cached masking 14 | - allows multiple masking fields (different graphics need to mask on different criteria) 15 | - removal of nan/inf values 16 | - option for single value shared by entire column 17 | - cached downsampling 18 | - cached min / max / hasnan / isuniform 19 | """ 20 | def __init__(self): 21 | self.fields = {} 22 | 23 | self.maxVals = {} ## cache for max/min 24 | self.minVals = {} 25 | 26 | def addFields(self, **fields): 27 | for f in fields: 28 | if f not in self.fields: 29 | self.fields[f] = None 30 | 31 | def hasField(self, f): 32 | return f in self.fields 33 | 34 | def __getitem__(self, field): 35 | return self.fields[field] 36 | 37 | def __setitem__(self, field, val): 38 | self.fields[field] = val 39 | 40 | def max(self, field): 41 | mx = self.maxVals.get(field, None) 42 | if mx is None: 43 | mx = np.max(self[field]) 44 | self.maxVals[field] = mx 45 | return mx 46 | 47 | def min(self, field): 48 | mn = self.minVals.get(field, None) 49 | if mn is None: 50 | mn = np.min(self[field]) 51 | self.minVals[field] = mn 52 | return mn 53 | 54 | 55 | 56 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/util/garbage_collector.py: -------------------------------------------------------------------------------- 1 | import gc 2 | 3 | from ..Qt import QtCore 4 | 5 | class GarbageCollector(object): 6 | ''' 7 | Disable automatic garbage collection and instead collect manually 8 | on a timer. 9 | 10 | This is done to ensure that garbage collection only happens in the GUI 11 | thread, as otherwise Qt can crash. 12 | 13 | Credit: Erik Janssens 14 | Source: http://pydev.blogspot.com/2014/03/should-python-garbage-collector-be.html 15 | ''' 16 | 17 | def __init__(self, interval=1.0, debug=False): 18 | self.debug = debug 19 | if debug: 20 | gc.set_debug(gc.DEBUG_LEAK) 21 | 22 | self.timer = QtCore.QTimer() 23 | self.timer.timeout.connect(self.check) 24 | 25 | self.threshold = gc.get_threshold() 26 | gc.disable() 27 | self.timer.start(interval * 1000) 28 | 29 | def check(self): 30 | #return self.debug_cycles() # uncomment to just debug cycles 31 | l0, l1, l2 = gc.get_count() 32 | if self.debug: 33 | print('gc_check called:', l0, l1, l2) 34 | if l0 > self.threshold[0]: 35 | num = gc.collect(0) 36 | if self.debug: 37 | print('collecting gen 0, found: %d unreachable' % num) 38 | if l1 > self.threshold[1]: 39 | num = gc.collect(1) 40 | if self.debug: 41 | print('collecting gen 1, found: %d unreachable' % num) 42 | if l2 > self.threshold[2]: 43 | num = gc.collect(2) 44 | if self.debug: 45 | print('collecting gen 2, found: %d unreachable' % num) 46 | 47 | def debug_cycles(self): 48 | gc.collect() 49 | for obj in gc.garbage: 50 | print(obj, repr(obj), type(obj)) 51 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/widgets/PathButton.py: -------------------------------------------------------------------------------- 1 | from ..Qt import QtGui, QtCore 2 | from .. import functions as fn 3 | 4 | __all__ = ['PathButton'] 5 | 6 | 7 | class PathButton(QtGui.QPushButton): 8 | """Simple PushButton extension that paints a QPainterPath centered on its face. 9 | """ 10 | def __init__(self, parent=None, path=None, pen='default', brush=None, size=(30,30), margin=7): 11 | QtGui.QPushButton.__init__(self, parent) 12 | self.margin = margin 13 | self.path = None 14 | if pen == 'default': 15 | pen = 'k' 16 | self.setPen(pen) 17 | self.setBrush(brush) 18 | if path is not None: 19 | self.setPath(path) 20 | if size is not None: 21 | self.setFixedWidth(size[0]) 22 | self.setFixedHeight(size[1]) 23 | 24 | def setBrush(self, brush): 25 | self.brush = fn.mkBrush(brush) 26 | 27 | def setPen(self, *args, **kwargs): 28 | self.pen = fn.mkPen(*args, **kwargs) 29 | 30 | def setPath(self, path): 31 | self.path = path 32 | self.update() 33 | 34 | def paintEvent(self, ev): 35 | QtGui.QPushButton.paintEvent(self, ev) 36 | margin = self.margin 37 | geom = QtCore.QRectF(0, 0, self.width(), self.height()).adjusted(margin, margin, -margin, -margin) 38 | rect = self.path.boundingRect() 39 | scale = min(geom.width() / float(rect.width()), geom.height() / float(rect.height())) 40 | 41 | p = QtGui.QPainter(self) 42 | p.setRenderHint(p.Antialiasing) 43 | p.translate(geom.center()) 44 | p.scale(scale, scale) 45 | p.translate(-rect.center()) 46 | p.setPen(self.pen) 47 | p.setBrush(self.brush) 48 | p.drawPath(self.path) 49 | p.end() 50 | 51 | 52 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/graphicsItems/ButtonItem.py: -------------------------------------------------------------------------------- 1 | from ..Qt import QtGui, QtCore 2 | from .GraphicsObject import GraphicsObject 3 | 4 | __all__ = ['ButtonItem'] 5 | class ButtonItem(GraphicsObject): 6 | """Button graphicsItem displaying an image.""" 7 | 8 | clicked = QtCore.Signal(object) 9 | 10 | def __init__(self, imageFile=None, width=None, parentItem=None, pixmap=None): 11 | self.enabled = True 12 | GraphicsObject.__init__(self) 13 | if imageFile is not None: 14 | self.setImageFile(imageFile) 15 | elif pixmap is not None: 16 | self.setPixmap(pixmap) 17 | 18 | if width is not None: 19 | s = float(width) / self.pixmap.width() 20 | self.scale(s, s) 21 | if parentItem is not None: 22 | self.setParentItem(parentItem) 23 | self.setOpacity(0.7) 24 | 25 | def setImageFile(self, imageFile): 26 | self.setPixmap(QtGui.QPixmap(imageFile)) 27 | 28 | def setPixmap(self, pixmap): 29 | self.pixmap = pixmap 30 | self.update() 31 | 32 | def mouseClickEvent(self, ev): 33 | if self.enabled: 34 | self.clicked.emit(self) 35 | 36 | def mouseHoverEvent(self, ev): 37 | if not self.enabled: 38 | return 39 | if ev.isEnter(): 40 | self.setOpacity(1.0) 41 | else: 42 | self.setOpacity(0.7) 43 | 44 | def disable(self): 45 | self.enabled = False 46 | self.setOpacity(0.4) 47 | 48 | def enable(self): 49 | self.enabled = True 50 | self.setOpacity(0.7) 51 | 52 | def paint(self, p, *args): 53 | p.setRenderHint(p.Antialiasing) 54 | p.drawPixmap(0, 0, self.pixmap) 55 | 56 | def boundingRect(self): 57 | return QtCore.QRectF(self.pixmap.rect()) 58 | 59 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/graphicsItems/GraphicsObject.py: -------------------------------------------------------------------------------- 1 | from ..Qt import QtGui, QtCore, QT_LIB 2 | if QT_LIB in ['PyQt4', 'PyQt5']: 3 | import sip 4 | from .GraphicsItem import GraphicsItem 5 | 6 | __all__ = ['GraphicsObject'] 7 | class GraphicsObject(GraphicsItem, QtGui.QGraphicsObject): 8 | """ 9 | **Bases:** :class:`GraphicsItem `, :class:`QtGui.QGraphicsObject` 10 | 11 | Extension of QGraphicsObject with some useful methods (provided by :class:`GraphicsItem `) 12 | """ 13 | _qtBaseClass = QtGui.QGraphicsObject 14 | def __init__(self, *args): 15 | self.__inform_view_on_changes = True 16 | QtGui.QGraphicsObject.__init__(self, *args) 17 | self.setFlag(self.ItemSendsGeometryChanges) 18 | GraphicsItem.__init__(self) 19 | 20 | def itemChange(self, change, value): 21 | ret = QtGui.QGraphicsObject.itemChange(self, change, value) 22 | if change in [self.ItemParentHasChanged, self.ItemSceneHasChanged]: 23 | self.parentChanged() 24 | try: 25 | inform_view_on_change = self.__inform_view_on_changes 26 | except AttributeError: 27 | # It's possible that the attribute was already collected when the itemChange happened 28 | # (if it was triggered during the gc of the object). 29 | pass 30 | else: 31 | if inform_view_on_change and change in [self.ItemPositionHasChanged, self.ItemTransformHasChanged]: 32 | self.informViewBoundsChanged() 33 | 34 | ## workaround for pyqt bug: 35 | ## http://www.riverbankcomputing.com/pipermail/pyqt/2012-August/031818.html 36 | if QT_LIB in ['PyQt4', 'PyQt5'] and change == self.ItemParentChange and isinstance(ret, QtGui.QGraphicsItem): 37 | ret = sip.cast(ret, QtGui.QGraphicsItem) 38 | 39 | return ret 40 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/__init__.py: -------------------------------------------------------------------------------- 1 | # Copyright 2022 by Serena Rosignoli. All rights reserved. 2 | # This code is part of the DockingPie package and governed by its license. Please 3 | # see the LICENSE file. 4 | 5 | 6 | import os 7 | import sys 8 | import shutil 9 | import re 10 | import json 11 | import datetime 12 | 13 | # PyMOL. 14 | from pymol import cmd 15 | 16 | from pymol.Qt import QtWidgets, QtCore, QtGui 17 | 18 | import os 19 | import shutil 20 | import warnings 21 | import math 22 | 23 | from .docking_program_gui.main_window import DockingProgram_main_window_qt 24 | 25 | def docking_program_launcher(app, docking_program_plugin_name, docking_program_version, docking_program_revision): 26 | docking_program = DockingProgram(app, docking_program_plugin_name, docking_program_version, docking_program_revision) 27 | 28 | class DockingProgram(): 29 | 30 | def __init__(self, app, docking_program_plugin_name, docking_program_version, docking_program_revision): 31 | 32 | self.docking_program_plugin_name = docking_program_plugin_name 33 | self.docking_program_version = docking_program_version 34 | self.docking_program_revision = docking_program_revision 35 | 36 | # Set to 'True' when developing, useful for debugging. 37 | self.DEVELOP = False 38 | # Set to 'True' to perform some tests on sequences/structures from the GUI. 39 | self.TEST = False 40 | 41 | self.app = app 42 | 43 | # If set to 'True' the most time consuming protocols will be run in a thread so 44 | # that the GUI is not freezed. When developing the code, it is better to set it to 'False', 45 | # in order to better track exceptions. 46 | if self.DEVELOP: 47 | self.use_protocol_threads = False 48 | else: 49 | self.use_protocol_threads = True 50 | 51 | 52 | #### MAIN WINDOW OF THE PLUGIN #### 53 | 54 | self.main_window = DockingProgram_main_window_qt(self) 55 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/multiprocess/bootstrap.py: -------------------------------------------------------------------------------- 1 | """For starting up remote processes""" 2 | import sys, pickle, os 3 | 4 | if __name__ == '__main__': 5 | if hasattr(os, 'setpgrp'): 6 | os.setpgrp() ## prevents signals (notably keyboard interrupt) being forwarded from parent to this process 7 | if sys.version[0] == '3': 8 | #name, port, authkey, ppid, targetStr, path, pyside = pickle.load(sys.stdin.buffer) 9 | opts = pickle.load(sys.stdin.buffer) 10 | else: 11 | #name, port, authkey, ppid, targetStr, path, pyside = pickle.load(sys.stdin) 12 | opts = pickle.load(sys.stdin) 13 | #print "key:", ' '.join([str(ord(x)) for x in authkey]) 14 | path = opts.pop('path', None) 15 | if path is not None: 16 | if isinstance(path, str): 17 | # if string, just insert this into the path 18 | sys.path.insert(0, path) 19 | else: 20 | # if list, then replace the entire sys.path 21 | ## modify sys.path in place--no idea who already has a reference to the existing list. 22 | while len(sys.path) > 0: 23 | sys.path.pop() 24 | sys.path.extend(path) 25 | 26 | pyqtapis = opts.pop('pyqtapis', None) 27 | if pyqtapis is not None: 28 | import sip 29 | for k,v in pyqtapis.items(): 30 | sip.setapi(k, v) 31 | 32 | qt_lib = opts.pop('qt_lib', None) 33 | if qt_lib == 'PySide': 34 | import PySide 35 | elif qt_lib == 'PySide2': 36 | import PySide2 37 | elif qt_lib == 'PyQt5': 38 | import PyQt5 39 | 40 | targetStr = opts.pop('targetStr') 41 | try: 42 | target = pickle.loads(targetStr) ## unpickling the target should import everything we need 43 | except: 44 | print("Current sys.path:", sys.path) 45 | raise 46 | target(**opts) ## Send all other options to the target function 47 | sys.exit(0) 48 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/exporters/tests/test_csv.py: -------------------------------------------------------------------------------- 1 | """ 2 | CSV export test 3 | """ 4 | from __future__ import division, print_function, absolute_import 5 | import pyqtgraph as pg 6 | import csv 7 | import os 8 | import tempfile 9 | 10 | app = pg.mkQApp() 11 | 12 | 13 | def approxeq(a, b): 14 | return (a-b) <= ((a + b) * 1e-6) 15 | 16 | 17 | def test_CSVExporter(): 18 | tempfilename = tempfile.NamedTemporaryFile(suffix='.csv').name 19 | print("using %s as a temporary file" % tempfilename) 20 | 21 | plt = pg.plot() 22 | y1 = [1,3,2,3,1,6,9,8,4,2] 23 | plt.plot(y=y1, name='myPlot') 24 | 25 | y2 = [3,4,6,1,2,4,2,3,5,3,5,1,3] 26 | x2 = pg.np.linspace(0, 1.0, len(y2)) 27 | plt.plot(x=x2, y=y2) 28 | 29 | y3 = [1,5,2,3,4,6,1,2,4,2,3,5,3] 30 | x3 = pg.np.linspace(0, 1.0, len(y3)+1) 31 | plt.plot(x=x3, y=y3, stepMode=True) 32 | 33 | ex = pg.exporters.CSVExporter(plt.plotItem) 34 | ex.export(fileName=tempfilename) 35 | 36 | with open(tempfilename, 'r') as csv_file: 37 | r = csv.reader(csv_file) 38 | lines = [line for line in r] 39 | header = lines.pop(0) 40 | assert header == ['myPlot_x', 'myPlot_y', 'x0001', 'y0001', 'x0002', 'y0002'] 41 | 42 | i = 0 43 | for vals in lines: 44 | vals = list(map(str.strip, vals)) 45 | assert (i >= len(y1) and vals[0] == '') or approxeq(float(vals[0]), i) 46 | assert (i >= len(y1) and vals[1] == '') or approxeq(float(vals[1]), y1[i]) 47 | 48 | assert (i >= len(x2) and vals[2] == '') or approxeq(float(vals[2]), x2[i]) 49 | assert (i >= len(y2) and vals[3] == '') or approxeq(float(vals[3]), y2[i]) 50 | 51 | assert (i >= len(x3) and vals[4] == '') or approxeq(float(vals[4]), x3[i]) 52 | assert (i >= len(y3) and vals[5] == '') or approxeq(float(vals[5]), y3[i]) 53 | i += 1 54 | 55 | os.unlink(tempfilename) 56 | 57 | if __name__ == '__main__': 58 | test_CSVExporter() 59 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/frozenSupport.py: -------------------------------------------------------------------------------- 1 | ## Definitions helpful in frozen environments (eg py2exe) 2 | import os, sys, zipfile 3 | 4 | def listdir(path): 5 | """Replacement for os.listdir that works in frozen environments.""" 6 | if not hasattr(sys, 'frozen'): 7 | return os.listdir(path) 8 | 9 | (zipPath, archivePath) = splitZip(path) 10 | if archivePath is None: 11 | return os.listdir(path) 12 | 13 | with zipfile.ZipFile(zipPath, "r") as zipobj: 14 | contents = zipobj.namelist() 15 | results = set() 16 | for name in contents: 17 | # components in zip archive paths are always separated by forward slash 18 | if name.startswith(archivePath) and len(name) > len(archivePath): 19 | name = name[len(archivePath):].split('/')[0] 20 | results.add(name) 21 | return list(results) 22 | 23 | def isdir(path): 24 | """Replacement for os.path.isdir that works in frozen environments.""" 25 | if not hasattr(sys, 'frozen'): 26 | return os.path.isdir(path) 27 | 28 | (zipPath, archivePath) = splitZip(path) 29 | if archivePath is None: 30 | return os.path.isdir(path) 31 | with zipfile.ZipFile(zipPath, "r") as zipobj: 32 | contents = zipobj.namelist() 33 | archivePath = archivePath.rstrip('/') + '/' ## make sure there's exactly one '/' at the end 34 | for c in contents: 35 | if c.startswith(archivePath): 36 | return True 37 | return False 38 | 39 | 40 | def splitZip(path): 41 | """Splits a path containing a zip file into (zipfile, subpath). 42 | If there is no zip file, returns (path, None)""" 43 | components = os.path.normpath(path).split(os.sep) 44 | for index, component in enumerate(components): 45 | if component.endswith('.zip'): 46 | zipPath = os.sep.join(components[0:index+1]) 47 | archivePath = ''.join([x+'/' for x in components[index+1:]]) 48 | return (zipPath, archivePath) 49 | else: 50 | return (path, None) 51 | 52 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/opengl/items/GLAxisItem.py: -------------------------------------------------------------------------------- 1 | from OpenGL.GL import * 2 | from .. GLGraphicsItem import GLGraphicsItem 3 | from ... import QtGui 4 | 5 | __all__ = ['GLAxisItem'] 6 | 7 | class GLAxisItem(GLGraphicsItem): 8 | """ 9 | **Bases:** :class:`GLGraphicsItem ` 10 | 11 | Displays three lines indicating origin and orientation of local coordinate system. 12 | 13 | """ 14 | 15 | def __init__(self, size=None, antialias=True, glOptions='translucent'): 16 | GLGraphicsItem.__init__(self) 17 | if size is None: 18 | size = QtGui.QVector3D(1,1,1) 19 | self.antialias = antialias 20 | self.setSize(size=size) 21 | self.setGLOptions(glOptions) 22 | 23 | def setSize(self, x=None, y=None, z=None, size=None): 24 | """ 25 | Set the size of the axes (in its local coordinate system; this does not affect the transform) 26 | Arguments can be x,y,z or size=QVector3D(). 27 | """ 28 | if size is not None: 29 | x = size.x() 30 | y = size.y() 31 | z = size.z() 32 | self.__size = [x,y,z] 33 | self.update() 34 | 35 | def size(self): 36 | return self.__size[:] 37 | 38 | 39 | def paint(self): 40 | 41 | #glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA) 42 | #glEnable( GL_BLEND ) 43 | #glEnable( GL_ALPHA_TEST ) 44 | self.setupGLState() 45 | 46 | if self.antialias: 47 | glEnable(GL_LINE_SMOOTH) 48 | glHint(GL_LINE_SMOOTH_HINT, GL_NICEST) 49 | 50 | glBegin( GL_LINES ) 51 | 52 | x,y,z = self.size() 53 | glColor4f(0, 1, 0, .6) # z is green 54 | glVertex3f(0, 0, 0) 55 | glVertex3f(0, 0, z) 56 | 57 | glColor4f(1, 1, 0, .6) # y is yellow 58 | glVertex3f(0, 0, 0) 59 | glVertex3f(0, y, 0) 60 | 61 | glColor4f(0, 0, 1, .6) # x is blue 62 | glVertex3f(0, 0, 0) 63 | glVertex3f(x, 0, 0) 64 | glEnd() 65 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/Transform3D.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from .Qt import QtCore, QtGui 3 | from . import functions as fn 4 | from .Vector import Vector 5 | import numpy as np 6 | 7 | 8 | class Transform3D(QtGui.QMatrix4x4): 9 | """ 10 | Extension of QMatrix4x4 with some helpful methods added. 11 | """ 12 | def __init__(self, *args): 13 | if len(args) == 1: 14 | if isinstance(args[0], (list, tuple, np.ndarray)): 15 | args = [x for y in args[0] for x in y] 16 | if len(args) != 16: 17 | raise TypeError("Single argument to Transform3D must have 16 elements.") 18 | elif isinstance(args[0], QtGui.QMatrix4x4): 19 | args = list(args[0].copyDataTo()) 20 | 21 | QtGui.QMatrix4x4.__init__(self, *args) 22 | 23 | def matrix(self, nd=3): 24 | if nd == 3: 25 | return np.array(self.copyDataTo()).reshape(4,4) 26 | elif nd == 2: 27 | m = np.array(self.copyDataTo()).reshape(4,4) 28 | m[2] = m[3] 29 | m[:,2] = m[:,3] 30 | return m[:3,:3] 31 | else: 32 | raise Exception("Argument 'nd' must be 2 or 3") 33 | 34 | def map(self, obj): 35 | """ 36 | Extends QMatrix4x4.map() to allow mapping (3, ...) arrays of coordinates 37 | """ 38 | if isinstance(obj, np.ndarray) and obj.shape[0] in (2,3): 39 | if obj.ndim >= 2: 40 | return fn.transformCoordinates(self, obj) 41 | elif obj.ndim == 1: 42 | v = QtGui.QMatrix4x4.map(self, Vector(obj)) 43 | return np.array([v.x(), v.y(), v.z()])[:obj.shape[0]] 44 | elif isinstance(obj, (list, tuple)): 45 | v = QtGui.QMatrix4x4.map(self, Vector(obj)) 46 | return type(obj)([v.x(), v.y(), v.z()])[:len(obj)] 47 | else: 48 | return QtGui.QMatrix4x4.map(self, obj) 49 | 50 | def inverted(self): 51 | inv, b = QtGui.QMatrix4x4.inverted(self) 52 | return Transform3D(inv), b 53 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/metaarray/readMeta.m: -------------------------------------------------------------------------------- 1 | function f = readMeta(file) 2 | info = hdf5info(file); 3 | f = readMetaRecursive(info.GroupHierarchy.Groups(1)); 4 | end 5 | 6 | 7 | function f = readMetaRecursive(root) 8 | typ = 0; 9 | for i = 1:length(root.Attributes) 10 | if strcmp(root.Attributes(i).Shortname, '_metaType_') 11 | typ = root.Attributes(i).Value.Data; 12 | break 13 | end 14 | end 15 | if typ == 0 16 | printf('group has no _metaType_') 17 | typ = 'dict'; 18 | end 19 | 20 | list = 0; 21 | if strcmp(typ, 'list') || strcmp(typ, 'tuple') 22 | data = {}; 23 | list = 1; 24 | elseif strcmp(typ, 'dict') 25 | data = struct(); 26 | else 27 | printf('Unrecognized meta type %s', typ); 28 | data = struct(); 29 | end 30 | 31 | for i = 1:length(root.Attributes) 32 | name = root.Attributes(i).Shortname; 33 | if strcmp(name, '_metaType_') 34 | continue 35 | end 36 | val = root.Attributes(i).Value; 37 | if isa(val, 'hdf5.h5string') 38 | val = val.Data; 39 | end 40 | if list 41 | ind = str2num(name)+1; 42 | data{ind} = val; 43 | else 44 | data.(name) = val; 45 | end 46 | end 47 | 48 | for i = 1:length(root.Datasets) 49 | fullName = root.Datasets(i).Name; 50 | name = stripName(fullName); 51 | file = root.Datasets(i).Filename; 52 | data2 = hdf5read(file, fullName); 53 | if list 54 | ind = str2num(name)+1; 55 | data{ind} = data2; 56 | else 57 | data.(name) = data2; 58 | end 59 | end 60 | 61 | for i = 1:length(root.Groups) 62 | name = stripName(root.Groups(i).Name); 63 | data2 = readMetaRecursive(root.Groups(i)); 64 | if list 65 | ind = str2num(name)+1; 66 | data{ind} = data2; 67 | else 68 | data.(name) = data2; 69 | end 70 | end 71 | f = data; 72 | return; 73 | end 74 | 75 | 76 | function f = stripName(str) 77 | inds = strfind(str, '/'); 78 | if isempty(inds) 79 | f = str; 80 | else 81 | f = str(inds(length(inds))+1:length(str)); 82 | end 83 | end 84 | 85 | 86 | 87 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/plots/pyqtgraph/canvas/TransformGuiTemplate.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | Form 4 | 5 | 6 | 7 | 0 8 | 0 9 | 224 10 | 117 11 | 12 | 13 | 14 | 15 | 0 16 | 0 17 | 18 | 19 | 20 | Form 21 | 22 | 23 | 24 | 1 25 | 26 | 27 | 0 28 | 29 | 30 | 31 | 32 | Translate: 33 | 34 | 35 | 36 | 37 | 38 | 39 | Rotate: 40 | 41 | 42 | 43 | 44 | 45 | 46 | Scale: 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | Mirror 59 | 60 | 61 | 62 | 63 | 64 | 65 | Reflect 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | -------------------------------------------------------------------------------- /DockingPie1/lib/docking_program_main/Functions/exceptions.py: -------------------------------------------------------------------------------- 1 | # Copyright 2022 by Serena Rosignoli. All rights reserved. 2 | # This code is part of the DockingPie package and governed by its license. Please 3 | # see the LICENSE file. 4 | 5 | """ 6 | Exceptions to be used within DockingPie. 7 | """ 8 | 9 | class DockingPieInvalidFile(Exception): 10 | """ 11 | Used when a sequence or structure file containing some error is opened. 12 | """ 13 | pass 14 | 15 | 16 | class DockingPieUnknownFile(Exception): 17 | """ 18 | Used when a sequence or structure file containing some error is opened. 19 | """ 20 | pass 21 | 22 | 23 | class DockingPieMissingStructure(Exception): 24 | """ 25 | Used when trying to access the 3D structure data of an element which lacks a 26 | structure. 27 | """ 28 | pass 29 | 30 | 31 | class DockingPieSequenceConflict(Exception): 32 | """ 33 | Used when updating the amino acid sequence of an element with a sequence with 34 | different amino acids. 35 | """ 36 | pass 37 | 38 | 39 | class DockingPieInterruptedProtocol(Exception): 40 | """ 41 | Used when interrupting a running protocol. 42 | """ 43 | pass 44 | 45 | 46 | def catch_protocol_exception(function): 47 | """ 48 | Function used as a decorator to catch the exceptions raised when running methods 49 | of protocols. 50 | """ 51 | 52 | def wrapper(self, *args, **kwargs): 53 | 54 | # Launches the method of the protocol. 55 | try: 56 | return function(self, *args, **kwargs) 57 | 58 | # The protocol is quitted by the user while the method is running, do not show any meesage. 59 | except DockingPieInterruptedProtocol as e: 60 | self.quit_protocol() 61 | return None 62 | 63 | # The protocol stops because an exception was raised in the method, show an error message. 64 | except Exception as e: 65 | # Shows an error message. 66 | title = "%s Error" % self.protocol_name 67 | message = "%s stopped because of the following error: %s" % (self.protocol_name, str(e)) 68 | self.DockingPie.main_window.show_error_message(title, message) 69 | self.quit_protocol() 70 | return None 71 | 72 | return wrapper 73 | --------------------------------------------------------------------------------