Index

A

Acquisition (class in pwem.objects.data) acquisitionToRow() (in module xmipp3.convert.convert) ACTION_BROWSE (pyworkflow.utils.properties.Icon attribute) ACTION_CIRCLE (pyworkflow.utils.properties.Icon attribute) ACTION_CLOSE (pyworkflow.utils.properties.Icon attribute) ACTION_COLLAPSE (pyworkflow.utils.properties.Icon attribute) ACTION_CONTINUE (pyworkflow.utils.properties.Icon attribute) ACTION_CONTRAST (pyworkflow.utils.properties.Icon attribute) ACTION_COPY (pyworkflow.utils.properties.Icon attribute) ACTION_DB (pyworkflow.utils.properties.Icon attribute) ACTION_DELETE (pyworkflow.utils.properties.Icon attribute) ACTION_DUPLICATE (pyworkflow.utils.properties.Icon attribute) ACTION_EDIT (pyworkflow.utils.properties.Icon attribute) ACTION_EXECUTE (pyworkflow.utils.properties.Icon attribute) ACTION_EXPAND (pyworkflow.utils.properties.Icon attribute) ACTION_EXPORT (pyworkflow.utils.properties.Icon attribute) ACTION_EXPORT_UPLOAD (pyworkflow.utils.properties.Icon attribute) ACTION_FILAMENT_PICKING (pyworkflow.utils.properties.Icon attribute) ACTION_FIND_NEXT (pyworkflow.utils.properties.Icon attribute) ACTION_FIND_PREVIOUS (pyworkflow.utils.properties.Icon attribute) ACTION_GRID (pyworkflow.utils.properties.Icon attribute) ACTION_HAND (pyworkflow.utils.properties.Icon attribute) ACTION_HELP (pyworkflow.utils.properties.Icon attribute) ACTION_IN (pyworkflow.utils.properties.Icon attribute) ACTION_NEW (pyworkflow.utils.properties.Icon attribute) ACTION_OUT (pyworkflow.utils.properties.Icon attribute) ACTION_PASTE (pyworkflow.utils.properties.Icon attribute) ACTION_PICKING (pyworkflow.utils.properties.Icon attribute) ACTION_REFERENCES (pyworkflow.utils.properties.Icon attribute) ACTION_REFRESH (pyworkflow.utils.properties.Icon attribute) ACTION_RENAME (pyworkflow.utils.properties.Icon attribute) ACTION_RESULTS (pyworkflow.utils.properties.Icon attribute) ACTION_SAVE (pyworkflow.utils.properties.Icon attribute) ACTION_SEARCH (pyworkflow.utils.properties.Icon attribute) ACTION_SELECT_FROM (pyworkflow.utils.properties.Icon attribute) ACTION_SELECT_TO (pyworkflow.utils.properties.Icon attribute) ACTION_STATS (pyworkflow.utils.properties.Icon attribute) ACTION_STOP (pyworkflow.utils.properties.Icon attribute) ACTION_STOP_WORKFLOW (pyworkflow.utils.properties.Icon attribute) ACTION_UNDO (pyworkflow.utils.properties.Icon attribute) ACTION_VISUALIZE (pyworkflow.utils.properties.Icon attribute) ACTION_WIZ (pyworkflow.utils.properties.Icon attribute) ACTION_ZOOM (pyworkflow.utils.properties.Icon attribute) activate() (pyworkflow.gui.plotter.Plotter method) (scipion.install.funcs.CondaCommandDef method) adaptShifts() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) add() (pyworkflow.gui.text.HyperlinkManager method) ADD_DATA_TRAIN_CUST (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ADD_DATA_TRAIN_CUSTOM_OPT (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ADD_DATA_TRAIN_CUSTOM_OPT_COORS (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ADD_DATA_TRAIN_CUSTOM_OPT_PARTS (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ADD_DATA_TRAIN_NONE (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ADD_DATA_TRAIN_PRECOMP (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ADD_DATA_TRAIN_TYPES (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ADD_MODEL_TRAIN_NEW (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ADD_MODEL_TRAIN_PRETRAIN (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ADD_MODEL_TRAIN_PREVRUN (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ADD_MODEL_TRAIN_TYPES (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) addActionsFrame() (pyworkflow.gui.project.viewprojects.ProjectsView method) addAdvancedParams() (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase method) addAttributeToFormula() (pwem.wizards.wizard.FormulaDialog method) addBinding() (pyworkflow.gui.text.TextFileViewer method) addBooleanParam() (pyworkflow.protocol.params.Form method) addButton() (pyworkflow.gui.dialog.ToolbarListDialog method) addChild() (pyworkflow.utils.graph.Node method) addCommand() (scipion.install.funcs.InstallHelper method) (scipion.install.funcs.Target method) addCommands() (scipion.install.funcs.InstallHelper method) addCommonFieldsToMap() (pyworkflow.mapper.sqlite.SqliteFlatDb method) addCondaPackages() (scipion.install.funcs.InstallHelper method) addCoordinate() (pwem.viewers.viewer_coordinates.MainWindow method) addCTF() (pwem.objects.data.DefocusGroup method) addDep() (scipion.install.funcs.Target method) addError() (pyworkflow.tests.tests.GTestResult method) addExtended() (pyworkflow.object.Pointer method) addFailure() (pyworkflow.tests.tests.GTestResult method) addFile() (pyworkflow.gui.text.TextFileViewer method) addFreqSlider() (pwem.wizards.wizard.BandPassFilterDialog method) addGeneralSection() (pyworkflow.protocol.params.Form method) addGroup() (pyworkflow.protocol.params.Form method) (pyworkflow.protocol.params.Section method) addHidden() (pyworkflow.protocol.params.ElementGroup method) (pyworkflow.protocol.params.Form method) addItem() (pyworkflow.gui.canvas.Canvas method) ADDITIONALVOLUMEDIR (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) ADDITIONALVOLUMENAME (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) addLabel() (pyworkflow.project.config.LabelsList method) addLibrary() (pyworkflow.utils.utils.Environ method) (scipion.install.funcs.Environment method) addLine() (pyworkflow.gui.text.OutputText method) (pyworkflow.gui.text.TaggedText method) (pyworkflow.gui.text.Text method) (pyworkflow.protocol.params.ElementGroup method) (pyworkflow.protocol.params.Form method) addLocalTemplates() (pyworkflow.template.TemplateList method) addNewline() (pyworkflow.gui.text.Text method) addNode() (pyworkflow.project.config.NodeConfigList method) (pyworkflow.project.config.ProjectSettings method) addNoise() (pwem.emlib.image.image_handler.ImageHandler method) addNoiseStep() (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoiseParticles method) (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoiseVolumes method) addObject() (pyworkflow.gui.form.MultiPointerTreeProvider method) addPackage() (scipion.install.funcs.Environment method) (scipion.install.funcs.InstallHelper method) addParallelSection() (pyworkflow.protocol.params.Form method) addParam() (pyworkflow.protocol.params.ElementGroup method) (pyworkflow.protocol.params.Form method) addPipModule() (scipion.install.funcs.Environment method) addPluginsVariables() (in module scipion.scripts.config) addPluginTemplates() (pyworkflow.template.TemplateList method) addPoint() (xmipp3.utils.Data method) addPositionListener() (pyworkflow.gui.canvas.Item method) addPrerequisites() (pyworkflow.protocol.protocol.Step method) addPyworkflowVariables() (in module scipion.scripts.config) addRadiusBox() (pwem.wizards.wizard.MaskPreviewDialog method) addReader() (pwem.emlib.image.image_readers.ImageReadersRegistry class method) addRow() (pyworkflow.utils.dataset.Table method) addScipionAttribute() (in module pwem.convert.atom_struct) addScipionTemplates() (pyworkflow.template.TemplateList method) addSearchWeight() (pyworkflow.gui.dialog.SearchBaseWindow method) addSection() (pyworkflow.protocol.params.Form method) addSelectionListener() (pyworkflow.gui.canvas.Item method) addSocket() (pyworkflow.gui.canvas.Item method) addStruct() (pwem.convert.atom_struct.AtomicStructHandler method) addSubMenu() (pyworkflow.gui.project.viewprotocols_extra.ProtocolConfig method) (pyworkflow.project.config.MenuConfig method) addSuccess() (pyworkflow.tests.tests.GTestResult method) addSummaryWarning() (pyworkflow.protocol.protocol.Protocol method) addTarget() (pwem.wizards.wizard.VariableWizard method) (scipion.install.funcs.CommandDef method) (scipion.install.funcs.Environment method) addTargetAlias() (scipion.install.funcs.Environment method) addTemplate() (pyworkflow.template.TemplateList method) addText() (pyworkflow.gui.text.Text method) addToMd() (pwem.emlib.metadata.utils.Row method)

addValidator() (pyworkflow.protocol.params.Param method) addVariablesToSection() (in module scipion.scripts.config) addViewList() (pyworkflow.gui.project.base.ProjectBaseWindow method) addWHTemplates() (pyworkflow.template.TemplateList method) adjustContent() (pyworkflow.gui.form.SectionFrame method) adjustSections() (pyworkflow.gui.form.FormWindow method) adjustSize() (pyworkflow.gui.form.FormWindow method) adjustStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolAdjust method) (xmipp3.protocols.protocol_volume_local_adjust.XmippProtLocalVolAdj method) ageColorMode() (pyworkflow.project.config.ProjectSettings method) AGG_AVERAGE (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes attribute) AGG_SUM (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes attribute) aggregate() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.object.Set method) aggregateSet() (pwem.protocols.protocol_sets.ProtSetAggregate method) ALERT (pyworkflow.utils.properties.Icon attribute) aliasFont() (in module pyworkflow.gui.gui) aliasNode() (pyworkflow.utils.graph.Graph method) alignabilityStep() (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) alignBioPairwise2Sequences() (in module pwem.convert.sequence) alignClustalSequences() (in module pwem.convert.sequence) ALIGNED_VOL (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D attribute) alignMaps() (xmipp3.protocols.protocol_volume_deform_zernike3d.XmippProtVolumeDeformZernike3D method) alignmentCorrelationMovieStep() (xmipp3.protocols.protocol_movie_alignment_consensus.XmippProtConsensusMovieAlignment method) alignmentToRow() (in module xmipp3.convert.convert) alignMuscleSequences() (in module pwem.convert.sequence) alignSeq() (pwem.convert.sequence.SequenceHandler method) alignStep() (xmipp3.protocols.protocol_structure_map.XmippProtStructureMap method) (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) alignTypeList (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) AlignVolPartOutputs (class in xmipp3.protocols.protocol_align_volume_and_particles) alignVolumeStep() (xmipp3.protocols.protocol_align_volume.XmippProtAlignVolume method) (xmipp3.protocols.protocol_align_volume_and_particles.XmippProtAlignVolumeParticles method) ALL_PROTOCOLS (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig attribute) allCtfGroups() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) allFree() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) allIters() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) allowsDelete() (pwem.protocols.protocol.EMProtocol method) (pyworkflow.protocol.protocol.Protocol method) allowsGpu() (pyworkflow.protocol.protocol.Protocol method) allowsRenderable() (pwem.viewers.showj.ColumnProperties method) allRefs() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) Alphabet (class in pwem.objects.data) alphabets (pwem.objects.data.Alphabet attribute) alphabetsLabels (pwem.objects.data.Alphabet attribute) ALT_COLOR (pyworkflow.constants.Color attribute) ALT_COLOR_2 (pyworkflow.constants.Color attribute) ALT_COLOR_DARK (pyworkflow.constants.Color attribute) AMBIGOUS_DNA_ALPHABET (pwem.objects.data.Alphabet attribute) AMBIGOUS_RNA_ALPHABET (pwem.objects.data.Alphabet attribute) AMINOACIDS (pwem.objects.data.Alphabet attribute) analyzeCore() (xmipp3.protocols.protocol_core_analysis.XmippProtCoreAnalysis method) analyzeDefocus() (xmipp3.protocols.protocol_analyze_local_ctf.XmippProtAnalyzeLocalCTF method) analyzeDistanceStep() (xmipp3.protocols.protocol_compare_angles.XmippProtCompareAngles method) analyzeFormattingTypeError() (in module pyworkflow.protocol.launch) analyzeOutOfCores() (xmipp3.protocols.protocol_cl2d.XmippProtCL2D method) anglePsi (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) angleRot (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) Angles (class in pwem.objects.data_tiltpairs) anglesDifference() (in module xmipp3.protocols.protocol_ctf_consensus) angleTilt (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) angularAccuracyStep() (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) AngularDistributionViewer (class in pwem.viewers.viewer_angular_dist) angularProjectLibraryStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) annotateClassName() (pyworkflow.mapper.mapper.Mapper static method) ansi() (in module pyworkflow.utils.utils) (in module scipion.install.funcs) (in module scipion.scripts.config) append() (pwem.convert.trigonometry.FibonacciSphere method) (pwem.emlib.image.image_readers.ImageStack method) (pwem.objects.data.SetOfImages method) (pyworkflow.object.PointerList method) (pyworkflow.object.Set method) (scipion.install.funcs.CommandDef method) (xmipp3.base.XmippSet method) appendFile() (pwem.convert.sequence.SequenceHandler method) appendFromClasses() (pwem.objects.data.SetOfClasses method) (pwem.objects.data.SetOfImages method) appendFromImages() (pwem.objects.data.SetOfImages method) appendJobId() (pyworkflow.protocol.protocol.Protocol method) appendToFile() (pwem.objects.data.Sequence method) apply() (pyworkflow.gui.dialog.Dialog method) (pyworkflow.gui.dialog.EditObjectDialog method) (pyworkflow.gui.dialog.EntryDialog method) (pyworkflow.gui.dialog.ListDialog method) (pyworkflow.gui.form.QueueDialog method) (pyworkflow.gui.project.labels.EditLabelDialog method) (pyworkflow.gui.project.variables.EditVariableDialog method) (pyworkflow.gui.project.variables.VariablesDialog method) applyAlignmentStep() (xmipp3.protocols.protocol_apply_alignment.XmippProtApplyAlignment method) applyBandpassFilter() (pwem.viewers.viewer_coordinates.MainWindow method) applyComparisonStep() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) applyContrast() (pwem.viewers.viewer_coordinates.MainWindow method) applyFormulaStep() (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) applyGaussianBlur() (pwem.viewers.viewer_coordinates.MainWindow method) applyInvertContrast() (pwem.viewers.viewer_coordinates.MainWindow method) applyMatrix() (pwem.protocols.protocol_projection_edit.ProtProjectionEditor method) applyOperations() (scipion.install.plugin_manager.OperationList method) applyPowerHistogram() (pwem.viewers.viewer_coordinates.MainWindow method) applyTransform() (in module xmipp3.protocols.protocol_tilt_analysis) (in module xmipp3.utils) (pwem.emlib.image.image_handler.ImageHandler static method) argsForTransformMask() (xmipp3.protocols.protocol_preprocess.geometrical_mask.XmippGeometricalMask2D method) (xmipp3.protocols.protocol_preprocess.geometrical_mask.XmippGeometricalMask3D method) array_zeros_to_median() (in module xmipp3.protocols.protocol_movie_gain) arrays_correlation_FT() (in module xmipp3.protocols.protocol_movie_gain) ARROW_UP (pyworkflow.utils.properties.Icon attribute) ask() (in module pyworkflow.apps.pw_sync_data) askColor() (in module pyworkflow.gui.dialog) askPath() (in module pyworkflow.gui.dialog) askSingleAllCancel() (in module pyworkflow.gui.dialog) askString() (in module pyworkflow.gui.dialog) askYesNo() (in module pyworkflow.gui.dialog) (pyworkflow.gui.gui.Window method) askYesNoCancel() (in module pyworkflow.gui.dialog) assertIsNotEmpty() (pyworkflow.tests.tests.BaseTest method) assertSetSize() (pyworkflow.tests.tests.BaseTest method) assignAllParams() (in module scipion.scripts.kickoff) assignImagesToReferencesStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) assignmentStep() (xmipp3.protocols.protocol_assignment_tilt_pair.XmippProtAssignmentTiltPair method) assignPdbStep() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) assignStep() (pwem.protocols.protocol_origin_sampling_volume.ProtOrigSampling method) AtomicStructHandler (class in pwem.convert.atom_struct) AtomStruct (class in pwem.objects.data) AtomStructFlex (class in pwem.objects.data_flexhub) ATTRIBUTES (pyworkflow.protocol.params.FormElement attribute) AttributesTreeProvider (class in pyworkflow.gui.tree) AUTOMATIC_ALIGNMENT (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes attribute) AutoScrollbar (class in pyworkflow.gui.widgets) AVAILABLE_RELEASE (pyworkflow.utils.properties.PluginStates attribute) averageAngles() (in module xmipp3.protocols.protocol_ctf_consensus) AVERAGES (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering attribute) averageStep() (xmipp3.protocols.protocol_reconstruct_fourier.XmippProtReconstructFourier method) awakeStep() (pwem.protocols.parallel.ProtTestParallel method)

B

backend (pyworkflow.gui.plotter.Plotter attribute) backup() (in module pyworkflow.utils.path) (in module scipion.scripts.config) BACKWARD (pyworkflow.utils.properties.Icon attribute) balanced_sampling() (in module xmipp3.protocols.protocol_mics_defocus_balancer) BandPassFilterDialog (class in pwem.wizards.wizard) BaseTest (class in pyworkflow.tests.tests) BasicMDViewer (class in pwem.viewers.viewers_data) BatchProtocol (class in pwem.protocols.protocol_batch) BEGIN (pyworkflow.utils.utils.Environ attribute) BETA (pyworkflow.utils.properties.Icon attribute) BG_COLOR (pyworkflow.constants.Color attribute) BINARY (pyworkflow.utils.properties.PluginStates attribute) binaryCondition (pwem.viewers.viewer_localres.LocalResolutionViewer attribute) Binding (class in pyworkflow.gui.form) bindWidget() (pyworkflow.gui.widgets.Scrollable method) black() (in module pyworkflow.utils.utils) (in module scipion.install.funcs) (in module scipion.scripts.config) blackB() (in module pyworkflow.utils.utils) blackList (pyworkflow.utils.profiler.Timer attribute) blue (pyworkflow.constants.StrColors attribute) BLUE (pyworkflow.utils.properties.colorText attribute) blue() (in module pyworkflow.utils.utils) (in module scipion.install.funcs) (in module scipion.scripts.config) blueB() (in module pyworkflow.utils.utils) blueStr() (in module pyworkflow.utils.utils) body() (pwem.wizards.wizard.ColorScaleDialog method) (pwem.wizards.wizard.FormulaDialog method) (pwem.wizards.wizard.PreviewDialog method) (pyworkflow.gui.dialog.Dialog method) (pyworkflow.gui.dialog.EditObjectDialog method) (pyworkflow.gui.dialog.EntryDialog method) (pyworkflow.gui.dialog.ExceptionDialog method) (pyworkflow.gui.dialog.GenericDialog method) (pyworkflow.gui.dialog.ListDialog method) (pyworkflow.gui.dialog.MessageDialog method) (pyworkflow.gui.dialog.ToolbarListDialog method) (pyworkflow.gui.form.QueueDialog method) (pyworkflow.gui.project.labels.EditLabelDialog method) (pyworkflow.gui.project.variables.EditVariableDialog method)

BOLD (pyworkflow.utils.properties.colorText attribute) Boolean (class in pyworkflow.object) BOOLEAN (pyworkflow.config.VarTypes attribute) BooleanParam (class in pyworkflow.protocol.params) BoolVar (class in pyworkflow.gui.form) boostingStep() (xmipp3.protocols.protocol_subtract_projection.XmippProtBoostParticles method) BOTH (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering attribute) (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections attribute) BOTTOM (pyworkflow.gui.canvas.Item attribute) BoundTree (class in pyworkflow.gui.tree) breakSymmetryStep() (xmipp3.protocols.protocol_break_symmetry.XmippProtAngBreakSymmetry method) BROOM (pyworkflow.utils.properties.Icon attribute) BrowserWindow (class in pyworkflow.gui.browser) buildRunCommand() (in module pyworkflow.utils.process) buildSearchList() (pyworkflow.gui.text.TextFileViewer method) Button (class in pyworkflow.gui.widgets) BUTTON_CANCEL (pyworkflow.utils.properties.Icon attribute) BUTTON_CLOSE (pyworkflow.utils.properties.Icon attribute) BUTTON_SAVE (pyworkflow.utils.properties.Icon attribute) BUTTON_SELECT (pyworkflow.utils.properties.Icon attribute) buttonbox() (pyworkflow.gui.dialog.Dialog method) (pyworkflow.gui.dialog.EditObjectDialog method) buttonClicked() (pyworkflow.gui.project.variables.EditVariableDialog method)

C

Cable (class in pyworkflow.gui.canvas) calculateAngStep() (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) calculateAutodownsampling() (xmipp3.protocols.protocol_ctf_micrographs.XmippProtCTFMicrographs method) calculateAverage() (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) calculateAveragePixel() (pwem.viewers.viewer_coordinates.MainWindow method) calculateConsensusParams() (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) calculateConsensusResolution() (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method) calculateConsensusStep() (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking method) calculateCoorConsensusStep() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) calculateDeviationsStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) calculateDPRResolution() (xmipp3.protocols.protocol_resolution3d.XmippProtResolution3D method) calculateFSCResolution() (xmipp3.protocols.protocol_resolution3d.XmippProtResolution3D method) calculateFscStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) (xmipp3.protocols.protocol_resolution3d.XmippProtResolution3D method) calculateGautomatchParams() (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) calculateParticleExtractionParams() (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) calculateRelionParams() (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) calculateResolution() (pwem.objects.data.FSC method) calculateStrain() (xmipp3.protocols.protocol_volume_strain.XmippProtVolumeStrain method) calculateTiltCorrelationStep() (xmipp3.protocols.protocol_tilt_analysis.XmippProtTiltAnalysis method) calculateTopazParams() (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) cancel() (pyworkflow.gui.dialog.Dialog method) CANCEL_SELECTED_OPERATION (pyworkflow.utils.properties.Message attribute) canPick() (pwem.viewers.viewer_coordinates.MainWindow method) Canvas (class in pyworkflow.gui.canvas) captureLastPosition() (pyworkflow.gui.canvas.Canvas method) CASTING_INDEX (pyworkflow.gui.dialog.SearchBaseWindow attribute) Ccp4Header (class in pwem.convert.headers) cd() (scipion.install.funcs.CommandDef method) centerOfMass() (pwem.convert.atom_struct.AtomicStructHandler method) centerStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles method) centerWindows() (in module pyworkflow.gui.gui) change_view() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) changeExtension() (xmipp3.protocols.protocol_enrich.XmippProtEnrich method) changeFont() (pyworkflow.gui.text.TextFileViewer method) changeFontSize() (in module pyworkflow.gui.gui) changeFontSizeByDeltha() (in module pyworkflow.gui.gui) changeHandStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) ChangeOriginSamplingWizard (class in pwem.wizards.wizards) changePosition() (pyworkflow.gui.text.TextFileViewer method) changeThreshold() (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) check() (in module pyworkflow.apps.pw_sync_data) (pyworkflow.template.Validations class method) check_item() (scipion.install.plugin_manager.PluginTree method) checkBackgroundStep() (xmipp3.protocols.protocol_volume_local_sharpening.XmippProtLocSharp method) checkConf() (in module scipion.scripts.config) CHECKED (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) checkIfNewMics() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) checkIfParentsFinished() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) checkInfoField() (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) checkIsAlive() (pyworkflow.project.project.Project method) checkJobId() (pyworkflow.project.project.Project method) checkLabelInFile() (pwem.convert.atom_struct.AtomicStructHandler method) checkLib() (in module scipion.install.funcs) checkNotify() (in module scipion.scripts.config) checkPaths() (in module scipion.scripts.config) checkPid() (pyworkflow.project.project.Project method) checkPlugin() (in module pyworkflow.utils.reflection) checkRead() (pwem.convert.atom_struct.AtomicStructHandler method) checkRejectedCriteria() (xmipp3.protocols.protocol_ctf_micrographs.XmippProtCTFMicrographs method) checkSummaryWarnings() (pyworkflow.protocol.protocol.Protocol method) Chimera (class in pwem.viewers.viewer_chimera) CHIMERA (pyworkflow.utils.properties.Icon attribute) CHIMERA_OLD_BINARY_PATH (pwem.Config attribute) ChimeraAngDist (class in pwem.viewers.viewer_chimera) ChimeraAttributeViewer (class in pwem.viewers.viewer_localres) ChimeraHandler (class in pwem.viewers.filehandlers) chimeraInstalled() (in module pwem.viewers.viewer_localres) ChimeraOldView (class in pwem.viewers.viewer_chimera) ChimeraOldViewer (class in pwem.viewers.viewer_chimera) ChimeraView (class in pwem.viewers.viewer_chimera) ChimeraViewer (class in pwem.viewers.viewer_chimera) CHOICE_DIHEDRAL (pwem.protocols.protocol_projection_edit.ProtProjectionEditor attribute) CHOICE_DISTANCE_BETWEEN_COORDS (pwem.protocols.protocol_set_filter.ProtSetFilter attribute) CHOICE_DISTANCE_CENTER (pwem.protocols.protocol_set_filter.ProtSetFilter attribute) CHOICE_FORMULA (pwem.protocols.protocol_set_filter.ProtSetFilter attribute) CHOICE_ICOSAHEDRAL (pwem.protocols.protocol_projection_edit.ProtProjectionEditor attribute) CHOICE_LABEL (pwem.protocols.protocol_projection_edit.ProtProjectionEditor attribute) (pwem.protocols.protocol_set_filter.ProtSetFilter attribute) CHOICE_MOVE_UC (pwem.protocols.protocol_projection_edit.ProtProjectionEditor attribute) CHOICE_MOVE_VECTOR (pwem.protocols.protocol_projection_edit.ProtProjectionEditor attribute) CHOICE_RANKED (pwem.protocols.protocol_set_filter.ProtSetFilter attribute) CHOICE_ROTATE_VECTOR (pwem.protocols.protocol_projection_edit.ProtProjectionEditor attribute) CHOICE_TETRAHEDRAL (pwem.protocols.protocol_projection_edit.ProtProjectionEditor attribute) chooseTemplate() (in module scipion.scripts.kickoff) CIF (pwem.convert.atom_struct.AtomicStructHandler attribute) cifToPdb() (in module pwem.convert.atom_struct) citations() (pyworkflow.protocol.protocol.Protocol method) Class2D (class in pwem.objects.data) class2DToRow() (in module xmipp3.convert.convert) Class3D (class in pwem.objects.data) CLASS_MAP (pyworkflow.mapper.sqlite.SqliteFlatDb attribute) classCount (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) CLASSES (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering attribute) Classes3DView (class in pwem.viewers.views) CLASSES_MD (xmipp3.protocols.protocol_classes_2d_mapping.XmippProtCL2DMap attribute) ClassesView (class in pwem.viewers.views) ClassFlex (class in pwem.objects.data_flexhub) classification() (xmipp3.protocols.protocol_classify_pca.XmippProtClassifyPca method) (xmipp3.protocols.protocol_classify_pca_streaming.XmippProtClassifyPcaStreaming method) classifyItems() (pwem.objects.data.SetOfClasses method) ClassStructFlex (class in pwem.objects.data_flexhub) ClassVol (class in pwem.objects.data) cleanDirectory() (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) cleanExecutionAttributes() (pyworkflow.protocol.protocol.Protocol method) cleanExtraAttributes() (pwem.protocols.protocol_sets.ProtUnionSet method) cleanFileName() (in module pwem.utils) cleanFileNameAnnotation() (pwem.convert.headers.Ccp4Header method) cleanInfo() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) cleanObjId() (pyworkflow.object.Object method) cleanPath() (in module pyworkflow.utils.path) cleanPattern() (in module pyworkflow.utils.path) cleanProjectName() (pyworkflow.project.project.Project static method) cleanSequence() (in module pwem.convert.sequence) cleanSequenceScipion() (in module pwem.convert.sequence) cleanTmp() (pyworkflow.protocol.protocol.Protocol method) cleanUpNodes() (pyworkflow.project.config.ProjectSettings method) cleanVoidGPUs() (pyworkflow.protocol.executor.ThreadStepExecutor method) cleanVolume() (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) cleanVolumeStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) cleanWeights() (pwem.convert.trigonometry.FibonacciSphere method) cleanWorkingDir() (pyworkflow.protocol.protocol.Protocol method) clear() (pyworkflow.gui.canvas.Canvas method) (pyworkflow.gui.form.MultiPointerTreeProvider method) (pyworkflow.gui.form.MultiPointerVar method) (pyworkflow.gui.form.ParamWidget method) (pyworkflow.gui.matplotlib_image.Preview method) (pyworkflow.gui.plotter.Plotter method) (pyworkflow.gui.text.Text method) (pyworkflow.gui.text.TextFileViewer method) (pyworkflow.gui.tree.Tree method) (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.object.CsvList method) (pyworkflow.object.List method) (pyworkflow.object.Set method) (pyworkflow.project.config.LabelsList method) (pyworkflow.project.config.NodeConfigList method) (xmipp3.utils.Data method) clearImageGrid() (pwem.viewers.viewer_coordinates.MainWindow method) clearOldName() (pyworkflow.project.config.Label method) clearOperations() (scipion.install.plugin_manager.OperationList method) clone() (pwem.emlib.metadata.utils.Row method) (pwem.objects.data.Class2D method) (pwem.objects.data.Class3D method) (pwem.objects.data.EMSet method) (pwem.objects.data_flexhub.ClassFlex method) (pwem.objects.data_flexhub.ClassStructFlex method) (pyworkflow.object.Object method) close() (pwem.objects.data.Class2D method) (pwem.objects.data.Class3D method) (pwem.objects.data.ClassVol method) (pwem.objects.data_flexhub.ClassFlex method) (pwem.objects.data_flexhub.ClassStructFlex method) (pwem.objects.data_tiltpairs.CoordinatesTiltPair method) (pwem.objects.data_tiltpairs.TiltPairSet method) (pyworkflow.gui.dialog.FlashMessage method) (pyworkflow.gui.dialog.FloatingMessage method) (pyworkflow.gui.gui.Window method) (pyworkflow.gui.plotter.Plotter method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) (pyworkflow.mapper.sqlite_db.SqliteDb method) (pyworkflow.object.Set method) (scipion.install.plugin_manager.PluginManagerWindow method) closeConnection() (pyworkflow.mapper.sqlite_db.SqliteDb class method) closeMapper() (pyworkflow.project.project.Project method) closeMappers() (pyworkflow.protocol.protocol.Protocol method) closeOutputStep() (xmipp3.protocols.protocol_classify_pca_streaming.XmippProtClassifyPcaStreaming method) clusterClasses() (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering method) cmd() (in module scipion.install.clean) cnnFree() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) coarseSearch() (xmipp3.protocols.protocol_helical_parameters.XmippProtHelicalParameters method) (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry method) CODE_BRANCH (pyworkflow.utils.properties.Icon attribute) Color (class in pyworkflow.constants) COLOR_MODE_AGE (pyworkflow.project.config.ProjectSettings attribute) COLOR_MODE_LABELS (pyworkflow.project.config.ProjectSettings attribute) COLOR_MODE_SIZE (pyworkflow.project.config.ProjectSettings attribute) COLOR_MODE_STATUS (pyworkflow.project.config.ProjectSettings attribute) COLOR_MODES (pyworkflow.project.config.ProjectSettings attribute) ColoredConnector (class in pyworkflow.gui.canvas) ColorScaleDialog (class in pwem.wizards.wizard) ColorScaleWizardBase (class in pwem.wizards.wizard) ColorScaleWizardRMSD (class in pwem.wizards.wizards) colorsInTerminal() (pyworkflow.config.Config class method) colorText (class in pyworkflow.utils.properties) Column (class in pyworkflow.utils.dataset) COLUMN_KWARGS_INDEX (pyworkflow.gui.dialog.SearchBaseWindow attribute) COLUMN_TEXT_INDEX (pyworkflow.gui.dialog.SearchBaseWindow attribute) columnConfig (pyworkflow.gui.dialog.SearchBaseWindow attribute) (pyworkflow.gui.project.searchprotocol.SearchProtocolWindow attribute) (pyworkflow.gui.project.searchrun.SearchRunWindow attribute) ColumnProperties (class in pwem.viewers.showj) ColumnsConfig (class in pwem.viewers.showj) ComboBox (class in pyworkflow.gui.widgets) ComboVar (class in pyworkflow.gui.form) Command (class in scipion.install.funcs) CommandDef (class in scipion.install.funcs) commandExists() (in module pyworkflow.utils.which) CommandView (class in pyworkflow.viewer) commit() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) (pyworkflow.project.config.ProjectSettings method) (xmipp3.programs.ProgramDb method) commonAttributes() (pwem.protocols.protocol_sets.ProtUnionSet method) commonPath() (in module pyworkflow.utils.path) compareConfig() (in module scipion.scripts.config) compareConfigVariable() (in module scipion.scripts.config) compareData() (pwem.emlib.image.image_handler.ImageHandler method) compareDefocus() (xmipp3.protocols.protocol_consensus_local_ctf.XmippProtConsensusLocalCTF method) compareSetProperties() (pyworkflow.tests.tests.BaseTest method) compareSets() (pyworkflow.tests.tests.BaseTest class method) compareVolumeStep() (xmipp3.protocols.protocol_multiple_fscs.XmippProtMultipleFSCs method) composePSD() (pwem.protocols.protocol_align_movies.ProtAlignMovies method) composePSDImages() (pwem.protocols.protocol_align_movies.ProtAlignMovies method) composeTransform() (pwem.objects.data.Transform method) compute_statistics() (in module xmipp3.protocols.protocol_mics_defocus_balancer) computeAverage() (pwem.emlib.image.image_handler.ImageHandler method) computeBfactorStep() (xmipp3.protocols.protocol_resolution3d.XmippProtResolution3D method) computeCorr() (xmipp3.protocols.protocol_structure_map.XmippProtStructureMap method) (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) computeMappingStep() (xmipp3.protocols.protocol_classes_2d_mapping.XmippProtCL2DMap method) computePSD() (pwem.protocols.protocol_align_movies.ProtAlignMovies method) computePSDImages() (pwem.protocols.protocol_align_movies.ProtAlignMovies method) computePSDs() (pwem.protocols.protocol_align_movies.ProtAlignMovies method) computeRankingVolumes() (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) computeSampling() (pwem.convert.headers.Ccp4Header method) computeStats() (in module xmipp3.protocols.protocol_movie_dose_analysis) (in module xmipp3.protocols.protocol_tilt_analysis) computeStep() (pwem.protocols.protocol_mathematical_operator.ProtMathematicalOperator method) computeThumbnail() (pwem.emlib.image.image_handler.ImageHandler method) (pwem.protocols.protocol_align_movies.ProtAlignMovies method) CONDA_ACTIVATION_CMD (pyworkflow.config.Config attribute) CondaCommandDef (class in scipion.install.funcs) condaInstall() (scipion.install.funcs.CondaCommandDef method) Conditional (class in pyworkflow.protocol.params) Config (class in pwem) (class in pyworkflow.config) (class in pyworkflow.gui.gui) config (pwem.viewers.viewers_data.RegistryViewerConfig attribute) CONFIG (pyworkflow.constants.DOCSITEURLS attribute) config() (pyworkflow.protocol.params.FormElement method) Config.Root (class in pyworkflow.config) CONFIG_SECTION (pyworkflow.constants.DOCSITEURLS attribute) configColumn() (pwem.viewers.showj.ColumnsConfig method) configure() (pyworkflow.gui.tooltip.ToolTip method) configureColorTags() (in module pyworkflow.gui.text) configureLogging() (pyworkflow.project.project.Project method) configureTags() (pyworkflow.gui.project.labels.LabelsTreeProvider method) (pyworkflow.gui.text.OutputText method) (pyworkflow.gui.text.TaggedText method) (pyworkflow.gui.text.Text method) (pyworkflow.gui.tree.TreeProvider method) configureWeights() (pyworkflow.gui.gui.Window method) configureWeigths() (in module pyworkflow.gui.gui) connect() (pwem.wizards.wizards_3d.callbacks.DraggablePoint method) Connector (class in pyworkflow.gui.canvas) CONSENSUS_COOR_PATH_TEMPLATE (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) CONSENSUS_PARTS_PATH_TEMPLATE (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) consensusCoordinates (xmipp3.protocols.protocol_particle_pick_consensus.ProtPickingConsensusOutput attribute) consensusWorker() (in module xmipp3.protocols.protocol_particle_pick_consensus) CONTACTUS (pyworkflow.constants.DOCSITEURLS attribute) containsAll() (pwem.emlib.metadata.utils.Row method) containsAny() (pwem.emlib.metadata.utils.Row method) containsCTF() (pwem.objects.data.DefocusGroup method) containsLabel() (pwem.emlib.metadata.utils.Row method) (pwem.emlib.metadata.utils.RowMetaData method) continueFromInteractive() (pyworkflow.protocol.protocol.Protocol method) continueProtocol() (pyworkflow.project.project.Project method) CONTROL (pyworkflow.utils.properties.KEYSYM attribute) controlPressed() (pyworkflow.viewer.Viewer method) convert() (pwem.emlib.image.image_handler.ImageHandler method) (pyworkflow.utils.dataset.Column method) (xmipp3.base.XmippSet method) CONVERT_TO_MRC (pwem.protocols.protocol_movies.ProtProcessMovies attribute) convertCTFXmippStep() (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterParticles method) convertInputStep() (pwem.protocols.protocol_movies.ProtProcessMovies method) (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_apply_alignment.XmippProtApplyAlignment method) (xmipp3.protocols.protocol_assignment_tilt_pair.XmippProtAssignmentTiltPair method) (xmipp3.protocols.protocol_break_symmetry.XmippProtAngBreakSymmetry method) (xmipp3.protocols.protocol_cl2d.XmippProtCL2D method) (xmipp3.protocols.protocol_cl2d_align.XmippProtCL2DAlign method) (xmipp3.protocols.protocol_classify_pca.XmippProtClassifyPca method) (xmipp3.protocols.protocol_classify_pca_streaming.XmippProtClassifyPcaStreaming method) (xmipp3.protocols.protocol_compare_angles.XmippProtCompareAngles method) (xmipp3.protocols.protocol_ctf_correct_wiener2d.XmippProtCTFCorrectWiener2D method) (xmipp3.protocols.protocol_ctf_defocus_group.XmippProtCTFDefocusGroup method) (xmipp3.protocols.protocol_deep_center.XmippProtDeepCenter method) (xmipp3.protocols.protocol_deep_center_predict.XmippProtDeepCenterPredict method) (xmipp3.protocols.protocol_kerdensom.KendersomBaseClassify method) (xmipp3.protocols.protocol_ml2d.XmippProtML2D method) (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) (xmipp3.protocols.protocol_particle_pick_pairs.XmippProtParticlePickingPairs method) (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc method) (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoiseParticles method) (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoiseVolumes method) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeParticles method) (xmipp3.protocols.protocol_preprocess.protocol_image_operate.XmippProtImageOperateParticles method) (xmipp3.protocols.protocol_preprocess.protocol_image_operate.XmippProtImageOperateVolumes method) (xmipp3.protocols.protocol_preprocess.protocol_process.XmippProcessParticles method) (xmipp3.protocols.protocol_preprocess.protocol_process.XmippProcessVolumes method) (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) (xmipp3.protocols.protocol_ransac.XmippProtRansac method) (xmipp3.protocols.protocol_reconstruct_fourier.XmippProtReconstructFourier method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) (xmipp3.protocols.protocol_reconstruct_significant.XmippProtReconstructSignificant method) (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) (xmipp3.protocols.protocol_resolution_bfactor.XmippProtbfactorResolution method) (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes method) (xmipp3.protocols.protocol_resolution_directional.XmippProtMonoDir method) (xmipp3.protocols.protocol_resolution_fso.XmippProtFSO method) (xmipp3.protocols.protocol_resolution_monogenic_signal.XmippProtMonoRes method) (xmipp3.protocols.protocol_screen_deeplearning.XmippProtScreenDeepLearning method) (xmipp3.protocols.protocol_simulate_ctf.XmippProtSimulateCTF method) (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) (xmipp3.protocols.protocol_validate_nontilt.XmippProtValidateNonTilt method) (xmipp3.protocols.protocol_volume_deform_zernike3d.XmippProtVolumeDeformZernike3D method) (xmipp3.protocols.protocol_volume_local_sharpening.XmippProtLocSharp method) convertInputToXmipp() (xmipp3.base.XmippProtocol method) convertInputVolume() (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) convertOutputStep() (xmipp3.protocols.protocol_volume_deform_zernike3d.XmippProtVolumeDeformZernike3D method) convertPdbStep() (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolSubtraction method) convertPixToLength() (in module pwem.utils) convertStack() (pwem.emlib.image.image_handler.ImageHandler method) convertStep() (xmipp3.protocols.protocol_align_volume_and_particles.XmippProtAlignVolumeParticles method) (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering method) (xmipp3.protocols.protocol_classes_2d_mapping.XmippProtCL2DMap method) (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) (xmipp3.protocols.protocol_generate_reprojections.XmippProtGenerateReprojections method) (xmipp3.protocols.protocol_local_ctf.XmippProtLocalCTF method) (xmipp3.protocols.protocol_shift_particles.XmippProtShiftParticles method) (xmipp3.protocols.protocol_structure_map.XmippProtStructureMap method) (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) (xmipp3.protocols.protocol_subtract_projection.XmippProtBoostParticles method) (xmipp3.protocols.protocol_subtract_projection.XmippProtSubtractProjection method)

convertToMrc() (in module xmipp3.convert.convert) convertXmdToStackStep() (xmipp3.protocols.protocol_movie_split_frames.XmippProtSplitFrames method) convolution() (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) Coordinate (class in pwem.objects.data) COORDINATEFILENAME (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) CoordinatesObjectView (class in pwem.viewers.views) CoordinatesTiltPair (class in pwem.objects.data_tiltpairs) coordinateSystemTransform() (pwem.convert.symmetry.Dihedral method) (pwem.convert.symmetry.Icosahedron method) (pwem.convert.symmetry.Tetrahedral method) coordinateToRow() (in module xmipp3.convert.convert) CoordinateView (class in pwem.viewers.viewer_coordinates) CoordinateViewer (class in pwem.viewers.viewer_coordinates) coords() (pyworkflow.gui.tooltip.ToolTip method) copy() (pyworkflow.object.Object method) (pyworkflow.object.Set method) (pyworkflow.protocol.protocol.Protocol method) copy_image() (in module xmipp3.utils) copyAttribute() (in module xmipp3.protocols.protocol_ctf_consensus) copyAttributes() (pyworkflow.object.Object method) copyBasicInformation() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) copyCCP4Header() (pwem.convert.headers.Ccp4Header method) copyDefinitionAttributes() (pyworkflow.protocol.protocol.Protocol method) copyFile() (in module pyworkflow.utils.path) copyFromRow() (pwem.emlib.metadata.utils.Row method) copyInfo() (pwem.objects.data.Acquisition method) (pwem.objects.data.Class2D method) (pwem.objects.data.Class3D method) (pwem.objects.data.Coordinate method) (pwem.objects.data.CTFModel method) (pwem.objects.data.EMSet method) (pwem.objects.data.Image method) (pwem.objects.data.Micrograph method) (pwem.objects.data.SetOfClasses method) (pwem.objects.data.SetOfCoordinates method) (pwem.objects.data.SetOfImages method) (pwem.objects.data.SetOfMicrographsBase method) (pwem.objects.data.SetOfMovies method) (pwem.objects.data.SetOfNormalModes method) (pwem.objects.data.SetOfParticles method) (pwem.objects.data_flexhub.AtomStructFlex method) (pwem.objects.data_flexhub.ClassFlex method) (pwem.objects.data_flexhub.ClassStructFlex method) (pwem.objects.data_flexhub.FlexInfo method) (pwem.objects.data_flexhub.ParticleFlex method) (pwem.objects.data_flexhub.SetOfAtomStructFlex method) (pwem.objects.data_flexhub.SetOfParticlesFlex method) (pwem.objects.data_flexhub.VolumeFlex method) copyInput() (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery method) (xmipp3.protocols.protocol_helical_parameters.XmippProtHelicalParameters method) (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry method) copyInputFilesStep() (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) copyItems() (pwem.objects.data.EMSet method) copyLocation() (pwem.objects.data.Image method) copyMaskFileStep() (xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMask method) copyObjId() (pyworkflow.object.Object method) copyPattern() (in module pyworkflow.utils.path) copyProtocol() (pyworkflow.project.project.Project method) copyToClipboard() (pyworkflow.gui.text.Text method) copyTree() (in module pyworkflow.utils.path) CORRECT_GAIN (pwem.protocols.protocol_movies.ProtProcessMovies attribute) correctCoordinatePosition() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs method) correctGain() (pwem.protocols.protocol_align_movies.ProtAlignMovies method) correlationMatrix() (xmipp3.protocols.protocol_structure_map.XmippProtStructureMap method) (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) cosine() (pwem.convert.trigonometry.TrigonometricMemoization method) count() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) countChildren() (pyworkflow.utils.graph.Node method) counter (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) countSockets() (pyworkflow.gui.canvas.Item method) cpuTime (pyworkflow.protocol.protocol.Protocol property) create() (pwem.objects.data.EMSet class method) (pwem.objects.data.Transform class method) (pyworkflow.project.project.Project method) (scipion.install.funcs.CondaCommandDef method) (xmipp3.programs.ProgramDb method) CREATE_CLASSES (xmipp3.protocols.protocol_classify_pca.XmippProtClassifyPca attribute) (xmipp3.protocols.protocol_classify_pca_streaming.XmippProtClassifyPcaStreaming attribute) create_contents() (pyworkflow.gui.tooltip.ToolTip method) createAbsLink() (in module pyworkflow.utils.path) createActionToolbar() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) createAlignmentPlot() (in module pwem.protocols.protocol_align_movies) createAngDistributionSqlite() (pwem.viewers.viewer_base.EmProtocolViewer method) createAngularDistributionFile() (pwem.viewers.viewer_chimera.ChimeraAngDist method) createAttributesFile() (pwem.viewers.viewer_localres.ChimeraAttributeViewer method) createBgImage() (in module pyworkflow.gui.matplotlib_image) createBoolWidget() (pyworkflow.gui.form.ParamWidget static method) createCable() (pyworkflow.gui.canvas.Canvas method) createCanvas() (pyworkflow.gui.plotter.Plotter method) createChimeraOutput() (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes method) createChimeraScript() (pwem.viewers.viewer_localres.LocalResolutionViewer method) (xmipp3.protocols.protocol_volume_consensus.XmippProtVolConsensus method) (xmipp3.protocols.protocol_volume_strain.XmippProtVolumeStrain method) createCircularMask() (pwem.emlib.image.image_handler.ImageHandler method) createClassesFromImages() (in module xmipp3.convert.convert) createClassesFromImages2() (in module xmipp3.convert.convert) createCloseButton() (pyworkflow.gui.gui.Window method) createConf() (in module scipion.scripts.config) createContent() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) createCoordinateAxisFile() (pwem.viewers.viewer_chimera.Chimera class method) createCoordinatesStep() (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData method) createCopy() (pwem.objects.data.EMSet method) createDirectoryStep() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) createDiscardedStep() (xmipp3.protocols.protocol_particle_pick.XmippProtParticlePicking method) createEdge() (pyworkflow.gui.canvas.Canvas method) createEllipsoid() (xmipp3.protocols.protocol_resolution_directional.XmippProtMonoDir method) createEmptyImage() (pwem.emlib.image.image_handler.ImageHandler class method) createEmptyPoint() (xmipp3.utils.PathData method) createFilenameTemplates() (in module xmipp3.protocols.protocol_projmatch.projmatch_initialize) createFinalOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) createFromFile() (pwem.viewers.plotter.EmPlotter class method) createFSCObject() (pwem.viewers.viewer_fsc.FscViewer method) createGallery() (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery method) createHeaderFrame() (pyworkflow.gui.project.base.ProjectBaseWindow method) (pyworkflow.gui.project.project.ProjectWindow method) createHelp() (scipion.install.plugin_manager.PluginHelp method) createHistogram() (xmipp3.protocols.protocol_resolution_monogenic_signal.XmippProtMonoRes method) createHistrogram() (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes method) (xmipp3.protocols.protocol_resolution_directional.XmippProtMonoDir method) createHistrogramStep() (xmipp3.protocols.protocol_resolution_directional.XmippProtMonoDir method) createImage() (pwem.emlib.image.image_handler.ImageHandler method) createItemMatrix() (in module xmipp3.convert.convert) createIterDirsStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) createLink() (in module pyworkflow.utils.path) createMainMenu() (pyworkflow.gui.gui.Window method) createMANIFEST() (in module pyworkflow.apps.pw_sync_data) createMapper() (pyworkflow.project.project.Project method) createMaskFromFeatureFile() (xmipp3.protocols.protocol_preprocess.protocol_create_mask3d.XmippProtCreateMask3D method) createMaskFromGeometryStep() (xmipp3.protocols.protocol_preprocess.protocol_create_mask2d.XmippProtCreateMask2D method) (xmipp3.protocols.protocol_preprocess.protocol_create_mask3d.XmippProtCreateMask3D method) createMaskFromVolumeStep() (xmipp3.protocols.protocol_preprocess.protocol_create_mask3d.XmippProtCreateMask3D method) createMaskStep() (pwem.protocols.protocol_batch.ProtCreateMask method) (xmipp3.protocols.protocol_volume_local_sharpening.XmippProtLocSharp method) createMessageBody() (in module pyworkflow.gui.dialog) createMetadataImageStep() (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) createNewProject() (pyworkflow.gui.project.viewprojects.ProjectsView method) createNode() (pyworkflow.utils.graph.Graph method) createOutput() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) (pwem.protocols.protocol_projection_edit.ProtProjectionEditor method) (pwem.protocols.protocol_set_editor.ProtSetEditor method) (pwem.protocols.protocol_set_filter.ProtSetFilter method) (pwem.protocols.protocol_wait.ProtWait method) (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb method) (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery method) (xmipp3.protocols.protocol_helical_parameters.XmippProtHelicalParameters method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry method) createOutputAverages() (xmipp3.protocols.protocol_classify_pca.XmippProtClassifyPca method) createOutputClasses() (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyClasses method) createOutputs() (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase method) (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyClasses method) (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyParticles method) (xmipp3.protocols.protocol_mics_defocus_balancer.XmippProtMicDefocusSampler method) createOutputSetOfAverages() (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering method) createOutputSetOfClasses() (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering method) createOutputStep() (pwem.protocols.protocol_2d.ProtEvenClassify2D method) (pwem.protocols.protocol_align_movies.ProtAlignMovies method) (pwem.protocols.protocol_align_movies.ProtAverageFrames method) (pwem.protocols.protocol_alignment_assign.ProtAlignmentAssign method) (pwem.protocols.protocol_alignment_invertHand.ProtAlignmentInvertHand method) (pwem.protocols.protocol_batch.ProtCreateFSC method) (pwem.protocols.protocol_ctf_assign.ProtCTFAssign method) (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs method) (pwem.protocols.protocol_import.sequence.ProtImportSequence method) (pwem.protocols.protocol_import.volumes.ProtImportPdb method) (pwem.protocols.protocol_import.volumes.ProtImportSetOfAtomStructs method) (pwem.protocols.protocol_micrographs.ProtCTFMicrographs method) (pwem.protocols.protocol_movies.ProtMovieAssignGain method) (pwem.protocols.protocol_particles.ProtExtractParticles method) (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (pwem.protocols.protocol_particles_picking.ProtParticlePickingAuto method) (pwem.protocols.protocol_particles_picking.ProtPickingDifference method) (pwem.protocols.protocol_sets.ProtCrossSubSet method) (pwem.protocols.protocol_sets.ProtSplitSet method) (pwem.protocols.protocol_sets.ProtSubSet method) (pwem.protocols.protocol_sets.ProtSubSetByCoord method) (pwem.protocols.protocol_sets.ProtSubSetByMic method) (pwem.protocols.protocol_sets.ProtUnionSet method) (xmipp3.protocols.protocol_align_volume.XmippProtAlignVolume method) (xmipp3.protocols.protocol_align_volume_and_particles.XmippProtAlignVolumeParticles method) (xmipp3.protocols.protocol_analyze_local_ctf.XmippProtAnalyzeLocalCTF method) (xmipp3.protocols.protocol_apply_alignment.XmippProtApplyAlignment method) (xmipp3.protocols.protocol_apply_tilt_to_ctf.XmippProtApplyTiltToCtf method) (xmipp3.protocols.protocol_apply_transformation_matrix.XmippProtApplyTransformationMatrix method) (xmipp3.protocols.protocol_apply_zernike3d.XmippApplyZernike3D method) (xmipp3.protocols.protocol_assignment_tilt_pair.XmippProtAssignmentTiltPair method) (xmipp3.protocols.protocol_break_symmetry.XmippProtAngBreakSymmetry method) (xmipp3.protocols.protocol_center_particles.XmippProtCenterParticles method) (xmipp3.protocols.protocol_cl2d.XmippProtCL2D method) (xmipp3.protocols.protocol_cl2d_align.XmippProtCL2DAlign method) (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering method) (xmipp3.protocols.protocol_classify_pca.XmippProtClassifyPca method) (xmipp3.protocols.protocol_compare_angles.XmippProtCompareAngles method) (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) (xmipp3.protocols.protocol_consensus_local_ctf.XmippProtConsensusLocalCTF method) (xmipp3.protocols.protocol_core_analysis.XmippProtCoreAnalysis method) (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method) (xmipp3.protocols.protocol_ctf_correct_wiener2d.XmippProtCTFCorrectWiener2D method) (xmipp3.protocols.protocol_ctf_defocus_group.XmippProtCTFDefocusGroup method) (xmipp3.protocols.protocol_deep_center.XmippProtDeepCenter method) (xmipp3.protocols.protocol_deep_center_predict.XmippProtDeepCenterPredict method) (xmipp3.protocols.protocol_deep_hand.XmippProtDeepHand method) (xmipp3.protocols.protocol_denoise_particles.XmippProtDenoiseParticles method) (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase method) (xmipp3.protocols.protocol_enrich.XmippProtEnrich method) (xmipp3.protocols.protocol_extract_asymmetric_unit.XmippProtExtractUnit method) (xmipp3.protocols.protocol_extract_particles_movies.XmippProtExtractMovieParticles method) (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) (xmipp3.protocols.protocol_generate_reprojections.XmippProtGenerateReprojections method) (xmipp3.protocols.protocol_kerdensom.KendersomBaseClassify method) (xmipp3.protocols.protocol_local_ctf.XmippProtLocalCTF method) (xmipp3.protocols.protocol_mics_defocus_balancer.XmippProtMicDefocusSampler method) (xmipp3.protocols.protocol_ml2d.XmippProtML2D method) (xmipp3.protocols.protocol_movie_alignment_consensus.XmippProtConsensusMovieAlignment method) (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis method) (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) (xmipp3.protocols.protocol_movie_max_shift.XmippProtMovieMaxShift method) (xmipp3.protocols.protocol_movie_split_frames.XmippProtSplitFrames method) (xmipp3.protocols.protocol_multiple_fscs.XmippProtMultipleFSCs method) (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) (xmipp3.protocols.protocol_particle_pick.XmippProtParticlePicking method) (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking method) (xmipp3.protocols.protocol_phantom_create.XmippProtPhantom method) (xmipp3.protocols.protocol_pick_noise.XmippProtPickNoise method) (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc method) (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoiseParticles method) (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoiseVolumes method) (xmipp3.protocols.protocol_preprocess.protocol_create_mask2d.XmippProtCreateMask2D method) (xmipp3.protocols.protocol_preprocess.protocol_create_mask3d.XmippProtCreateMask3D method) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeParticles method) (xmipp3.protocols.protocol_preprocess.protocol_movie_resize.XmippProtMovieResize method) (xmipp3.protocols.protocol_preprocess.protocol_process.XmippProcessParticles method) (xmipp3.protocols.protocol_preprocess.protocol_process.XmippProcessVolumes method) (xmipp3.protocols.protocol_preprocess_micrographs.XmippProtPreprocessMicrographs method) (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) (xmipp3.protocols.protocol_random_conical_tilt.XmippProtRCT method) (xmipp3.protocols.protocol_ransac.XmippProtRansac method) (xmipp3.protocols.protocol_reconstruct_fourier.XmippProtReconstructFourier method) (xmipp3.protocols.protocol_reconstruct_significant.XmippProtReconstructSignificant method) (xmipp3.protocols.protocol_resolution3d.XmippProtResolution3D method) (xmipp3.protocols.protocol_resolution_bfactor.XmippProtbfactorResolution method) (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes method) (xmipp3.protocols.protocol_resolution_directional.XmippProtMonoDir method) (xmipp3.protocols.protocol_resolution_fso.XmippProtFSO method) (xmipp3.protocols.protocol_resolution_monogenic_signal.XmippProtMonoRes method) (xmipp3.protocols.protocol_rotate_volume.XmippProtRotateVolume method) (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) (xmipp3.protocols.protocol_screen_deeplearning.XmippProtScreenDeepLearning method) (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles method) (xmipp3.protocols.protocol_shift_particles.XmippProtShiftParticles method) (xmipp3.protocols.protocol_shift_volume.XmippProtShiftVolume method) (xmipp3.protocols.protocol_subtract_projection.XmippProtSubtractProjectionBase method) (xmipp3.protocols.protocol_tilt_analysis.XmippProtTiltAnalysis method) (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) (xmipp3.protocols.protocol_validate_nontilt.XmippProtValidateNonTilt method) (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolAdjBase method) (xmipp3.protocols.protocol_volume_consensus.XmippProtVolConsensus method) (xmipp3.protocols.protocol_volume_deform_zernike3d.XmippProtVolumeDeformZernike3D method) (xmipp3.protocols.protocol_volume_local_adjust.XmippProtLocalVolAdj method) (xmipp3.protocols.protocol_volume_local_sharpening.XmippProtLocSharp method) createPackageLink() (scipion.install.funcs.Link method) createParamPhantomFile() (in module xmipp3.convert.convert) createParticles() (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) createParticlesStep() (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData method) createPhantomsStep() (xmipp3.protocols.protocol_phantom_create.XmippProtPhantom method) createPlot2D() (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) createPreliminarOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) createProgramsAutocomplete() (in module xmipp3.programs) createProgramsDb() (in module xmipp3.programs) createProject() (pyworkflow.project.manager.Manager method) createProjectFromWorkflow() (in module scipion.scripts.kickoff) createProjectLabel() (pyworkflow.gui.project.viewprojects.ProjectsView method) createProjectList() (pyworkflow.gui.project.viewprojects.ProjectsView method) createRandomMicStep() (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData method) createRctImagesStep() (xmipp3.protocols.protocol_random_conical_tilt.XmippProtRCT method) createReferenceStep() (xmipp3.protocols.protocol_write_testP.XmippProtWriteTestP method) createReport() (pwem.protocols.protocol_pdf_report.ProtPDFReport method) createRepresentativeVolume() (in module xmipp3.protocols.protocol_compare_reprojections) createResultOutput() (pwem.protocols.protocol_mathematical_operator.ProtMathematicalOperator method) createResultsOutput() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) createRing() (pyworkflow.gui.matplotlib_image.PsdPreview method) createRoundedTextbox() (pyworkflow.gui.canvas.Canvas method) createRunItem() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) createRunsGraph() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) createRunsTree() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) createSetFromImages() (in module pwem.protocols.protocol_classes_selector) createSetFromRepresentative() (in module pwem.protocols.protocol_classes_selector) createSetObject() (pwem.protocols.protocol_batch.ProtUserSubSet method) createSetOfParticles() (in module xmipp3.protocols.protocol_compare_reprojections) createSetStep() (pwem.protocols.protocol_batch.ProtUserSubSet method) createSettings() (pyworkflow.project.project.Project method) createStep() (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData method) createSubPlot() (pyworkflow.gui.plotter.Plotter method) createSummaryStep() (xmipp3.protocols.protocol_resolution3d.XmippProtResolution3D method) createTables() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (xmipp3.programs.ProgramDb method) createTemplateFile() (in module scipion.scripts.kickoff) (pyworkflow.template.Template method) createTextbox() (pyworkflow.gui.canvas.Canvas method) createTextCircle() (pyworkflow.gui.canvas.Canvas method) createTiltedPairsStep() (pwem.protocols.protocol_tiltpairs.ProtImportMicrographsTiltPairs method) createUniqueFileName() (in module pyworkflow.utils.path) createVolumesSqlite() (pwem.viewers.viewer_base.EmProtocolViewer method) createWidgets() (pyworkflow.gui.text.TextFileViewer method) CREATION_COLUMN (pyworkflow.gui.form.ScalarTreeProvider attribute) (pyworkflow.gui.form.SubclassesTreeProvider attribute) CsvList (class in pyworkflow.object) ctfCritFitting (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) ctfCritMaxFreq (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) ctfDefocusAngle (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) ctfDefocusU (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) ctfDefocusV (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) CtfDialog (class in pwem.wizards.wizard) CtfDownsampleDialog (class in pwem.wizards.wizard) CTFModel (class in pwem.objects.data) ctfModelToRow() (in module xmipp3.convert.convert) ctfQ0 (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) ctfSphericalAberration (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) CtfView (class in pwem.viewers.views) ctfVoltage (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) CtfWizard (class in pwem.wizards.wizard) CUDA_BIN (pwem.Config attribute) CUDA_LIB (pwem.Config attribute) currentTable() (pyworkflow.utils.dataset.DataSet method) customizeheader() (pyworkflow.gui.project.base.ProjectBaseWindow method) (pyworkflow.gui.project.project.ProjectWindow method) customLoggingActive (pyworkflow.utils.log.LoggingConfigurator attribute) cyan (pyworkflow.constants.StrColors attribute) CYAN (pyworkflow.utils.properties.colorText attribute) cyan() (in module pyworkflow.utils.utils) (in module scipion.install.funcs) (in module scipion.scripts.config) cyanB() (in module pyworkflow.utils.utils) cyanStr() (in module pyworkflow.utils.utils) Cyclic (class in pwem.convert.symmetry)

D

DARKCYAN (pyworkflow.utils.properties.colorText attribute) Data (class in xmipp3.utils) DataSet (class in pyworkflow.tests.tests) (class in pyworkflow.utils.dataset) DataTextBox (class in pyworkflow.gui.project.viewdata) DataView (class in pwem.viewers.views) DataViewer (class in pwem.viewers.viewers_data) dateStr() (in module pyworkflow.utils.utils) datetime() (pyworkflow.object.String method) DATETIME_FORMAT (pyworkflow.object.String attribute) DB (pyworkflow.utils.properties.Icon attribute) DB_TIMEOUT (xmipp3.programs.ProgramDb attribute) DbTreeProvider (class in pyworkflow.gui.tree) DEBUG (pyworkflow.utils.properties.Icon attribute) debug() (pyworkflow.protocol.protocol.Protocol method) debugOn() (pyworkflow.config.Config static method) debugSQLOn() (pyworkflow.config.Config static method) DECIMAL (pyworkflow.config.VarTypes attribute) deepVolPostProStep() (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc method) DEFAULT (pyworkflow.utils.progressbar.ProgressBar attribute) DEFAULT_VERSION (scipion.install.funcs.InstallHelper attribute) DEFAULT_WIDTH (pyworkflow.utils.properties.Sprite attribute) defineBinaries() (pwem.Plugin class method) (pyworkflow.plugin.Plugin class method) (xmipp3.Plugin class method) defineBinariesMaxit() (pwem.Plugin class method) defineColorScaleParams() (pwem.wizards.wizard.ColorScaleWizardBase static method) defineParams() (xmipp3.protocols.protocol_preprocess.geometrical_mask.XmippGeometricalMask2D method) (xmipp3.protocols.protocol_preprocess.geometrical_mask.XmippGeometricalMask3D method) defineRelations() (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking method) (xmipp3.protocols.protocol_particle_pick_remove_duplicates.XmippProtPickingRemoveDuplicates method) defineStyle() (in module pyworkflow.gui.gui) defineTargets() (pwem.wizards.wizard.ColorScaleWizardBase class method) DEFOCUS_RATIO_ERROR_VALUE (pwem.objects.data.CTFModel attribute) DEFOCUS_V_MINIMUM_VALUE (pwem.objects.data.CTFModel attribute) DefocusGroup (class in pwem.objects.data) defocusGroupSetToRow() (in module xmipp3.convert.convert) deformationMatrix() (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) deformStep() (xmipp3.protocols.protocol_apply_zernike3d.XmippApplyZernike3D method) (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) (xmipp3.protocols.protocol_volume_deform_zernike3d.XmippProtVolumeDeformZernike3D method) delayStep() (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData method) (pwem.protocols.protocol_tests.ProtStress method) (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) DELETE (pyworkflow.mapper.sqlite.SqliteObjectsDb attribute) (pyworkflow.utils.properties.KEYSYM attribute) delete() (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) DELETE_OPERATION (pyworkflow.utils.properties.Icon attribute) DELETE_SEQUENCE (pyworkflow.mapper.sqlite.SqliteObjectsDb attribute) deleteAll() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) (pyworkflow.mapper.sqlite.SqliteObjectsDb method) deleteChildObjects() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) deleteChilds() (pyworkflow.mapper.sqlite.SqliteMapper method) deleteLabel() (pyworkflow.project.config.LabelsList method) deleteMissingObjectsByAncestor() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) deleteMoviesCoorStep() (pwem.protocols.protocol_movie_eraser.ProtMovieEraser method) deleteMoviesMicStep() (pwem.protocols.protocol_movie_eraser.ProtMovieEraser method) deleteMoviesStep() (pwem.protocols.protocol_movie_eraser.ProtMovieEraser method) deleteObject() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteObjectsDb method) deleteOperation() (scipion.install.plugin_manager.PluginBrowser method) deleteOutput() (pyworkflow.protocol.protocol.Protocol method) deleteProject() (pyworkflow.gui.project.viewprojects.ProjectsView method) (pyworkflow.project.manager.Manager method) deleteProperty() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method)

deleteProtocol() (pyworkflow.project.project.Project method) deleteProtocolOutput() (pyworkflow.project.project.Project method) deleteRelations() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) deleteRelationsByCreator() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) denoiseImages() (xmipp3.protocols.protocol_denoise_particles.XmippProtDenoiseParticles method) DeprecatedParam (class in pyworkflow.protocol.params) desiredDimensions() (pyworkflow.gui.gui.Window method) destroy() (pyworkflow.gui.dialog.Dialog method) Dialog (class in pyworkflow.gui.dialog) Dict (class in pyworkflow.object) DigFreqParam (class in pyworkflow.protocol.params) Dihedral (class in pwem.convert.symmetry) DIHEDRAL_SYM_NAME (pwem.protocols.protocol_projection_edit.ProtProjectionEditor attribute) directionalResolutionStep() (xmipp3.protocols.protocol_resolution_directional.XmippProtMonoDir method) disable() (scipion.install.plugin_manager.PluginTree method) DISCARDED (xmipp3.utils.Point attribute) disconnect() (pwem.wizards.wizards_3d.callbacks.DraggablePoint method) display() (pyworkflow.gui.form.ParamWidget method) DISPLAY_CHECKBOX (pyworkflow.protocol.params.BooleanParam attribute) DISPLAY_COMBO (pyworkflow.protocol.params.EnumParam attribute) DISPLAY_HLIST (pyworkflow.protocol.params.EnumParam attribute) DISPLAY_LIST (pyworkflow.protocol.params.EnumParam attribute) DISPLAY_YES_NO (pyworkflow.protocol.params.BooleanParam attribute) distanceBetweenCoorStep() (pwem.protocols.protocol_set_filter.ProtSetFilter method) distanceCenterStep() (pwem.protocols.protocol_set_filter.ProtSetFilter method) distances (xmipp3.protocols.protocol_classes_2d_mapping.XmippProtCL2DMap attribute) DOCS (pyworkflow.constants.DOCSITEURLS attribute) DOCSITEURLS (class in pyworkflow.constants) doesProtocolExists() (pyworkflow.project.project.Project method) doesRowExist() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteObjectsDb method) doGainProcess() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) doIteration000() (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) Domain (class in pwem) (class in pyworkflow.plugin) doRefresh() (pyworkflow.gui.text.OutputText method) doReport() (pyworkflow.tests.tests.GTestResult method) doShow2DPolar() (pwem.viewers.viewer_angular_dist.AngularDistributionViewer method) doShow3DPlot() (pwem.viewers.viewer_angular_dist.AngularDistributionViewer method) doShowHeatMap() (pwem.viewers.viewer_angular_dist.AngularDistributionViewer method) DOT (pyworkflow.utils.progressbar.ProgressBar attribute) doTraining() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) doWeightSSNR() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) downKeyPress() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.MaskRadiiPreviewDialog method) DOWNLOAD (pyworkflow.utils.properties.Icon attribute) download() (in module pyworkflow.apps.pw_sync_data) download_pdb_files() (pwem.convert.pdb_list.PDBList method) downloadPdb() (in module pwem.convert.utils) downloadSeqFromDatabase() (pwem.convert.sequence.SequenceHandler method) DownsampleDialog (class in pwem.wizards.wizard) downSampleStep() (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) DownsampleWizard (class in pwem.wizards.wizard) downsamplingPC() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) DraggablePoint (class in pwem.wizards.wizards_3d.callbacks) draw() (pyworkflow.gui.graph_layout.GraphLayout method) (pyworkflow.gui.graph_layout.LevelTreeLayout method) (pyworkflow.gui.plotter.Plotter method) drawCoordinates() (pwem.viewers.viewer_coordinates.MainWindow method) drawGraph() (pyworkflow.gui.canvas.Canvas method) drawRangeLines() (pwem.viewers.viewer_coordinates.MainWindow method) drawRunsGraph() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) dropColumns() (in module pwem.emlib.metadata.utils) dstMoved() (pyworkflow.gui.canvas.Cable method) DUMMY_ALPHABET (pwem.objects.data.Alphabet attribute) duplicatedIds() (pwem.protocols.protocol_sets.ProtUnionSet method)

E

echo() (in module pyworkflow.utils.echo) echo_class() (in module pyworkflow.utils.echo) echo_instancemethod() (in module pyworkflow.utils.echo) echo_module() (in module pyworkflow.utils.echo) Edge (class in pyworkflow.gui.canvas) editionListOfChains() (pwem.wizards.wizards.GetStructureChainsWizard method) (pwem.wizards.wizards.SelectChainWizard method) editionListOfResidues() (pwem.wizards.wizards.SelectResidueWizard method) EditLabelDialog (class in pyworkflow.gui.project.labels) editObject() (in module pyworkflow.gui.form) EditObjectDialog (class in pyworkflow.gui.dialog) EditVariableDialog (class in pyworkflow.gui.project.variables) ElementGroup (class in pyworkflow.protocol.params) eliminationStep() (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase method) EM_ROOT (pwem.Config attribute) EMANImageReader (class in pwem.emlib.image.image_readers) EMFile (class in pwem.objects.data) EMObject (class in pwem.objects.data) EmPlotter (class in pwem.viewers.plotter) EMProtocol (class in pwem.protocols.protocol) EmProtocolViewer (class in pwem.viewers.viewer_base) empty() (pyworkflow.object.String method) EMPTY_OLD_NAME (pyworkflow.project.config.Label attribute) EMSet (class in pwem.objects.data) EmWizard (class in pwem.wizards.wizard) enable() (scipion.install.plugin_manager.PluginTree method) enableAppend() (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.object.Set method) enabled (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) END (pyworkflow.utils.properties.colorText attribute) (pyworkflow.utils.utils.Environ attribute) ENDED (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) endPredictingStep() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) endProtocolStep() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) endStep() (pwem.protocols.parallel.ProtTestParallel method) endTrainingStep() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) enqueue() (pyworkflow.gui.gui.Window method) ENTER (pyworkflow.constants.TK attribute) enter() (pyworkflow.gui.tooltip.ToolTip method) entropyConsensus() (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) EntryDialog (class in pyworkflow.gui.dialog) EnumParam (class in pyworkflow.protocol.params) ENV_CREATED (scipion.install.funcs.CondaCommandDef attribute) Environ (class in pyworkflow.utils.utils) environAdd() (in module pyworkflow.utils.utils) Environment (class in scipion.install.funcs) envVarOn() (in module pyworkflow.utils.utils) EQUAL_PRECISION (pyworkflow.object.Float attribute) equalAttributes() (pwem.objects.data.CTFModel method) (pyworkflow.object.CsvList method) (pyworkflow.object.Float method) (pyworkflow.object.Object method) (pyworkflow.object.Scalar method) equalItemAttributes() (pyworkflow.object.Set method) eraserActivate() (pwem.viewers.viewer_coordinates.MainWindow method) ERROR (pyworkflow.utils.properties.Icon attribute) error() (pyworkflow.protocol.protocol.Protocol method) ERROR_DIMENSIONS (pyworkflow.utils.properties.Message attribute) ERROR_IMPORT_VOL (pyworkflow.utils.properties.Message attribute) ERROR_NO_EST_CTF (pyworkflow.utils.properties.Message attribute) ERROR_PATTERN_EMPTY (pyworkflow.utils.properties.Message attribute) ERROR_PATTERN_FILES (pyworkflow.utils.properties.Message attribute) ERROR_WEBGL (pyworkflow.utils.properties.Message attribute) errorList() (pyworkflow.viewer.Viewer method) errorMessage() (pyworkflow.viewer.Viewer method) ERRORS (pyworkflow.utils.properties.PluginStates attribute) errorWindow() (in module pwem.viewers.viewer_volumes) escapeStr() (in module xmipp3.programs) estimateCtfListStep() (pwem.protocols.protocol_micrographs.ProtCTFMicrographs method) estimateCtfStep() (pwem.protocols.protocol_micrographs.ProtCTFMicrographs method)

estimatedDatabase (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain attribute) estimateGainFun() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) estimateOrientationStep() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) estimatePoissonCount() (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis method) eulerAngles_to_2D() (in module pwem.viewers.plotter) eval() (xmipp3.utils.Point method) evalCondition() (pyworkflow.object.Object method) evalExpertLevel() (pyworkflow.protocol.protocol.Protocol method) evalParamCondition() (pyworkflow.protocol.params.Form method) (pyworkflow.protocol.protocol.Protocol method) evalParamExpertLevel() (pyworkflow.protocol.protocol.Protocol method) evaluate_callback() (pyworkflow.utils.utils.LazyDict method) evaluateClassesStep() (xmipp3.protocols.protocol_cl2d.XmippProtCL2D method) evaluateFormula() (pwem.wizards.wizard.FormulaDialog method) evaluateIndividuals() (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) evaluateReconstructions() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) evaluateResiduals() (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) evaluateSingleMicrograph() (xmipp3.protocols.protocol_ctf_micrographs.XmippProtCTFMicrographs method) evaluateVolumesStep() (xmipp3.protocols.protocol_ransac.XmippProtRansac method) evenOddCapable (pwem.protocols.protocol_align_movies.ProtAlignMovies attribute) EVENT (pyworkflow.utils.log.STATUS attribute) ExceptionDialog (class in pyworkflow.gui.dialog) execute() (pyworkflow.gui.form.FormWindow method) (scipion.install.funcs.Command method) (scipion.install.funcs.Environment method) (scipion.install.funcs.Target method) EXECUTE_PLUGINS_MANAGER_OPERATION (pyworkflow.utils.properties.Message attribute) executeCtfGroupsStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) executeProtocol() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) EXISTS (pyworkflow.mapper.sqlite.SqliteObjectsDb attribute) exists() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) existsLocation() (pwem.emlib.image.image_handler.ImageHandler class method) existsVariablePaths() (in module pyworkflow.utils.utils) expandPattern() (in module pyworkflow.utils.path) ExplanationText (class in pyworkflow.gui.widgets) exportAdditionalVolumeStep() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) exportAtomStructStep() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) exportFSCStep() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) exportImageStep() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) exportMasksStep() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) exportProtocols() (pyworkflow.project.project.Project method) exportSymmetryStep() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) exportToFile() (pwem.objects.data.Sequence method) (pwem.objects.data.SetOfSequences method) exportVolumeStep() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) EXPOSE_ITEMS (pwem.objects.data.SetOfAtomStructs attribute) (pwem.objects.data.SetOfVolumes attribute) (pwem.objects.data_flexhub.SetOfAtomStructFlex attribute) (pwem.objects.data_flexhub.SetOfVolumesFlex attribute) EXTENDED_ATTR (pyworkflow.object.Pointer attribute) EXTENDED_DNA_ALPHABET (pwem.objects.data.Alphabet attribute) EXTENDED_ITEMID (pyworkflow.object.Pointer attribute) EXTENDED_PROTEIN_ALPHABET (pwem.objects.data.Alphabet attribute) EXTRA_LABELS (pwem.viewers.views.CtfView attribute) (pwem.viewers.views.MicrographsView attribute) extractBalancedDefocus() (xmipp3.protocols.protocol_mics_defocus_balancer.XmippProtMicDefocusSampler method) extractChain() (pwem.convert.atom_struct.AtomicStructHandler method) extractCoordinates() (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) extractCoordsStep() (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) extractElements() (pwem.protocols.protocol_classes_selector.ProtClassesSelector method) extractImages() (pwem.viewers.viewer_coordinates.MainWindow method) EXTRACTING (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) extractMicrographListStep() (pwem.protocols.protocol_particles.ProtExtractParticles method) extractMicrographListStepOwn() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) extractMicrographStep() (pwem.protocols.protocol_particles.ProtExtractParticles method) extractParticles() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) extractParticlesStep() (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) extractRegion() (pwem.viewers.viewer_coordinates.MainWindow method) extractUnit() (xmipp3.protocols.protocol_extract_asymmetric_unit.XmippProtExtractUnit method)

F

factory() (pyworkflow.gui.browser.ShortCut static method) FAILURE (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) failure_item() (scipion.install.plugin_manager.PluginTree method) FAVORITE (pyworkflow.utils.properties.Icon attribute) fetch_emdb_map() (in module pwem.protocols.protocol_import.volumes) fetch_file() (in module pwem.protocols.protocol_import.volumes) fibonacci_sphere() (pwem.convert.trigonometry.FibonacciSphere static method) FibonacciSphere (class in pwem.convert.trigonometry) FigureFrame (class in pyworkflow.gui.matplotlib_image) filamentActivate() (pwem.viewers.viewer_coordinates.MainWindow method) FILE (pyworkflow.utils.properties.Icon attribute) FILE_COLUMN (pyworkflow.gui.browser.FileTreeProvider attribute) FILE_IMAGE (pyworkflow.utils.properties.Icon attribute) FILE_IMAGE_LINK (pyworkflow.utils.properties.Icon attribute) FILE_LINK (pyworkflow.utils.properties.Icon attribute) FILE_METADATA (pyworkflow.utils.properties.Icon attribute) FILE_METADATA_LINK (pyworkflow.utils.properties.Icon attribute) FILE_STACK (pyworkflow.utils.properties.Icon attribute) FILE_STACK_LINK (pyworkflow.utils.properties.Icon attribute) FILE_VOL (pyworkflow.utils.properties.Icon attribute) FileBrowser (class in pyworkflow.gui.browser) FileBrowserWindow (class in pyworkflow.gui.browser) fileDownloadStep() (pwem.protocols.protocol_import.sequence.ProtImportSequence method) FileHandler (class in pyworkflow.gui.browser) FileInfo (class in pyworkflow.gui.browser) fileKey() (pyworkflow.gui.browser.FileTreeProvider method) fileModified() (pwem.protocols.protocol_import.base.ProtImportFiles method) FILENAME (pyworkflow.config.VarTypes attribute) FILENAMENUMBERLENGTH (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch attribute) FileParam (class in pyworkflow.protocol.params) filesToCopy (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic attribute) FileTreeProvider (class in pyworkflow.gui.browser) fillAcquisition() (pwem.protocols.protocol_import.images.ProtImportImages method) fillClasses() (in module xmipp3.convert.convert) fillMessageText() (in module pyworkflow.gui.dialog) fillObjDict() (pyworkflow.object.Object static method) fillObject() (pyworkflow.mapper.sqlite.SqliteMapper method) fillObjectWithRow() (pyworkflow.mapper.sqlite.SqliteMapper method) fillOutput() (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method) (xmipp3.protocols.protocol_mics_defocus_balancer.XmippProtMicDefocusSampler method) (xmipp3.protocols.protocol_movie_alignment_consensus.XmippProtConsensusMovieAlignment method) fillToolBar() (pyworkflow.gui.project.steps.StepsWindow method) filter() (pyworkflow.utils.log.LevelFilter method) FilterParticlesWizard (class in pwem.wizards.wizard) filterPresentInputs() (pwem.wizards.wizard.VariableWizard method) filterStep() (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeParticles method) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeVolumes method) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippResizeHelper class method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterParticles method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterVolumes method) filterVolumeStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) (xmipp3.protocols.protocol_validate_nontilt.XmippProtValidateNonTilt method) FilterVolumesWizard (class in pwem.wizards.wizard) FilterWizard (class in pwem.wizards.wizard) FIND (pyworkflow.utils.properties.Icon attribute) find_prog() (in module pyworkflow.gui.text) findAttributeName() (pyworkflow.protocol.protocol.Protocol method) findClass() (pyworkflow.plugin.Domain class method) findClosestConnectors() (in module pyworkflow.gui.canvas) findClosestPoints() (in module pyworkflow.gui.canvas) findElbowsStep() (xmipp3.protocols.protocol_consensus_classes.XmippProtConsensusClasses method) findFile() (in module pyworkflow.utils.path) findFileRecursive() (in module pyworkflow.utils.path) findFolderWithPattern() (in module pwem) findPrevText() (pyworkflow.gui.text.TextFileViewer method) findResource() (in module pyworkflow.config) findRootFrom() (in module pyworkflow.utils.path) findRow() (in module xmipp3.base) findRowById() (in module xmipp3.base) findStrictClosestConnectors() (in module pyworkflow.gui.canvas) findSubClasses() (pyworkflow.plugin.Domain class method)

findText() (pyworkflow.gui.text.TextFileViewer method) findUpDownClosestConnectors() (in module pyworkflow.gui.canvas) findViewers() (pyworkflow.plugin.Domain class method) findWizards() (pyworkflow.plugin.Domain class method) fineSearch() (xmipp3.protocols.protocol_helical_parameters.XmippProtHelicalParameters method) (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry method) finish() (pyworkflow.utils.progressbar.ProgressBar method) finished (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis attribute) fixFile() (pwem.convert.headers.Ccp4Header class method) fixLinks() (pyworkflow.project.project.Project method) fixMRCVolume() (pwem.objects.data.Volume method) fixVolume() (in module pwem.convert.headers) fixVolumeFileName() (in module xmipp3.convert.convert) fixXmippVolumeFileName() (pwem.emlib.image.image_handler.ImageHandler class method) flag2Value() (in module scipion.scripts.kickoff) FlashMessage (class in pyworkflow.gui.dialog) FlexInfo (class in pwem.objects.data_flexhub) flip (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) flipStep() (xmipp3.protocols.protocol_deep_hand.XmippProtDeepHand method) flipYImage() (in module xmipp3.utils) Float (class in pyworkflow.object) FLOAT32_BYTES (pwem.emlib.image.image_readers.STKImageReader attribute) FloatingMessage (class in pyworkflow.gui.dialog) FloatParam (class in pyworkflow.protocol.params) FM_ADAPTIVE_SOFT (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_BAND_PASS (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_BAYESIAN (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_CENTRAL (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_CTF (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_DAUB12 (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_DAUB20 (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_DAUB4 (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_HIGH_PASS (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_LOW_PASS (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_MEDIAN (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_REMOVE_SCALE (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) FM_SOFT_THRESHOLDING (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper attribute) fmtDate() (pyworkflow.mapper.sqlite.SqliteFlatMapper static method) (pyworkflow.object.Set method) FN_PREFIX (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking attribute) (xmipp3.protocols.protocol_particle_pick_remove_duplicates.XmippProtPickingRemoveDuplicates attribute) fnMatching() (in module pwem.utils) FOLDER (pyworkflow.config.VarTypes attribute) (pyworkflow.utils.properties.Icon attribute) FOLDER_LINK (pyworkflow.utils.properties.Icon attribute) FOLDER_OPEN (pyworkflow.utils.properties.Icon attribute) FolderParam (class in pyworkflow.protocol.params) Font_wm (class in scipion.scripts.fontbrowser) Form (class in pyworkflow.protocol.params) Format (class in pyworkflow.protocol.params) format_args() (in module pyworkflow.utils.echo) formatExceptionInfo() (in module pyworkflow.utils.utils) FormElement (class in pyworkflow.protocol.params) FormulaDialog (class in pwem.wizards.wizard) formulaNeedsInput() (pwem.protocols.protocol_mathematical_operator.ProtMathematicalOperator method) formulaNeedsParam() (pwem.protocols.protocol_mathematical_operator.ProtMathematicalOperator method) formulaStep() (pwem.protocols.protocol_set_editor.ProtSetEditor method) (pwem.protocols.protocol_set_filter.ProtSetFilter method) FormWindow (class in pyworkflow.gui.form) FramesRange (class in pwem.objects.data) frameToRow() (in module xmipp3.convert.convert) freeGpusSlot() (pyworkflow.protocol.executor.ThreadStepExecutor method) fromCIFTommCIF() (in module pwem.convert.atom_struct) fromCIFToPDB() (in module pwem.convert.atom_struct) fromPDBToCIF() (in module pwem.convert.atom_struct) FS (pyworkflow.object.String attribute) FSC (class in pwem.objects.data) FscViewer (class in pwem.viewers.viewer_fsc) FSOestimationStep() (xmipp3.protocols.protocol_resolution_fso.XmippProtFSO method) FULL (pyworkflow.utils.progressbar.ProgressBar attribute) FunctionStep (class in pyworkflow.protocol.protocol) fusionStep() (xmipp3.protocols.protocol_volume_consensus.XmippProtVolConsensus method)

G

gatherResultsStep() (xmipp3.protocols.protocol_validate_overfitting.XmippProtValidateOverfitting method) gatherResultsStepCorr() (xmipp3.protocols.protocol_structure_map.XmippProtStructureMap method) (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) gatherResultsStepDef() (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) GAUSSIAN_NOISE (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoise attribute) GaussianFilterDialog (class in pwem.wizards.wizard) gaussianKernel() (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) GaussianParticlesWizard (class in pwem.wizards.wizard) GaussianVolumesWizard (class in pwem.wizards.wizard) GaussianWizard (class in pwem.wizards.wizard) GE (class in pyworkflow.protocol.params) generateColorLegend() (in module pwem.viewers.viewer_chimera) generateMask2Step() (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolSubtraction method) GenericDialog (class in pyworkflow.gui.dialog) genFromStrList() (pyworkflow.template.TemplateList method) genNotesHeading() (in module pyworkflow.config) genProjectName() (pyworkflow.template.Template method) GEOMETRY_BASECLASS (xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMaskParticles attribute) (xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMaskVolumes attribute) geometryFromMatrix() (in module xmipp3.convert.convert) (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) get() (pyworkflow.gui.form.BoolVar method) (pyworkflow.gui.form.ComboVar method) (pyworkflow.gui.form.MultiPointerVar method) (pyworkflow.gui.form.ParamWidget method) (pyworkflow.gui.form.PointerVar method) (pyworkflow.gui.form.ScalarWithPointerVar method) (pyworkflow.gui.form.SectionWidget method) (pyworkflow.gui.form.TextVar method) (pyworkflow.gui.widgets.LabelSlider method) (pyworkflow.object.CsvList method) (pyworkflow.object.Object method) (pyworkflow.object.Pointer method) (pyworkflow.object.Scalar method) (pyworkflow.project.config.Label method) (pyworkflow.project.config.NodeConfig method) get2foldAxis() (pwem.convert.symmetry.Icosahedron method) get3foldAxis() (pwem.convert.symmetry.Icosahedron method) get_all_entries() (pwem.convert.pdb_list.PDBList method) get_all_obsolete() (pwem.convert.pdb_list.PDBList method) get_parser() (in module pyworkflow.apps.pw_sync_data) get_recent_changes() (pwem.convert.pdb_list.PDBList method) get_sphere_params() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) get_status_list() (pwem.convert.pdb_list.PDBList static method) get_wh_templates() (in module pyworkflow.webservices.workflowhub) get_workflow_file_url() (in module pyworkflow.webservices.workflowhub) getAcquisition() (pwem.objects.data.Image method) (pwem.objects.data.SetOfImages method) (pwem.protocols.protocol_import.images.ProtImportImages method) getAction() (scipion.scripts.kickoff.KickoffWindow method) getActions() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) (pwem.protocols.protocol_import.images.ProtImportImages method) (pwem.protocols.protocol_tools.ProtManualCheckpoint method) getActionsFromSelection() (pyworkflow.gui.project.searchrun.RunsTreeProvider method) getActiveColor() (pyworkflow.config.Config class method) getActiveVersion() (pyworkflow.plugin.Plugin class method) getAddress() (pyworkflow.protocol.hosts.HostConfig method) getAlias() (pyworkflow.template.TemplateParam method) getAlignment() (pwem.objects.data.Movie method) (pwem.objects.data.SetOfImages method) getAlignmentMatrix() (xmipp3.protocols.protocol_align_volume_and_particles.XmippProtAlignVolumeParticles method) getAllCoordsInputMicrographs() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getAllSetsAttributes() (pwem.protocols.protocol_sets.ProtUnionSet method) getAlphabet() (pwem.objects.data.Sequence method) getAmplitudeContrast() (pwem.objects.data.Acquisition method) getAngles() (pwem.objects.data_tiltpairs.Angles method) (pwem.objects.data_tiltpairs.CoordinatesTiltPair method) (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry method) getAppsPath() (in module pyworkflow.config) getArchitecture() (in module pwem.viewers.showj) getArgs() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getArray() (pwem.emlib.image.image_readers.MRCImageReader class method) (pwem.emlib.image.image_readers.STKImageReader class method) getAtomStructObject() (pwem.viewers.viewer_localres.ChimeraAttributeViewer method) getAttr() (pwem.objects.data_flexhub.FlexInfo method) getAttributeName() (pyworkflow.protocol.params.RelationParam method) getAttributes() (pyworkflow.object.List method) (pyworkflow.object.Object method) (pyworkflow.object.Pointer method) getAttributes2Store() (pyworkflow.mapper.sqlite.SqliteFlatMapper method) getAttributesToStore() (pyworkflow.object.Object method) getAttributeValue() (pyworkflow.object.Object method) getAuthor() (scipion.install.plugin_funcs.PluginInfo method) getAutoSuffix() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) getAvailableExtensions() (pwem.emlib.image.image_readers.ImageReadersRegistry class method) getAvailablePalettes() (pwem.wizards.wizard.ColorScaleDialog method) getAvgSet() (pwem.objects.data.SetOfDefocusGroup method) getBaseName() (pwem.objects.data.Image method) getBestVolumesStep() (xmipp3.protocols.protocol_ransac.XmippProtRansac method) getBigFont() (in module pyworkflow.gui.gui) getBin() (scipion.install.funcs.Environment static method) getBindingsFolder() (pyworkflow.config.Config class method) getBinFolder() (scipion.install.funcs.Environment static method) getBinToPluginDict() (scipion.install.plugin_funcs.PluginRepository static method) getBinVersions() (scipion.install.plugin_funcs.PluginInfo method) getBlacklistedItems() (pwem.protocols.protocol_import.micrographs.ProtImportMicBase method) getBoolListFromValues() (in module pyworkflow.utils.utils) getBottomConnectorCoordinates() (pyworkflow.gui.canvas.Item method) getBoundingBox() (pwem.convert.atom_struct.AtomicStructHandler method) getBoxScale() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) (xmipp3.protocols.protocol_extract_particles_movies.XmippProtExtractMovieParticles method) (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) getBoxSize() (pwem.objects.data.SetOfCoordinates method) (pwem.objects.data_tiltpairs.CoordinatesTiltPair method) (xmipp3.convert.dataimport.XmippImport method) (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) getCancelCommand() (pyworkflow.protocol.hosts.HostConfig method) (pyworkflow.protocol.hosts.QueueSystemConfig method) getCanvas() (pyworkflow.gui.matplotlib_image.FigureFrame method) (pyworkflow.gui.plotter.Plotter method) getCCThreshold() (xmipp3.protocols.protocol_ransac.XmippProtRansac method) getCellDimensions() (pwem.convert.headers.Ccp4Header method) getCenter() (pyworkflow.gui.canvas.Item method) getCheckCommand() (pyworkflow.protocol.hosts.HostConfig method) (pyworkflow.protocol.hosts.QueueSystemConfig method) getChildren() (pyworkflow.utils.graph.Node method) getChimeraError() (in module pwem.viewers.viewer_localres) getCifKeyName() (in module pwem.viewers.viewer_localres) getCitations() (pyworkflow.protocol.protocol.Protocol method) getClass() (pyworkflow.object.Object method) (pyworkflow.protocol.params.Form method) getClassDomain() (pyworkflow.protocol.protocol.LegacyProtocol class method) (pyworkflow.protocol.protocol.Protocol class method) getClassId() (pwem.objects.data.Particle method) (pwem.objects.data.Volume method) getClassLabel() (pyworkflow.protocol.protocol.Protocol class method) getClassName() (pyworkflow.object.Object class method) getClassNameStr() (pwem.objects.data.SetOfImages method) (pwem.objects.data.SetOfParticles method) getClassPackage() (pyworkflow.protocol.protocol.Protocol class method) getClassPackageName() (pyworkflow.protocol.protocol.Protocol class method) getClassPlugin() (pyworkflow.protocol.protocol.Protocol class method) getClassRows() (pyworkflow.mapper.sqlite.SqliteFlatDb method) getCloneCommand() (scipion.install.funcs.InstallHelper method) getClusterImagesPlot() (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering method) getClusterPlot() (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering method) getCmdPath() (in module pwem.utils) getCollectivity() (pwem.objects.data.NormalMode method) getColor() (pyworkflow.project.config.Label method) getColorBar() (pyworkflow.gui.plotter.Plotter method) getColorMap() (pwem.viewers.viewer_angular_dist.AngularDistributionViewer method) getColorMode() (pyworkflow.project.config.ProjectSettings method) getColorPalette() (pwem.wizards.wizard.ColorScaleDialog method) getColors() (pwem.viewers.viewer_localres.ChimeraAttributeViewer method) getColorStr() (in module pyworkflow.utils.utils) getColumn() (pyworkflow.utils.dataset.Table method) getColumnKeyByColumnName() (pyworkflow.gui.tree.BoundTree method) getColumnKeys() (pyworkflow.gui.dialog.SearchBaseWindow method) getColumnProperty() (pwem.viewers.showj.ColumnsConfig method) getColumns() (pyworkflow.gui.form.MultiPointerTreeProvider method) (pyworkflow.gui.form.ProtocolClassTreeProvider method) (pyworkflow.gui.form.ScalarTreeProvider method) (pyworkflow.gui.form.SubclassesTreeProvider method) (pyworkflow.gui.project.labels.LabelsTreeProvider method) (pyworkflow.gui.project.variables.VariablesTreeProvider method) (pyworkflow.gui.project.viewprotocols_extra.RunIOTreeProvider static method) (pyworkflow.gui.tree.ProjectRunsTreeProvider method) (pyworkflow.gui.tree.TreeProvider method) (pyworkflow.utils.dataset.Table method) getColumnType() (pwem.viewers.showj.ColumnProperties method) getColumnValues() (pyworkflow.utils.dataset.Table method) getCommandList() (scipion.install.funcs.InstallHelper method) getCommands() (scipion.install.funcs.CommandDef method) (scipion.install.funcs.Target method) getComment() (pyworkflow.gui.dialog.EditObjectDialog method) (pyworkflow.project.project.Project method) getCompatibilityDict() (pyworkflow.object.Set class method) getCompatibleExtensions() (pwem.emlib.image.image_readers.EMANImageReader static method) (pwem.emlib.image.image_readers.ImageReader static method) (pwem.emlib.image.image_readers.MRCImageReader static method) (pwem.emlib.image.image_readers.PILImageReader static method) (pwem.emlib.image.image_readers.STKImageReader class method) (pwem.emlib.image.image_readers.TiffImageReader static method) (pwem.emlib.image.image_readers.XMIPPImageReader static method) getCompatiblePipReleases() (scipion.install.plugin_funcs.PluginInfo method) getCondaActivationCmd() (pyworkflow.plugin.Plugin class method) getCondaEnv() (xmipp3.base.XmippProtocol class method) getCondaEnvCommand() (scipion.install.funcs.InstallHelper method) getConfig() (pwem.viewers.viewers_data.RegistryViewerConfig class method) getConfigPathFromConfigFile() (in module scipion.scripts.config) getConfigVariable() (in module scipion.scripts.config) getConnectors() (in module pyworkflow.gui.canvas) getConnectorsCoordinates() (pyworkflow.gui.canvas.Item method) getConsensusRadius() (xmipp3.protocols.protocol_particle_pick_remove_duplicates.XmippProtPickingRemoveDuplicates method) getContent() (pyworkflow.template.Template method) getConvertedInput() (xmipp3.base.XmippProtocol method) getCoordinate() (pwem.objects.data.Particle method) getCoordinates() (pwem.objects.data.SetOfParticles method) (pyworkflow.gui.canvas.Canvas method) getCoordinatesOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getCoords() (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) (xmipp3.protocols.protocol_extract_particles_movies.XmippProtExtractMovieParticles method) (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) (xmipp3.protocols.protocol_particle_pick_pairs.XmippProtParticlePickingPairs method) getCoordSampling() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) (xmipp3.protocols.protocol_extract_particles_movies.XmippProtExtractMovieParticles method) (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) getCoordsDir() (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (xmipp3.protocols.protocol_particle_pick.XmippProtParticlePicking method) (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) getCoordsPair() (pwem.objects.data_tiltpairs.ParticlesTiltPair method) getCoordsTiltPair() (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) getCopyOrLink() (pwem.protocols.protocol_import.base.ProtImportFiles method) (pwem.protocols.protocol_import.micrographs.ProtImportMovies method) getCorners() (pyworkflow.gui.canvas.Item method) getCorrThreshStep() (xmipp3.protocols.protocol_ransac.XmippProtRansac method) getCreationTime() (pyworkflow.project.config.ProjectSettings method) (pyworkflow.project.manager.ProjectInfo method) (pyworkflow.project.project.Project method) getCTF() (pwem.objects.data.Image method) getCtfParamsDict() (pwem.protocols.protocol_micrographs.ProtCTFMicrographs method) getCTFViews() (xmipp3.viewers.viewer.XmippViewer method) getCurrentDir() (pyworkflow.gui.browser.FileBrowser method) (pyworkflow.gui.browser.FileBrowserWindow method) getCurrentProtocolView() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) getDark() (pwem.objects.data.SetOfMovies method) (pwem.protocols.protocol_import.micrographs.ProtImportMovies method) getData() (pwem.objects.data.FSC method) (xmipp3.utils.Point method) getDataSet() (pyworkflow.tests.tests.DataSet class method) getDataToRender() (pyworkflow.utils.dataset.Table method) getDataToRenderAndExtra() (pyworkflow.utils.dataset.Table method) getDataType() (pwem.emlib.image.image_handler.ImageHandler method) (pwem.objects.data.Image method) getDate() (pyworkflow.gui.browser.FileInfo method) getDateStr() (pyworkflow.gui.browser.FileInfo method) getDatetime() (pyworkflow.object.String class method) getDbLastModificationDate() (pyworkflow.project.project.Project method) getDbName() (pyworkflow.mapper.sqlite_db.SqliteDb method) (pyworkflow.project.project.Project class method) getDbPath() (pyworkflow.project.project.Project method) (pyworkflow.protocol.protocol.Protocol method) getDefault() (pyworkflow.protocol.params.Param method) (pyworkflow.utils.dataset.Column method) getDefaultBoxSize() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs method) getDefaultFont() (in module pyworkflow.gui.gui) getDefaultRunName() (pyworkflow.protocol.protocol.Protocol method) getDefaults() (pyworkflow.gui.text.OutputText method) (pyworkflow.gui.text.TaggedText method) (pyworkflow.gui.text.Text method) getDefaultSummary() (pwem.protocols.protocol_batch.ProtUserSubSet method) getDefinition() (pyworkflow.protocol.protocol.Protocol method) getDefinitionDict() (pyworkflow.protocol.protocol.Protocol method) getDefocus() (pwem.objects.data.CTFModel method) getDefocusAngle() (pwem.objects.data.CTFModel method) getDefocusAvg() (pwem.objects.data.DefocusGroup method) (pwem.objects.data.SetOfDefocusGroups method) getDefocusMax() (pwem.objects.data.DefocusGroup method) (pwem.objects.data.SetOfDefocusGroups method) getDefocusMin() (pwem.objects.data.DefocusGroup method) getDefocusRatio() (pwem.objects.data.CTFModel method) getDefocusU() (pwem.objects.data.CTFModel method) getDefocusV() (pwem.objects.data.CTFModel method) getDeps() (scipion.install.funcs.Target method) getDescription() (pwem.objects.data.Sequence method) (pyworkflow.template.LocalTemplate static method) getDim() (pwem.objects.data.Image method) (pwem.objects.data.Movie method) (pwem.objects.data.SetOfImages method) (pwem.objects.data.Volume method) getDimensions() (pwem.emlib.image.image_handler.ImageHandler class method) (pwem.emlib.image.image_readers.EMANImageReader static method) (pwem.emlib.image.image_readers.ImageReader static method) (pwem.emlib.image.image_readers.MRCImageReader static method) (pwem.emlib.image.image_readers.PILImageReader static method) (pwem.emlib.image.image_readers.STKImageReader static method) (pwem.emlib.image.image_readers.TiffImageReader static method) (pwem.emlib.image.image_readers.XMIPPImageReader static method) (pwem.objects.data.Image method) (pwem.objects.data.SetOfClasses method) (pwem.objects.data.SetOfImages method) (pyworkflow.gui.canvas.Item method) (pyworkflow.gui.canvas.RoundedTextBox method) getDims() (pwem.convert.headers.Ccp4Header method) getDir() (pyworkflow.gui.browser.FileTreeProvider method) getDirection() (pyworkflow.protocol.params.RelationParam method) getDirName() (scipion.install.plugin_funcs.PluginInfo method) getDiscardedSize() (xmipp3.utils.Data method) getDistro() (pyworkflow.utils.utils.OS class method) getDoc() (pyworkflow.object.Object class method) getDomain() (pyworkflow.config.Config class method) (pyworkflow.project.project.Project method) getDoneMics() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) getDoseDiffPlot() (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis method) getDoseInitial() (pwem.objects.data.Acquisition method) getDosePerFrame() (pwem.objects.data.Acquisition method) getDosePlot() (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis method) getDownsample() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.CtfDownsampleDialog method) (pwem.wizards.wizard.DownsampleDialog method) getEdges() (pwem.convert.symmetry.Icosahedron method) getElapsedTime() (pyworkflow.project.project.Project method) (pyworkflow.protocol.protocol.Step method) (pyworkflow.utils.utils.Timer method) getEm() (scipion.install.funcs.Environment static method) getEmFolder() (scipion.install.funcs.Environment static method) getEntryFromWebservice() (pyworkflow.webservices.notifier.ProjectWorkflowNotifier method) getEntryValue() (pyworkflow.gui.browser.FileBrowser method) (pyworkflow.gui.browser.FileBrowserWindow method) getEnumText() (pyworkflow.protocol.protocol.Protocol method) getEnviron() (in module pwem.convert.atom_struct) (pwem.viewers.viewer_chimera.Chimera class method) (pwem.viewers.viewer_chimera.ChimeraOldView method) (pwem.viewers.viewer_chimera.ChimeraView method) (pwem.viewers.viewer_vmd.Vmd class method) (pyworkflow.plugin.Plugin class method) (xmipp3.Plugin class method) getEnvVariable() (in module pyworkflow.utils.utils) getError() (pyworkflow.protocol.protocol.Step method) getErrorMessage() (pyworkflow.protocol.protocol.Step method) getEstimatedGainPath() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getEulerAngles() (pwem.objects.data.Transform method) getEven() (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) getExt() (in module pyworkflow.utils.path) getExtended() (pyworkflow.object.Pointer method) getExtendedParts() (pyworkflow.object.Pointer method) getExternalJsonTemplates() (in module scipion.utils) (pyworkflow.config.Config class method) getExtractedMicFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getExtraFile() (scipion.install.funcs.InstallHelper method) getExtraFiles() (scipion.install.funcs.InstallHelper method) getExtraLogInfo() (in module pyworkflow.utils.log) getFigure() (pyworkflow.gui.matplotlib_image.FigureFrame method) (pyworkflow.gui.plotter.Plotter method) getFile() (pyworkflow.tests.tests.DataSet method) getFileActions() (pwem.viewers.filehandlers.ChimeraHandler method) (pwem.viewers.filehandlers.ImageFileHandler method) (pwem.viewers.filehandlers.ImajeJFileHandler method) (pyworkflow.gui.browser.FileHandler method) getFileDict() (scipion.install.funcs.InstallHelper method) getFileFormat() (in module pwem.convert.headers) getFileHandlers() (pyworkflow.gui.browser.FileTreeProvider method) getFileIcon() (pwem.viewers.filehandlers.ChimeraHandler method) (pwem.viewers.filehandlers.ImajeJFileHandler method) (pwem.viewers.filehandlers.MdFileHandler method) (pwem.viewers.filehandlers.ParticleFileHandler method) (pwem.viewers.filehandlers.StackHandler method) (pwem.viewers.filehandlers.VolFileHandler method) (pyworkflow.gui.browser.FileHandler method) (pyworkflow.gui.browser.SqlFileHandler method) (pyworkflow.gui.browser.TextFileHandler method) getFileLastModificationDate() (in module pyworkflow.utils.path) getFileList() (pyworkflow.viewer.TextView method) getFileName() (pwem.objects.data.EMFile method) (pwem.objects.data.Image method) (pyworkflow.gui.browser.FileInfo method) (pyworkflow.object.Set method) getFileNameNoisyStk() (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoiseParticles method) getFileNamesList() (pwem.protocols.protocol_import.images.ProtImportImages method) getFilePreview() (pwem.viewers.filehandlers.ImageFileHandler method) (pwem.viewers.filehandlers.MdFileHandler method) (pyworkflow.gui.browser.FileHandler method) getFiles() (in module pyworkflow.utils.path) (pwem.objects.data.EMObject method) (pwem.objects.data.EMSet method) (pwem.objects.data.Image method) (pwem.objects.data.SetOfAtomStructs method) (pwem.objects.data.SetOfClasses method) (pwem.objects.data.SetOfCoordinates method) (pwem.objects.data.SetOfImages method) (pwem.objects.data_tiltpairs.CoordinatesTiltPair method) (pwem.objects.data_tiltpairs.ParticlesTiltPair method) (pwem.objects.data_tiltpairs.TiltPairSet method) (pwem.protocols.protocol_import.images.ProtImportImages method) (pwem.protocols.protocol_tiltpairs.ProtImportMicrographsTiltPairs method) (pyworkflow.object.Set method) (pyworkflow.protocol.protocol.Protocol method) getFileSize() (in module pyworkflow.utils.path) getFileTag() (pyworkflow.protocol.protocol.Protocol method) getFinalCorrectionImagePath() (pwem.protocols.protocol_movies.ProtProcessMovies method) getFinalGainPath() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getFinalProjId() (in module pyworkflow.utils.log) getFinalProtId() (in module pyworkflow.utils.log) getFirst() (pyworkflow.gui.tree.Tree method) (pyworkflow.utils.utils.Environ method) getFirstFrame() (pwem.objects.data.FramesRange method) getFirstFrameIndex() (pwem.objects.data.FramesRange method) getFirstItem() (pwem.objects.data.SetOfClasses method) (pwem.wizards.wizards.SelectAttributeWizard method) (pyworkflow.object.Set method) getFirstLine() (in module pyworkflow.apps.pw_protocol_list) (in module scipion.install.inspect_plugins) getFirstRow() (in module pwem.emlib.metadata.utils) getFitQuality() (pwem.objects.data.CTFModel method) getFlagArg() (in module scipion.scripts.kickoff) getFlexInfo() (pwem.objects.data_flexhub.AtomStructFlex method) (pwem.objects.data_flexhub.ParticleFlex method) (pwem.objects.data_flexhub.SetOfAtomStructFlex method) (pwem.objects.data_flexhub.SetOfParticlesFlex method) (pwem.objects.data_flexhub.SetOfVolumesFlex method) (pwem.objects.data_flexhub.VolumeFlex method) getFlippedOrientedGainPath() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getFloatListFromValues() (in module pyworkflow.utils.utils) getFnPath() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) (pwem.protocols.protocol_origin_sampling_volume.ProtOrigSampling method) getFontScaleFactor() (pyworkflow.gui.graph_layout.GraphLayout method) getFormat() (pwem.objects.data.Image method) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) (pwem.protocols.protocol_import.ctfs.ProtImportCTF method) getFormula() (pwem.wizards.wizard.FormulaDialog method) getFrameId() (pwem.objects.data.MovieParticle method) getFramesRange() (pwem.objects.data.Movie method) (pwem.objects.data.SetOfMovies method) getFreeGpuSlot() (pyworkflow.protocol.executor.ThreadStepExecutor method) getFreePort() (in module pyworkflow.utils.utils) getFreq() (pwem.wizards.wizard.CtfDialog static method) getFreqDecay() (pwem.wizards.wizard.BandPassFilterDialog method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper class method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterParticles method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterVolumes method) getFreqSigma() (pwem.wizards.wizard.GaussianFilterDialog method) getFscqAttrDic() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) getFSCQFile() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) getFullID() (pwem.convert.atom_struct.AtomicStructHandler method) getFullName() (pyworkflow.mapper.mapper.Mapper method) getGain() (pwem.objects.data.SetOfMovies method) (pwem.protocols.protocol_import.micrographs.ProtImportMovies method) getGainAndDark() (pwem.protocols.protocol_movies.ProtProcessMovies method) getGainOrDark() (pwem.protocols.protocol_import.micrographs.ProtImportMovies method) getGeometry() (in module pyworkflow.gui.gui) getGPUArgs() (xmipp3.protocols.protocol_flexalign.XmippProtFlexAlign method) getGpuList() (pyworkflow.protocol.executor.StepExecutor method) (pyworkflow.protocol.executor.ThreadStepExecutor method) (pyworkflow.protocol.protocol.Protocol method) getGraphFromRuns() (pyworkflow.project.project.Project method) getGridSampling() (pwem.convert.headers.Ccp4Header method) getGroupByCTF() (pwem.objects.data.SetOfDefocusGroups method) getGroupByName() (pwem.objects.data.SetOfDefocusGroups method) getHalfMaps() (pwem.objects.data.Volume method) getHeader() (pwem.convert.headers.Ccp4Header method) getHelp() (pyworkflow.protocol.params.FormElement method) getHelpText() (pyworkflow.protocol.protocol.Protocol class method) getHexColorList() (in module pyworkflow.gui.plotter) getHighest() (pwem.wizards.wizard.ColorScaleDialog method) getHighFreq() (pwem.wizards.wizard.BandPassFilterDialog method) (pwem.wizards.wizard.CtfDialog method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper class method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterParticles method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterVolumes method) getHome() (pwem.viewers.viewer_chimera.Chimera class method) (pyworkflow.plugin.Plugin class method) getHomePage() (scipion.install.plugin_funcs.PluginInfo method) getHomePath() (in module pyworkflow.utils.path) getHostConfig() (pyworkflow.project.project.Project method) (pyworkflow.protocol.protocol.Protocol method) getHostFullName() (in module pyworkflow.utils.utils) (pyworkflow.protocol.protocol.Protocol method) getHostName() (in module pyworkflow.utils.utils) (pyworkflow.protocol.hosts.HostConfig method) (pyworkflow.protocol.protocol.Protocol method) getHostNames() (pyworkflow.project.project.Project method) getHostPath() (pyworkflow.protocol.hosts.HostConfig method) getHScroll() (pyworkflow.gui.widgets.Scrollable method) getId() (pwem.objects.data.Sequence method) (pyworkflow.project.config.NodeConfig method) (xmipp3.utils.Point method) getIdColumn() (pyworkflow.utils.dataset.Table method) getIdSet() (pyworkflow.object.Set method) getImage() (in module pyworkflow.gui.gui) (pwem.emlib.image.image_readers.ImageStack method) (pwem.objects.data.Image method) (pyworkflow.gui.canvas.Canvas method) (pyworkflow.gui.dialog.Dialog method) (pyworkflow.gui.gui.Window method) (pyworkflow.gui.tree.Tree method) (pyworkflow.utils.properties.Sprite class method) getImageFromPath() (in module pwem.viewers.filehandlers) getImageLocation() (in module xmipp3.convert.convert) getImagePath() (pwem.viewers.views.ImageView method) getImages() (pwem.emlib.image.image_readers.ImageStack method) (pwem.objects.data.SetOfClasses method) getImagesClass() (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) getImagesPointer() (pwem.objects.data.SetOfClasses method) getImagesType() (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) getImgData() (pwem.viewers.viewer_localres.LocalResolutionViewer method) getImportClass() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs method) (pwem.protocols.protocol_import.ctfs.ProtImportCTF method) (pwem.protocols.protocol_import.micrographs.ProtImportMicrographs method) (pwem.protocols.protocol_import.particles.ProtImportParticles method) getImportFrom() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) getIncludeFolder() (scipion.install.funcs.Environment static method) getIndex() (pwem.objects.data.Image method) (pyworkflow.gui.text.TextFileViewer method) (pyworkflow.gui.widgets.ComboBox method) (pyworkflow.protocol.protocol.Step method) (pyworkflow.template.TemplateParam method) getIndexFromValue() (pyworkflow.utils.dataset.Table method) getInitialSleepTime() (pyworkflow.apps.pw_schedule_run.RunScheduler method) getInpCoordsFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getInput() (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase method) (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyClasses method) (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyParticles method) getInputAttributes() (pwem.wizards.wizards.SelectAttributeWizard method) getInputConnectorCoordinates() (pyworkflow.gui.canvas.Item method) getInputGain() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getInputMicrographs() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs method) (pwem.protocols.protocol_micrographs.ProtCTFMicrographs method) (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (pwem.protocols.protocol_particles_picking.ProtPickingDifference method) (xmipp3.protocols.protocol_ctf_micrographs.XmippProtCTFMicrographs method) (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) (xmipp3.protocols.protocol_particle_pick_pairs.XmippProtParticlePickingPairs method) (xmipp3.protocols.protocol_pick_noise.XmippProtPickNoise method) (xmipp3.protocols.protocol_tilt_analysis.XmippProtTiltAnalysis method) getInputMicrographsPointer() (pwem.protocols.protocol_micrographs.ProtCTFMicrographs method) (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) (xmipp3.protocols.protocol_pick_noise.XmippProtPickNoise method) getInputMicsFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getInputOutput() (pwem.wizards.wizard.VariableWizard method) getInputParticles() (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) getInputSampling() (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterParticles method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterVolumes method) getInputSet() (pwem.wizards.wizards.SelectAttributeWizard method) getInputStatus() (pyworkflow.protocol.protocol.Protocol method) getInputStruct() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) getInputStructCIF() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) getInputStructFile() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) getInstallenv() (scipion.install.plugin_funcs.PluginInfo method) getInstallPath() (in module scipion.utils) getInstance() (pyworkflow.mapper.sqlite.SqliteFlatMapper method) getInstancesCount() (in module pyworkflow.utils.profiler) getIntervals() (pwem.wizards.wizard.ColorScaleDialog method) getIsAminoacids() (pwem.objects.data.Sequence method) getISPG() (pwem.convert.headers.Ccp4Header method) getIsSubparticles() (pwem.objects.data.SetOfParticles method) getItem() (pwem.wizards.wizard.FormulaDialog method) (pyworkflow.object.Set method) getItemClass() (xmipp3.base.XmippSet method) getItemsToBlacklistFromFile() (pwem.protocols.protocol_import.micrographs.ProtImportMicBase method) getIterTmpVolume() (xmipp3.protocols.protocol_reconstruct_significant.XmippProtReconstructSignificant method) getIterVolume() (xmipp3.protocols.protocol_reconstruct_significant.XmippProtReconstructSignificant method) getJavaBin() (in module pwem.viewers.showj) getJavaIJappArguments() (in module pwem.viewers.showj) getJavaVersion() (in module pwem.viewers.showj) getJobDoneRegex() (pyworkflow.protocol.hosts.HostConfig method) getJobIds() (pyworkflow.protocol.protocol.Protocol method) getJvmMaxMemory() (in module pwem.viewers.showj) getKeyPressed() (pyworkflow.viewer.Viewer method) getLabel() (in module pwem.emlib.metadata.utils) (pwem.viewers.showj.ColumnProperties method) (pyworkflow.gui.dialog.EditObjectDialog method) (pyworkflow.project.config.LabelsList method) (pyworkflow.protocol.hosts.HostConfig method) (pyworkflow.protocol.params.FormElement method) (pyworkflow.utils.dataset.Column method) (pyworkflow.utils.graph.Node method) getLabelPythonType() (in module xmipp3.base) getLabels() (pyworkflow.project.config.NodeConfig method) (pyworkflow.project.config.ProjectSettings method) getLastFile() (in module pyworkflow.utils.path) getLastFinishedIter() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) getLastFrame() (pwem.objects.data.FramesRange method) getLastIter() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) getLastIteration() (xmipp3.protocols.protocol_reconstruct_significant.XmippProtReconstructSignificant method) getLastName() (pyworkflow.object.Object method) getLastSelection() (pyworkflow.gui.browser.FileBrowserWindow method) getLastSubPlot() (pyworkflow.gui.plotter.Plotter method) getLatestRelease() (scipion.install.plugin_funcs.PluginInfo method) getLeftConnectorCoordinates() (pyworkflow.gui.canvas.Item method) getLeftTime() (pyworkflow.project.project.Project method) getLib() (scipion.install.funcs.Environment method) getLibFolder() (pyworkflow.config.Config class method) (scipion.install.funcs.Environment static method) getLibSuffix() (scipion.install.funcs.Environment method) getLifeTime() (pyworkflow.project.config.ProjectSettings method) getLimitIntervals() (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis method) getLineInFile() (in module pyworkflow.utils.utils) getListFromRange() (pyworkflow.object.String method) getListFromRangeString() (in module pyworkflow.utils.utils) getListFromValues() (in module pyworkflow.utils.utils) (pyworkflow.object.String method) getLocalConfigHosts() (pyworkflow.project.project.Project method) getLocalHostName() (in module pyworkflow.utils.utils) getLocalUserName() (in module pyworkflow.utils.utils) getLocation() (pwem.objects.data.Image method) getLogFolder() (scipion.install.funcs.Environment static method) getLogPath() (pyworkflow.project.project.Project method) getLogPaths() (pyworkflow.protocol.protocol.Protocol method) getLogsAsStrings() (pyworkflow.protocol.protocol.Protocol method) getLogsFolder() (pyworkflow.config.Config class method) getLogsLastLines() (pyworkflow.protocol.protocol.Protocol method) getLowest() (pwem.wizards.wizard.ColorScaleDialog method) getLowFreq() (pwem.wizards.wizard.BandPassFilterDialog method) (pwem.wizards.wizard.CtfDialog method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper class method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterParticles method) (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterVolumes method) getMagnification() (pwem.objects.data.Acquisition method) getMainInput() (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking method) (xmipp3.protocols.protocol_particle_pick_remove_duplicates.XmippProtPickingRemoveDuplicates method) getMainSetField() (pwem.protocols.protocol_sets.ProtCrossSubSet method) getMandatory() (pyworkflow.protocol.hosts.QueueSystemConfig method) getMappedDict() (pyworkflow.object.Object method) getMapper() (pyworkflow.protocol.protocol.Protocol method) getMapperDict() (pyworkflow.plugin.Domain class method) getMatchFiles() (pwem.protocols.protocol_import.base.ProtImportFiles method) getMatchingCoord() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs method) getMatchingFiles() (in module pwem.utils) getMatchingMic() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) getMatlabEnviron() (xmipp3.Plugin class method) getMatrix() (pwem.objects.data.Matrix method) (pwem.objects.data.Transform method) getMatrixAsList() (pwem.objects.data.Transform method) getMaxitBin() (pwem.Plugin class method) getMaxitHome() (pwem.Plugin class method) getMaxSet() (pwem.objects.data.SetOfDefocusGroup method)

getMdFirstRow() (in module xmipp3.base) getMemoryAvailable() (in module pyworkflow.utils.utils) getMessage() (pyworkflow.viewer.MessageView method) getMethods() (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) getMicCTF() (pwem.protocols.protocol_import.dataimport.ScipionImport method) getMicId() (pwem.objects.data.Coordinate method) (pwem.objects.data.Particle method) (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking class method) getMicName() (pwem.objects.data.Coordinate method) (pwem.objects.data.Micrograph method) getMicNameOrId() (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) getMicrograph() (pwem.objects.data.Coordinate method) (pwem.objects.data.CTFModel method) getMicrographFnsWithCoordinates() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getMicrographs() (pwem.objects.data.SetOfCoordinates method) (pwem.objects.data.SetOfCTF method) getMicSampling() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) getMicsIds() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getMicsPair() (pwem.objects.data_tiltpairs.CoordinatesTiltPair method) getMinMax() (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes method) (xmipp3.protocols.protocol_resolution_monogenic_signal.XmippProtMonoRes method) getMinSet() (pwem.objects.data.SetOfDefocusGroup method) getModeFile() (pwem.objects.data.NormalMode method) getModel() (xmipp3.base.XmippProtocol class method) getModelsChains() (pwem.convert.atom_struct.AtomicStructHandler method) getModelsChainsStep() (pwem.wizards.wizards.GetStructureChainsWizard class method) (pwem.wizards.wizards.SelectChainWizard class method) getModesCondition() (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper class method) getModificationTime() (pyworkflow.project.manager.ProjectInfo method) getModuleClasses() (pyworkflow.plugin.Domain class method) getModuleFolder() (in module pyworkflow.config) (in module scipion.utils) getModules() (in module pyworkflow.utils.reflection) getMovieFileName() (in module xmipp3.convert.convert) getMpiCommand() (pyworkflow.protocol.hosts.HostConfig method) getMrcImage() (pwem.emlib.image.image_readers.MRCImageReader class method) getName() (pwem.viewers.showj.ColumnProperties method) (pyworkflow.object.Object method) (pyworkflow.plugin.Domain class method) (pyworkflow.plugin.Plugin method) (pyworkflow.project.config.Label method) (pyworkflow.project.manager.ProjectInfo method) (pyworkflow.project.project.Project method) (pyworkflow.protocol.hosts.QueueSystemConfig method) (pyworkflow.protocol.package.Package method) (pyworkflow.protocol.params.RelationParam method) (pyworkflow.utils.dataset.Column method) (pyworkflow.utils.graph.Node method) (pyworkflow.viewer.Viewer class method) (scipion.install.funcs.Target method) getNamedFont() (in module pyworkflow.gui.gui) getNameId() (pyworkflow.object.Object method) getNestedValue() (pyworkflow.object.Object method) getNextOutputName() (pyworkflow.protocol.protocol.Protocol method) getNode() (pyworkflow.project.config.NodeConfigList method) (pyworkflow.utils.graph.Graph method) getNodeById() (pyworkflow.project.config.ProjectSettings method) getNodeNames() (pyworkflow.utils.graph.Graph method) getNodes() (pyworkflow.project.config.ProjectSettings method) (pyworkflow.utils.graph.Graph method) getNormFSCQFile() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) getNumberOfColumns() (pyworkflow.utils.dataset.Table method) getNumberOfFrames() (pwem.objects.data.Movie method) getNumberOfObjects() (pwem.convert.headers.Ccp4Header method) getNumberOfPreviousIterations() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) getNumberSlices() (pyworkflow.utils.dataset.DataSet method) getNumberSlicesForTemplate() (pyworkflow.utils.dataset.DataSet method) getObjComment() (pyworkflow.object.Object method) getObjCreation() (pyworkflow.object.Object method) getObjCreationAsDate() (pyworkflow.object.Object method) getObjDict() (pyworkflow.object.Object method) getObject() (pyworkflow.project.project.Project method) getObjectActions() (pyworkflow.gui.browser.FileTreeProvider method) (pyworkflow.gui.form.SubclassesTreeProvider method) (pyworkflow.gui.project.labels.LabelsTreeProvider method) (pyworkflow.gui.project.searchrun.RunsTreeProvider method) (pyworkflow.gui.project.viewprotocols_extra.RunIOTreeProvider method) (pyworkflow.gui.tree.ObjectTreeProvider method) (pyworkflow.gui.tree.TreeProvider method) getObjectFromId() (pyworkflow.gui.tree.BoundTree method) (pyworkflow.gui.tree.ProjectRunsTreeProvider method) getObjectInfo() (pyworkflow.gui.browser.FileTreeProvider method) (pyworkflow.gui.form.MultiPointerTreeProvider method) (pyworkflow.gui.form.ProtocolClassTreeProvider method) (pyworkflow.gui.form.ScalarTreeProvider method) (pyworkflow.gui.form.SubclassesTreeProvider method) (pyworkflow.gui.project.labels.LabelsTreeProvider method) (pyworkflow.gui.project.steps.StepsTreeProvider static method) (pyworkflow.gui.project.variables.VariablesTreeProvider method) (pyworkflow.gui.project.viewprotocols_extra.RunIOTreeProvider method) (pyworkflow.gui.tree.AttributesTreeProvider method) (pyworkflow.gui.tree.ListTreeProvider method) (pyworkflow.gui.tree.ListTreeProviderTemplate method) (pyworkflow.gui.tree.ObjectTreeProvider method) (pyworkflow.gui.tree.ProjectRunsTreeProvider method) (pyworkflow.gui.tree.TreeProvider method) getObjectLabel() (in module pyworkflow.gui.form) (pyworkflow.gui.project.viewprotocols_extra.RunIOTreeProvider static method) getObjectPersistingClassName() (pyworkflow.mapper.mapper.Mapper static method) getObjectPreview() (pyworkflow.gui.browser.FileTreeProvider method) (pyworkflow.gui.project.labels.LabelsTreeProvider method) (pyworkflow.gui.project.steps.StepsTreeProvider static method) (pyworkflow.gui.project.viewprotocols_extra.RunIOTreeProvider static method) (pyworkflow.gui.tree.ObjectTreeProvider method) (pyworkflow.gui.tree.TreeProvider method) getObjects() (pyworkflow.gui.browser.FileTreeProvider method) (pyworkflow.gui.form.MultiPointerTreeProvider method) (pyworkflow.gui.form.ProtocolClassTreeProvider method) (pyworkflow.gui.form.RelationsTreeProvider method) (pyworkflow.gui.form.ScalarTreeProvider method) (pyworkflow.gui.form.SubclassesTreeProvider method) (pyworkflow.gui.project.labels.LabelsTreeProvider method) (pyworkflow.gui.project.steps.StepsTreeProvider method) (pyworkflow.gui.project.variables.VariablesTreeProvider method) (pyworkflow.gui.project.viewprotocols_extra.RunIOTreeProvider method) (pyworkflow.gui.tree.ObjectTreeProvider method) (pyworkflow.gui.tree.ProjectRunsTreeProvider method) (pyworkflow.gui.tree.TreeProvider method) (pyworkflow.plugin.Domain class method) getObjectTag() (pyworkflow.protocol.protocol.Protocol method) getObjId() (pwem.emlib.metadata.utils.Row method) (pyworkflow.object.Object method) (pyworkflow.project.project.Project method) (pyworkflow.template.Template method) getObjLabel() (pyworkflow.object.Object method) getObjName() (pyworkflow.object.Object method) (scipion.install.plugin_manager.Operation method) getObjParent() (scipion.install.plugin_manager.Operation method) getObjParentId() (pyworkflow.object.Object method) getObjs() (pyworkflow.gui.tree.ListTreeProvider method) getObjStatus() (scipion.install.plugin_manager.Operation method) getObjText() (scipion.install.plugin_manager.Operation method) getObjType() (scipion.install.plugin_manager.Operation method) getObjValue() (pwem.objects.data.Matrix method) (pyworkflow.object.CsvList method) (pyworkflow.object.Object method) (pyworkflow.project.config.Label method) (pyworkflow.project.config.NodeConfig method) (pyworkflow.protocol.params.DeprecatedParam method) getOldName() (pyworkflow.project.config.Label method) getOperationByName() (scipion.install.plugin_manager.OperationList method) getOperations() (scipion.install.plugin_manager.OperationList method) getOrientedCorrectionPath() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getOrientedGainPath() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getOrigin() (pwem.convert.headers.Ccp4Header method) (pwem.objects.data.AtomStruct method) (pwem.objects.data.Image method) getOutput() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) getOutputAlignedVolumePath() (xmipp3.protocols.protocol_align_volume_and_particles.XmippProtAlignVolumeParticles method) getOutputConnectorCoordinates() (pyworkflow.gui.canvas.Item method) getOutputFiles() (pyworkflow.protocol.protocol.Protocol method) getOutputMics() (xmipp3.protocols.protocol_preprocess_micrographs.XmippProtPreprocessMicrographs method) getOutputName() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) getOutputNamesDict() (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) getOutputPath() (pyworkflow.tests.tests.BaseTest class method) getOutputsSize() (pyworkflow.protocol.protocol.Protocol method) getOutputSuffix() (pyworkflow.protocol.protocol.Protocol method) getOututName() (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) getPackage() (scipion.install.funcs.Environment method) getPackageCitations() (pyworkflow.protocol.protocol.Protocol method) getPackages() (scipion.install.funcs.Environment method) getPackagesStatus() (scipion.install.update_manager.UpdateManager class method) getPackageState() (scipion.install.update_manager.UpdateManager class method) getParam() (pyworkflow.protocol.params.Form method) (pyworkflow.protocol.protocol.Protocol method) getParam1() (pwem.protocols.protocol_mathematical_operator.ProtMathematicalOperator method) getParam2() (pwem.protocols.protocol_mathematical_operator.ProtMathematicalOperator method) getParamName() (pwem.viewers.viewer_angular_dist.AngularDistributionViewer method) getParams() (pyworkflow.template.Template method) getParent() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) (pyworkflow.utils.graph.Node method) (pyworkflow.viewer.Viewer method) getParentFolder() (in module pyworkflow.utils.path) getParents() (pyworkflow.utils.graph.Node method) getParsedMethods() (pyworkflow.protocol.protocol.Protocol method) getParticleId() (pwem.objects.data.MovieParticle method) getParticlesOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getPassword() (pyworkflow.protocol.hosts.HostConfig method) getPath() (pwem.viewers.views.DataView method) (pyworkflow.gui.browser.FileInfo method) (pyworkflow.plugin.Plugin method) (pyworkflow.project.project.Project method) (pyworkflow.protocol.protocol.Protocol method) (pyworkflow.tests.tests.DataSet method) getPattern() (pwem.protocols.protocol_import.base.ProtImportFiles method) getPdb() (pwem.objects.data.SetOfNormalModes method) getPhaseShift() (pwem.objects.data.CTFModel method) getPid() (pyworkflow.protocol.protocol.Protocol method) getPILImage() (in module pwem.viewers.filehandlers) getPipData() (scipion.install.plugin_funcs.PluginInfo method) getPipJsonData() (scipion.install.plugin_funcs.PluginInfo method) getPipName() (scipion.install.plugin_funcs.PluginInfo method) getPipVersion() (scipion.install.plugin_funcs.PluginInfo method) getPixelValue() (pwem.viewers.viewer_coordinates.MainWindow method) getPlatform() (pyworkflow.gui.project.utils.OS static method) (pyworkflow.utils.utils.OS static method) getPlugin() (pyworkflow.plugin.Domain class method) (pyworkflow.protocol.protocol.Protocol class method) getPluginClass() (scipion.install.plugin_funcs.PluginInfo method) getPluginDir() (pyworkflow.plugin.Plugin method) getPluginLogoPath() (pyworkflow.protocol.protocol.Protocol class method) getPluginModule() (pyworkflow.plugin.Domain class method) getPluginName() (scipion.install.plugin_funcs.PluginInfo method) getPlugins() (pyworkflow.plugin.Domain class method) (scipion.install.plugin_funcs.PluginRepository method) getPluginTemplateDir() (pyworkflow.plugin.Plugin method) getPngData() (in module pyworkflow.gui.matplotlib_image) getPoint() (xmipp3.utils.Data method) getPointer() (pyworkflow.gui.form.PointerVar method) (pyworkflow.gui.form.ScalarWithPointerVar method) (pyworkflow.object.Scalar method) getPointerLabelAndInfo() (in module pyworkflow.gui.form) getPosition() (pwem.objects.data.Coordinate method) (pyworkflow.project.config.NodeConfig method) getPossibleOutputs() (pyworkflow.protocol.protocol.Protocol method) getPreCoordinatesOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getPredictedMicFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getPreferredViewers() (pyworkflow.plugin.Domain class method) getPrefix() (pyworkflow.object.Set method) getPreParticlesOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getPrepend() (pyworkflow.utils.utils.Environ method) getPreprocessedMicFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getPreProcParamsFromForm() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getPrerequisites() (pyworkflow.protocol.protocol.Step method) getPreviousParameters() (xmipp3.protocols.protocol_ctf_micrographs.XmippProtCTFMicrographs method) getPreviousQuality() (in module xmipp3.protocols.protocol_reconstruct_highres) getPreviousValues() (xmipp3.protocols.protocol_ctf_micrographs.XmippProtCTFMicrographs method) getPriorityPackageList() (pyworkflow.config.Config class method) getProcessors() (scipion.install.funcs.Environment method) getProgName() (pwem.objects.data_flexhub.FlexInfo method) getProgram() (pwem.viewers.viewer_chimera.Chimera class method) (pwem.viewers.viewer_chimera.ChimeraOldView method) (pwem.viewers.viewer_chimera.ChimeraView method) getProgramsDbName() (in module xmipp3.programs) getProject() (pyworkflow.protocol.protocol.Protocol method) (pyworkflow.viewer.Viewer method) getProjectionMatchingArgs() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) getProjectLog() (pyworkflow.project.project.Project method) getProjectPath() (pyworkflow.project.manager.Manager method) getProperties() (pwem.emlib.image.image_readers.ImageStack method) getProperty() (pwem.emlib.image.image_readers.ImageStack method) (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.object.Set method) getPropertyKeys() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) getProtocol() (pyworkflow.project.project.Project method) getProtocolCompatibleOutputs() (pyworkflow.project.project.Project method) getProtocolFromDb() (in module pyworkflow.protocol.protocol) getProtocolFromRuns() (pyworkflow.project.project.Project method) getProtocolId() (pyworkflow.viewer.Viewer method) getProtocols() (pyworkflow.plugin.Domain class method) getProtocolsByClass() (pyworkflow.project.project.Project method) getProtocolsDict() (pyworkflow.project.project.Project method) getProtocolsJson() (pyworkflow.project.project.Project method) getProtocolsToUpdate() (pyworkflow.protocol.protocol.Protocol method) getProtocolTag() (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig class method) getProtocolView() (pyworkflow.project.config.ProjectSettings method) (pyworkflow.project.project.Project method) getProtocolViews() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) getProtWorkingDir() (pyworkflow.project.project.Project static method) getPsdFile() (pwem.objects.data.CTFModel method) getPSDs() (xmipp3.protocols.protocol_tilt_analysis.XmippProtTiltAnalysis static method) getPseudoAtoms() (pwem.objects.data.AtomStruct method) getPWEMPath() (in module pwem.utils) getPython() (in module pyworkflow.utils.utils) (scipion.install.funcs.Environment static method) getPythonLibFolder() (pyworkflow.config.Config static method) getPythonPackagesFolder() (in module pyworkflow.utils.utils) (scipion.install.funcs.Environment static method) getPyworkflowPath() (in module pyworkflow.config) getQuestion() (pyworkflow.protocol.params.Section method) getQuestionName() (pyworkflow.protocol.params.Section method) getQueueConfig() (pyworkflow.protocol.hosts.QueueSystemConfig method) getQueueParams() (pyworkflow.protocol.protocol.Protocol method) getQueues() (pyworkflow.protocol.hosts.QueueSystemConfig method) getQueuesDefault() (pyworkflow.protocol.hosts.HostConfig method) getQueueSystem() (pyworkflow.protocol.hosts.HostConfig method) getRadius() (pwem.wizards.wizard.MaskPreviewDialog static method) getRadiusAngstroms() (pwem.wizards.wizard.MaskPreviewDialog method) getRange() (pwem.objects.data.FramesRange method) (pwem.objects.data.MovieAlignment method) getRangeStringFromList() (in module pyworkflow.utils.utils) getRank() (xmipp3.programs.ProgramKeywordsRank method) getRawSequenceStep() (pwem.protocols.protocol_import.sequence.ProtImportSequence method) getReader() (pwem.emlib.image.image_readers.ImageReadersRegistry class method) getReadOnly() (pyworkflow.project.config.ProjectSettings method) getReadyMics() (in module xmipp3.protocols.protocol_particle_pick_consensus) getRecalCtfParamsDict() (pwem.protocols.protocol_micrographs.ProtCTFMicrographs method) getRelatedObjects() (pyworkflow.project.project.Project method) getRelationChilds() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) getRelationParents() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) getRelations() (pyworkflow.protocol.protocol.Protocol method) getRelationsByCreator() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) getRelationsByName() (pyworkflow.mapper.sqlite.SqliteMapper method) getReleaseDate() (scipion.install.plugin_funcs.PluginInfo method) getRelPath() (pyworkflow.tests.tests.BaseTest class method) getRenderableColumns() (pwem.viewers.showj.ColumnsConfig method) getRenderType() (pyworkflow.utils.dataset.Column method) getRepresentative() (pyworkflow.object.Set method) getResidualGainPath() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getResidueAverage() (in module pwem.viewers.viewer_localres) getResiduePositions() (in module pwem.viewers.viewer_localres) getResidues() (pwem.wizards.wizards.SelectResidueWizard method) getResolution() (pwem.objects.data.CTFModel method) getResourcesPath() (in module pyworkflow.config) getResult() (pyworkflow.gui.dialog.Dialog method) getRightConnectorCoordinates() (pyworkflow.gui.canvas.Item method) getRoi() (pwem.objects.data.MovieAlignment method) getRoot() (pyworkflow.gui.dialog.Dialog method) (pyworkflow.gui.gui.Window method) (pyworkflow.utils.graph.Graph method) getRootNodes() (pyworkflow.utils.graph.Graph method) getRotatingFileLogger() (in module scipion.install.plugin_manager) getRotationMatrix() (pwem.objects.data.Transform method) getRow() (pyworkflow.utils.dataset.Table method) getRows() (pyworkflow.utils.dataset.Table method) getRunMode() (pyworkflow.protocol.protocol.Protocol method) getRunName() (pyworkflow.protocol.protocol.Protocol method) getRuns() (pyworkflow.project.project.Project method) getRunsFont() (pyworkflow.gui.canvas.Canvas method) getRunsGraph() (pyworkflow.project.project.Project method) getRunsView() (pyworkflow.project.config.ProjectSettings method) getSampling() (pwem.convert.headers.Ccp4Header method) getSamplingRate() (pwem.objects.data.Image method) (pwem.objects.data.SetOfClasses method) (pwem.objects.data.SetOfImages method) (pwem.objects.data_flexhub.AtomStructFlex method) (pwem.objects.data_flexhub.SetOfAtomStructFlex method) getScannedPixelSize() (pwem.objects.data.SetOfMicrographsBase method) getScheduleLog() (pyworkflow.protocol.protocol.Protocol method) getScheduleScript() (in module pyworkflow.config) getScipionAppPath() (in module scipion.utils) getScipionConfig() (pyworkflow.protocol.hosts.HostConfig method) getScipionHome() (in module scipion.utils) (pyworkflow.protocol.hosts.HostConfig method) getScipionObj() (in module xmipp3.convert.convert) getScore() (pwem.objects.data.NormalMode method) getScriptsPath() (in module scipion.utils) getSecSetField() (pwem.protocols.protocol_sets.ProtCrossSubSet method) getSection() (pyworkflow.protocol.params.Form method) getSelected() (pyworkflow.gui.browser.ObjectBrowser method) (pyworkflow.gui.canvas.Item method) getSelectedObjects() (pyworkflow.gui.form.MultiPointerVar method) (pyworkflow.gui.tree.BoundTree method) getSelectedProtocol() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) getSelectedSize() (xmipp3.utils.Data method) getSelfClassName() (pyworkflow.mapper.sqlite.SqliteFlatDb method) getSeqName() (pwem.objects.data.Sequence method) getSequence() (pwem.convert.sequence.SequenceHandler method) (pwem.objects.data.Sequence method) (pwem.wizards.wizards.SelectResidueWizard method) getSequenceFromChain() (pwem.convert.atom_struct.AtomicStructHandler method) getSequenceOfChainStep() (pwem.protocols.protocol_import.sequence.ProtImportSequence method) getSettings() (pyworkflow.gui.project.project.ProjectWindow method) (pyworkflow.project.project.Project method) getSettingsCreationTime() (pyworkflow.project.project.Project method) getShifts() (pwem.objects.data.MovieAlignment method) (pwem.objects.data.Transform method) (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) getShiftsFromOrigin() (pwem.objects.data.Image method) getShortName() (pyworkflow.project.project.Project method) getShowJParams() (pwem.viewers.views.DataView method) (pwem.viewers.views.ObjectView method) getShowJWebParams() (pwem.viewers.views.DataView method) getSignificantArgs() (xmipp3.protocols.protocol_reconstruct_significant.XmippProtReconstructSignificant method) getSinglePreviousParameters() (xmipp3.protocols.protocol_ctf_micrographs.XmippProtCTFMicrographs method) getSize() (in module pwem.emlib.metadata.utils) (pwem.objects.data.DefocusGroup method) (pwem.objects.data.SetOfDefocusGroups method) (pyworkflow.gui.browser.FileInfo method) (pyworkflow.object.List method) (pyworkflow.object.Set method) (pyworkflow.protocol.protocol.Protocol method) (pyworkflow.utils.dataset.Table method) (xmipp3.base.XmippSet method) (xmipp3.utils.Data method) getSizeStr() (pyworkflow.gui.browser.FileInfo method) getSleepTime() (pyworkflow.apps.pw_schedule_run.RunScheduler method) getSlice() (pwem.viewers.viewer_localres.LocalResolutionViewer method) getSliceImage() (pwem.viewers.viewer_localres.LocalResolutionViewer method) getSocket() (pyworkflow.gui.canvas.Item method) getSocketCoords() (pyworkflow.gui.canvas.Item method) getSocketCoordsAt() (pyworkflow.gui.canvas.Item method) getSocketsAt() (pyworkflow.gui.canvas.Item method) getSoftware() (scipion.install.funcs.Environment static method) getSortingColumnName() (pyworkflow.gui.tree.TreeProvider method) getSourceChilds() (pyworkflow.project.project.Project method) getSourceGraph() (pyworkflow.project.project.Project method) getSourceParents() (pyworkflow.project.project.Project method) getSourceUrl() (scipion.install.plugin_funcs.PluginInfo method) getSphericalAberration() (pwem.objects.data.Acquisition method) getSpritesFile() (pyworkflow.config.Config class method) (pyworkflow.utils.properties.Sprite class method) getSrcDir() (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) getStartAngstrom() (pwem.convert.headers.Ccp4Header method) getStartPixel() (pwem.convert.headers.Ccp4Header method) getState() (xmipp3.utils.Point method) getStatus() (pyworkflow.protocol.protocol.Step method) getStatusColor() (in module pyworkflow.gui.project.utils) getStatusColorFromNode() (in module pyworkflow.gui.project.utils) getStatusColorFromRun() (in module pyworkflow.gui.project.utils) getStatusMessage() (pyworkflow.protocol.protocol.Protocol method) getStderrLog() (pyworkflow.protocol.protocol.Protocol method) getStdoutLog() (pyworkflow.protocol.protocol.Protocol method) getSteps() (pyworkflow.protocol.protocol.Protocol method) getStepsCheckSeconds() (pyworkflow.config.Config class method) getStepsFile() (pyworkflow.protocol.protocol.Protocol method) getStepsGraph() (pyworkflow.protocol.protocol.Protocol method) getStore() (pyworkflow.object.Object method) getStreamState() (pyworkflow.object.Set method) getStringListFromValues() (in module pyworkflow.utils.utils) getStructExtension() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) getStructFile() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) getStructure() (pwem.convert.atom_struct.AtomicStructHandler method) getStructureBFactorValues() (pwem.convert.atom_struct.AtomicStructHandler method) GetStructureChainsWizard (class in pwem.wizards.wizards) getStructureRecipient() (in module pwem.viewers.viewer_localres) getSubclasses() (in module pyworkflow.utils.reflection) getSubclassesFromModules() (in module pyworkflow.utils.reflection) getSubclassesFromPath() (in module pyworkflow.utils.reflection) getSubmitCommand() (pyworkflow.protocol.hosts.HostConfig method) (pyworkflow.protocol.hosts.QueueSystemConfig method) getSubmitDict() (pyworkflow.protocol.protocol.Protocol method) getSubmitPrefix() (pyworkflow.protocol.hosts.HostConfig method) getSubmitTemplate() (pyworkflow.protocol.hosts.HostConfig method) (pyworkflow.protocol.hosts.QueueSystemConfig method) getSubmodule() (in module scipion.install.inspect_plugins) getSubset() (pyworkflow.object.Set method) getSubsetByDefocus() (in module pwem.convert.utils) getSuffix() (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) getSummary() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs method) (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (scipion.install.plugin_funcs.PluginInfo method) (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoise method) getSupportedDataType() (pwem.emlib.image.image_handler.ImageHandler class method) getSupportedVersions() (pyworkflow.plugin.Plugin class method) getSymmetry() (pwem.viewers.viewer_chimera.Chimera class method) (xmipp3.base.HelicalFinder method) getSymmetryKey() (pwem.convert.symmetry.SymmetryHelper class method) getSymmetryMatrices() (in module pwem.convert.symmetry) getSymmetryMatricesAndPlanes() (pwem.convert.symmetry.SymmetryHelper class method) getSyncDataScript() (in module pyworkflow.config) getTable() (pyworkflow.utils.dataset.DataSet method) getTableColumns() (pyworkflow.mapper.sqlite_db.SqliteDb method) getTableName() (pwem.viewers.views.DataView method) getTables() (pyworkflow.mapper.sqlite_db.SqliteDb method) getTarget() (scipion.install.funcs.Environment method) getTargetList() (scipion.install.funcs.Environment method) getTargets() (scipion.install.funcs.Environment method) getTemplate() (scipion.scripts.kickoff.KickoffWindow method) getTemplateName() (in module scipion.scripts.config) getTemplatePath() (in module pwem.utils) getTemplates() (in module scipion.scripts.kickoff) (pyworkflow.plugin.Plugin method) getTemplatesPath() (in module scipion.utils) getTestName() (pyworkflow.tests.tests.GTestResult static method) getTestsCommand() (pyworkflow.apps.pw_run_tests.Tester method) getTestsScript() (in module pyworkflow.config) getText() (pyworkflow.gui.text.Text method) (pyworkflow.gui.tree.AttributesTreeProvider method) (pyworkflow.gui.tree.ListTreeProvider method) (pyworkflow.gui.tree.ListTreeProviderString method) (pyworkflow.gui.tree.ListTreeProviderTemplate method) (pyworkflow.gui.widgets.ComboBox method) getThreadJobId() (pyworkflow.protocol.executor.QueueStepExecutor method) getThumbnailFn() (pwem.emlib.image.image_handler.ImageHandler static method) (pwem.protocols.protocol_align_movies.ProtAlignMovies method) getTilted() (pwem.objects.data_tiltpairs.TiltPair method) (pwem.objects.data_tiltpairs.TiltPairSet method) getTimeInterval() (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData method) getTimeOutInSeconds() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) (pwem.protocols.protocol_tools.ProtManualCheckpoint method) getTitle() (pyworkflow.template.TemplateParam method) getTkImage() (in module pwem.viewers.filehandlers) getTkRoot() (pyworkflow.viewer.ProtocolViewer method) (pyworkflow.viewer.Viewer method) getTmpFolder() (scipion.install.funcs.Environment static method) getTmpOutputPath() (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) getTmpPath() (pyworkflow.project.project.Project method) getToc() (pyworkflow.utils.utils.Timer method) getTopConnectorCoordinates() (pyworkflow.gui.canvas.Item method) getTopRankItems() (pwem.protocols.protocol_set_filter.ProtSetFilter method) getTrainedMicFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getTransform() (pwem.objects.data.Image method) getTransformationFile() (xmipp3.protocols.protocol_align_volume_and_particles.XmippProtAlignVolumeParticles method) getTransformationMatrix() (pyworkflow.utils.dataset.Table method) getTransformGraph() (pyworkflow.project.project.Project method) getTransformMatrix() (pwem.convert.atom_struct.AtomicStructHandler method) getTriangles() (pwem.convert.symmetry.Icosahedron method) getType() (pyworkflow.template.TemplateParam method) (pyworkflow.utils.dataset.Column method) getTypeFromFile() (pwem.convert.sequence.SequenceHandler method) getTypeOfColumn() (pyworkflow.utils.dataset.DataSet method) getUniqueId() (pyworkflow.object.Pointer method) getUniqueItems() (in module pyworkflow.utils.utils) getUniqueValues() (pyworkflow.object.Set method) getUnitCell() (in module pwem.convert.symmetry) getUntilted() (pwem.objects.data_tiltpairs.TiltPair method) (pwem.objects.data_tiltpairs.TiltPairSet method) getUpdatedProtocol() (in module pyworkflow.protocol.protocol) getUpdateSetAttempts() (pyworkflow.config.Config class method) getUpdateSetAttemptsWait() (pyworkflow.config.Config class method) getUpDownConnectorsCoordinates() (pyworkflow.gui.canvas.Item method) getUrl() (pyworkflow.exceptions.PyworkflowException method) (pyworkflow.plugin.Plugin class method) (pyworkflow.protocol.protocol.Protocol class method) getUserAngle() (xmipp3.protocols.protocol_flexalign.XmippProtFlexAlign method) getUserFlip() (xmipp3.protocols.protocol_flexalign.XmippProtFlexAlign method) getUserName() (pyworkflow.protocol.hosts.HostConfig method) getValue() (pwem.emlib.metadata.utils.Row method) (pwem.emlib.metadata.utils.RowMetaData method) (pyworkflow.gui.widgets.ComboBox method) (pyworkflow.template.TemplateParam method) getValueAsObject() (pwem.emlib.metadata.utils.Row method) getValueFromIndex() (pyworkflow.utils.dataset.Table method) getValues() (pwem.viewers.showj.ColumnProperties method) (pyworkflow.gui.tree.AttributesTreeProvider method) (pyworkflow.gui.tree.ListTreeProviderTemplate method) getValuesFromDict() (pyworkflow.object.Object method) getValuesFromMappedDict() (pyworkflow.object.Object method) getValuesRange() (pwem.viewers.viewer_localres.ChimeraAttributeViewer method) getVar() (pyworkflow.plugin.Plugin class method) getVars() (pyworkflow.config.Config class method) (pyworkflow.plugin.Plugin class method) getVarValue() (pyworkflow.gui.form.FormWindow method) getVersion() (pyworkflow.mapper.sqlite_db.SqliteDb method) getVersionFromPath() (pwem.Plugin class method) getVersionFromVariable() (pwem.Plugin class method) getVertices() (pwem.convert.symmetry.Icosahedron method) getView() (pwem.wizards.wizard.CtfWizard class method) (pwem.wizards.wizard.DownsampleWizard class method) (pwem.wizards.wizard.MaskRadiiWizard class method) (pyworkflow.viewer.Viewer method) (pyworkflow.wizard.Wizard method) getViewers() (pyworkflow.plugin.Domain class method) getViewerScript() (in module pyworkflow.config) getViewParams() (pwem.viewers.views.DataView method) getViewWidget() (pyworkflow.gui.project.base.ProjectBaseWindow method) getVolFileName() (pwem.emlib.image.image_handler.ImageHandler class method) getVoltage() (pwem.objects.data.Acquisition method) getVolume() (pwem.objects.data.AtomStruct method) getVolumeName() (pyworkflow.utils.dataset.DataSet method) getVScroll() (pyworkflow.gui.widgets.Scrollable method) getWedgeExtraParams() (in module pyworkflow.gui.matplotlib_image) getWeight() (xmipp3.utils.Point method) getWeights() (xmipp3.utils.Data method) getWidgetValue() (pyworkflow.gui.form.FormWindow method) getWindow() (pyworkflow.viewer.ProtocolViewer method) getWindowSize() (xmipp3.protocols.protocol_tilt_analysis.XmippProtTiltAnalysis method) getWizardMaskColor() (pyworkflow.config.Config class method) getWizards() (pyworkflow.plugin.Domain class method) getWLSNAME() (pyworkflow.utils.utils.OS class method) getWorkflow() (in module scipion.scripts.tutorial) getWorkingDir() (pyworkflow.protocol.protocol.Protocol method) getX() (pwem.objects.data.Coordinate method) (pwem.objects.data.ImageDim method) (pyworkflow.project.config.NodeConfig method) (xmipp3.utils.Point method) getXData() (xmipp3.utils.Data method) getXDim() (pwem.objects.data.Image method) (pwem.objects.data.SetOfImages method) getXmippAttribute() (in module xmipp3.convert.convert) getXmippLabels() (in module xmipp3.programs) getXmippLabelsName() (in module xmipp3.programs) getXmippPath() (in module xmipp3.base) getXmippPrograms() (in module xmipp3.programs) getxyz() (pwem.wizards.wizards_3d.callbacks.DraggablePoint method) getXYZN() (pwem.convert.headers.Ccp4Header method) getY() (pwem.objects.data.Coordinate method) (pwem.objects.data.ImageDim method) (pyworkflow.gui.graph_layout.GraphLayout method) (pyworkflow.project.config.NodeConfig method) (xmipp3.utils.Point method) getYData() (xmipp3.utils.Data method) getYDim() (pwem.objects.data.Image method) getZ() (pwem.objects.data.ImageDim method) (xmipp3.utils.Point method) getZData() (xmipp3.utils.Data method) getZFlex() (pwem.objects.data_flexhub.AtomStructFlex method) (pwem.objects.data_flexhub.ParticleFlex method) (pwem.objects.data_flexhub.VolumeFlex method) getZRed() (pwem.objects.data_flexhub.AtomStructFlex method) (pwem.objects.data_flexhub.ParticleFlex method) (pwem.objects.data_flexhub.VolumeFlex method) GLOBAL_ALIGNMENT (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes attribute) GLOBAL_LOCAL_SEARCH (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry attribute) GLOBAL_SEARCH (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry attribute) globalAssignment() (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) goBegin() (pyworkflow.gui.text.Text method) goEnd() (pyworkflow.gui.text.Text method) GradientFrame (class in pyworkflow.gui.widgets) Graph (class in pyworkflow.utils.graph) GraphLayout (class in pyworkflow.gui.graph_layout) gray (pyworkflow.constants.StrColors attribute) grayStr() (in module pyworkflow.utils.utils) green (pyworkflow.constants.StrColors attribute) GREEN (pyworkflow.utils.properties.colorText attribute) green() (in module pyworkflow.utils.utils) (in module scipion.install.funcs) (in module scipion.scripts.config) greenB() (in module pyworkflow.utils.utils) greenStr() (in module pyworkflow.utils.utils) Group (class in pyworkflow.protocol.params) GROUP (pyworkflow.utils.properties.Icon attribute) GroupWidget (class in pyworkflow.gui.form) GT (class in pyworkflow.protocol.params) GTestResult (class in pyworkflow.tests.tests) guessCudaVersion() (pwem.Plugin class method) GUI (pyworkflow.constants.DOCSITEURLS attribute) gunzip() (in module pwem.protocols.protocol_import.volumes)

H

halfside (pyworkflow.gui.canvas.SquareConnector attribute) HALFVOLUMENAME (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) handle() (pwem.viewers.showj.ProtocolTCPRequestHandler method) (pyworkflow.gui.project.project.ProjectTCPRequestHandler method) handleImgHed() (pwem.protocols.protocol_import.images.ProtImportImages method) handleMove() (pyworkflow.gui.gui.Window method) handler() (pyworkflow.gui.project.utils.OS class method) handleResize() (pyworkflow.gui.gui.Window method) hasAcquisition() (pwem.objects.data.Image method) (pwem.objects.data.SetOfImages method) hasAlignment() (pwem.objects.data.Movie method) (pwem.objects.data.SetOfImages method) hasAlignment2D() (pwem.objects.data.SetOfImages method) hasAlignment3D() (pwem.objects.data.SetOfImages method) hasAlignmentProj() (pwem.objects.data.SetOfImages method) hasAnyFileChanged() (in module pyworkflow.utils.utils) hasAttribute() (pyworkflow.object.Object method) hasAttributeExt() (pyworkflow.object.Object method) hasChangedSince() (in module pyworkflow.utils.path) (pyworkflow.object.Set method) hasClassId() (pwem.objects.data.Particle method) (pwem.objects.data.Volume method) hasColumn() (pyworkflow.utils.dataset.Table method) hasCondition() (pyworkflow.protocol.params.FormElement method) hasCoordinate() (pwem.objects.data.Particle method) hasCoordinates() (pwem.objects.data.SetOfParticles method) hasCTF() (pwem.objects.data.Image method) (pwem.objects.data.SetOfImages method) hasDefault() (pyworkflow.utils.dataset.Column method) hasDefinition() (pyworkflow.protocol.protocol.Protocol static method) hasDoubleInheritance() (in module pyworkflow.apps.pw_protocol_list) hasEnableColumn() (pwem.viewers.showj.ColumnsConfig method) hasEnabledColumn() (pyworkflow.utils.dataset.Table method) hasExpert() (pyworkflow.protocol.protocol.Protocol method) hasExtended() (pyworkflow.object.Pointer method) hasFileChangedSince() (in module pyworkflow.utils.utils) hasFont() (in module pyworkflow.gui.gui) hasFractions() (pwem.protocols.protocol_alignment_assign.ProtAlignmentAssign method) hasHalfMaps() (pwem.objects.data.Volume method) hasLabel() (in module pyworkflow.tests.tests) (pwem.emlib.metadata.utils.Row method) hasMicId() (pwem.objects.data.Particle method) hasName() (pyworkflow.protocol.hosts.QueueSystemConfig method) hasObjId() (pyworkflow.object.Object method) hasObjParentId() (pyworkflow.object.Object method) hasOldName() (pyworkflow.project.config.Label method) hasOrigin() (pwem.objects.data.AtomStruct method) (pwem.objects.data.Image method) hasPackage() (scipion.install.funcs.Environment method) hasParam() (pyworkflow.protocol.params.Form method) hasParentHidden() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) hasPhaseShift() (pwem.objects.data.CTFModel method) hasPipPackage() (scipion.install.plugin_funcs.PluginInfo method)

hasPointer() (pyworkflow.gui.form.ScalarWithPointerVar method) (pyworkflow.object.Scalar method) hasProject() (pyworkflow.project.manager.Manager method) hasProperty() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.object.Set method) hasQuestion() (pyworkflow.protocol.params.Section method) hasQueueParams() (pyworkflow.protocol.protocol.Protocol method) hasRepresentative() (pyworkflow.object.Set method) hasRepresentatives() (pwem.objects.data.SetOfClasses method) hasResolution() (pwem.objects.data.CTFModel method) hasSummaryWarnings() (pyworkflow.protocol.protocol.Protocol method) hasTable() (pyworkflow.mapper.sqlite_db.SqliteDb method) hasTarget() (scipion.install.funcs.Environment method) hasTransform() (pwem.objects.data.Image method) hasValue() (pyworkflow.object.Object method) (pyworkflow.object.Pointer method) (pyworkflow.object.Scalar method) (pyworkflow.protocol.hosts.QueueSystemConfig method) hasVolume() (pwem.objects.data.AtomStruct method) header_info (pwem.emlib.image.image_readers.STKImageReader attribute) HEADER_OFFSET (pwem.emlib.image.image_readers.STKImageReader attribute) HelicalFinder (class in xmipp3.base) HELP_PARALLEL_HEADER (pyworkflow.utils.properties.Message attribute) HELP_PARALLEL_MPI (pyworkflow.utils.properties.Message attribute) HELP_PARALLEL_THREADS (pyworkflow.utils.properties.Message attribute) HELP_RUNMODE (pyworkflow.utils.properties.Message attribute) HELP_SCIPION_THREADS (pyworkflow.utils.properties.Message attribute) HELP_USEQUEUE (pyworkflow.utils.properties.Message attribute) HELP_USEQUEUEPERJOB (pyworkflow.utils.properties.Message attribute) HELP_WAIT_FOR (pyworkflow.utils.properties.Message attribute) hex_to_rgb() (in module pyworkflow.utils.utils) HI_RES (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc attribute) HiddenBooleanParam (class in pyworkflow.protocol.params) hide() (pyworkflow.gui.form.GroupWidget method) (pyworkflow.gui.form.ParamWidget method) (pyworkflow.gui.form.SectionWidget method) hideTooltip() (pyworkflow.gui.canvas.Canvas method) HIGH_RESOL (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes attribute) highlight() (pyworkflow.gui.text.Text method) highlightInnerSlider() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.MaskRadiiPreviewDialog method) highlightLabel() (pyworkflow.gui.widgets.LabelSlider method) highlightOuterSlider() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.MaskRadiiPreviewDialog method) histThresholding() (in module xmipp3.protocols.protocol_screen_particles) histWindowClose() (pwem.viewers.viewer_coordinates.MainWindow method) histWindowSaveClose() (pwem.viewers.viewer_coordinates.MainWindow method) HOME (pyworkflow.constants.DOCSITEURLS attribute) (pyworkflow.utils.properties.Icon attribute) HOST_CONFIG (pyworkflow.constants.DOCSITEURLS attribute) HostConfig (class in pyworkflow.protocol.hosts) HotButton (class in pyworkflow.gui.widgets) HyperlinkManager (class in pyworkflow.gui.text)

I

Icon (class in pyworkflow.utils.properties) IconButton (class in pyworkflow.gui.widgets) ICOSAHEDRAL_SYM_NAME (pwem.protocols.protocol_projection_edit.ProtProjectionEditor attribute) icosahedralMatrixTable() (pwem.convert.symmetry.Icosahedron method) icosahedralSymmetryMatrices() (pwem.convert.symmetry.Icosahedron method) Icosahedron (class in pwem.convert.symmetry) icosahedronAngles() (pwem.convert.symmetry.Icosahedron method) icosahedronEdgeLength() (pwem.convert.symmetry.Icosahedron method) icosahedronGeometry() (pwem.convert.symmetry.Icosahedron method) ID_COLUMN (pyworkflow.gui.form.SubclassesTreeProvider attribute) (pyworkflow.gui.tree.ProjectRunsTreeProvider attribute) ifNomask() (xmipp3.protocols.protocol_resolution_monogenic_signal.XmippProtMonoRes method) IGNORE_LABEL (pwem.protocols.protocol_alignment_assign.ProtAlignmentAssign attribute) ignoreCopy() (pwem.protocols.protocol_import.micrographs.ProtImportMovies method) Image (class in pwem.objects.data) image (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) ImageDim (class in pwem.objects.data) ImageFileHandler (class in pwem.viewers.filehandlers) ImageHandler (class in pwem.emlib.image.image_handler) IMAGEJ_BINARY_PATH (pwem.Config attribute) ImagePreview (class in pyworkflow.gui.matplotlib_image) ImagePreviewDialog (class in pwem.wizards.wizard) ImageReader (class in pwem.emlib.image.image_readers) ImageReadersRegistry (class in pwem.emlib.image.image_readers) ImageStack (class in pwem.emlib.image.image_readers) imageToRow() (in module xmipp3.convert.convert) ImageView (class in pwem.viewers.views) ImajeJFileHandler (class in pwem.viewers.filehandlers) IMG_BYTES (pwem.emlib.image.image_readers.STKImageReader attribute) IMG_FILENAME_ATTR (pwem.objects.data.Image attribute) IMPORT_FROM_AUTO (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates attribute) (pwem.protocols.protocol_import.ctfs.ProtImportCTF attribute) IMPORT_FROM_CRYOSPARC (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates attribute) (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) IMPORT_FROM_DOGPICKER (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates attribute) IMPORT_FROM_EMAN (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates attribute) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs attribute) (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) IMPORT_FROM_EMAN2 (pwem.protocols.protocol_import.ctfs.ProtImportCTF attribute) IMPORT_FROM_EMDB (pwem.protocols.protocol_import.volumes.ProtImportVolumes attribute) IMPORT_FROM_EMX (pwem.protocols.protocol_import.micrographs.ProtImportMicrographs attribute) (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) IMPORT_FROM_FILES (pwem.protocols.protocol_import.base.ProtImportFiles attribute) (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) (pwem.protocols.protocol_import.volumes.ProtImportPdb attribute) (pwem.protocols.protocol_import.volumes.ProtImportSetOfAtomStructs attribute) (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolAdjust attribute) (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolSubtraction attribute) IMPORT_FROM_FREALIGN (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) IMPORT_FROM_GCTF (pwem.protocols.protocol_import.ctfs.ProtImportCTF attribute) IMPORT_FROM_GRIGORIEFF (pwem.protocols.protocol_import.ctfs.ProtImportCTF attribute) IMPORT_FROM_ID (pwem.protocols.protocol_import.volumes.ProtImportPdb attribute) (pwem.protocols.protocol_import.volumes.ProtImportSetOfAtomStructs attribute) IMPORT_FROM_NUCLEOTIDE_FILES (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) IMPORT_FROM_NUCLEOTIDE_GENEBANK (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) IMPORT_FROM_NUCLEOTIDE_PLAIN_TEXT (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) IMPORT_FROM_NUCLEOTIDE_STRUCTURE (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) IMPORT_FROM_PLAIN_TEXT (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) IMPORT_FROM_PROTEIN_GENEBANK (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) IMPORT_FROM_RELION (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates attribute) (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) IMPORT_FROM_SCIPION (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates attribute) (pwem.protocols.protocol_import.ctfs.ProtImportCTF attribute) (pwem.protocols.protocol_import.micrographs.ProtImportMicrographs attribute) (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) IMPORT_FROM_STRUCTURE (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) IMPORT_FROM_UNIPROT (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) IMPORT_FROM_XMIPP (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates attribute) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs attribute) IMPORT_FROM_XMIPP3 (pwem.protocols.protocol_import.ctfs.ProtImportCTF attribute) (pwem.protocols.protocol_import.micrographs.ProtImportMicrographs attribute) (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) IMPORT_OBJ (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolAdjust attribute) (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolSubtraction attribute) IMPORT_STRUCTURE_FROM_FILES (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) IMPORT_STRUCTURE_FROM_ID (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) ImportAcquisitionWizard (class in pwem.wizards.wizards) importCommandList() (scipion.install.funcs.InstallHelper method) importCoordinates() (pwem.protocols.protocol_import.dataimport.ScipionImport method) (xmipp3.convert.dataimport.XmippImport method) ImportCoordinatesBoxSizeWizard (class in pwem.wizards.wizards) importCTF() (xmipp3.convert.dataimport.XmippImport method) importCTFStep() (pwem.protocols.protocol_import.ctfs.ProtImportCTF method) importExts (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) importFormats (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) importFromEMDBStep() (pwem.protocols.protocol_import.volumes.ProtImportVolumes method) importFromFile() (pwem.objects.data.Sequence method) (pwem.objects.data.SetOfSequences method) importFromFileStep() (pwem.protocols.protocol_import.volumes.ProtImportVolumes method) importFromPlugin() (pyworkflow.plugin.Domain static method) importFromTemplate() (in module scipion.guiplugin) importImagesStep() (pwem.protocols.protocol_import.images.ProtImportImages method) importImagesStreamStep() (pwem.protocols.protocol_import.images.ProtImportImages method) ImportMaskOutput (class in pwem.protocols.protocol_import.masks) importMaskStep() (pwem.protocols.protocol_import.masks.ProtImportMask method) importMicrographs() (pwem.protocols.protocol_import.dataimport.ScipionImport method) (pwem.protocols.protocol_tiltpairs.ProtImportMicrographsTiltPairs method) (xmipp3.convert.dataimport.XmippImport method) importMicrographsStep() (pwem.protocols.protocol_import.micrographs.ProtImportMicrographs method) ImportMicsOutput (class in pwem.protocols.protocol_import.micrographs) ImportMoviesOutput (class in pwem.protocols.protocol_import.micrographs) ImportOriginVolumeWizard (class in pwem.wizards.wizards) importParticles() (pwem.protocols.protocol_import.dataimport.ScipionImport method) (xmipp3.convert.dataimport.XmippImport method) importParticlesStep() (pwem.protocols.protocol_import.particles.ProtImportParticles method) importProject() (pyworkflow.gui.project.viewprojects.ProjectsView method) (pyworkflow.project.manager.Manager method) importTemplate() (in module scipion.scripts.kickoff) ImportVolumeOutputs (class in pwem.protocols.protocol_import.volumes) imScatter() (xmipp3.protocols.protocol_classes_2d_mapping.ScatterImageMarker method) increase() (pyworkflow.utils.progressbar.ProgressBar method) increment() (pyworkflow.object.Integer method) indentation (pyworkflow.utils.profiler.Timer attribute) inDevelMode() (pyworkflow.plugin.Plugin method) indexes (pyworkflow.object.Set attribute) INFO (pyworkflow.utils.properties.Icon attribute) info() (pyworkflow.gui.dialog.Dialog method) (pyworkflow.gui.project.viewprotocols.ProtocolsView method) (pyworkflow.protocol.protocol.Protocol method) INFO_COLUMN (pyworkflow.gui.form.ScalarTreeProvider attribute) (pyworkflow.gui.form.SubclassesTreeProvider attribute) infoMessage() (pyworkflow.viewer.Viewer method) INIT_REFRESH_SECONDS (in module pyworkflow.gui.project.viewprotocols) initAngularReferenceFileStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) initializeLists() (in module xmipp3.protocols.protocol_projmatch.projmatch_initialize) initializeParams() (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method) (xmipp3.protocols.protocol_mics_defocus_balancer.XmippProtMicDefocusSampler method) (xmipp3.protocols.protocol_movie_alignment_consensus.XmippProtConsensusMovieAlignment method) initializePlot() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) (xmipp3.protocols.protocol_classes_2d_mapping.ScatterImageMarker method) initializeRejDict() (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method) initializeStep() (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis method) (xmipp3.protocols.protocol_movie_max_shift.XmippProtMovieMaxShift method) (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) (xmipp3.protocols.protocol_tilt_analysis.XmippProtTiltAnalysis method) initialStep() (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) initMicrographs() (pwem.objects.data.SetOfCoordinates method) initParams() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) initProjectTCPServer() (pyworkflow.gui.project.project.ProjectWindow method) initProtocolTCPServer() (in module pwem.viewers.showj) initStep() (pwem.protocols.parallel.ProtTestParallel method) initVolumeData() (pwem.viewers.viewer_chimera.ChimeraAngDist method) INPUT_PARTICLES (xmipp3.protocols.protocol_subtract_projection.XmippProtBoostParticles attribute) (xmipp3.protocols.protocol_subtract_projection.XmippProtSubtractProjection attribute) INPUTARG (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability attribute) insert() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) (scipion.install.plugin_manager.PluginTree method) insertAngularClassAverageStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) insertAngularProjectLibraryStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) insertCaculateConsensusSteps() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) insertChild() (pyworkflow.mapper.sqlite.SqliteMapper method) insertChilds() (pyworkflow.mapper.sqlite.SqliteMapper method) insertComputeResolutionStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) insertExtractPartSteps() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) insertFilterVolumeStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) insertIteration() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) insertLabel() (xmipp3.programs.ProgramDb method) insertMaskReferenceStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) insertNewCoorsSteps() (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking method) (xmipp3.protocols.protocol_particle_pick_remove_duplicates.XmippProtPickingRemoveDuplicates method) insertObject() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteObjectsDb method) insertOperation() (scipion.install.plugin_manager.OperationList method) insertProgram() (xmipp3.programs.ProgramDb method) insertProjMatchStep() (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) insertReconstructionStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) insertRelation() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) (pyworkflow.mapper.sqlite.SqliteObjectsDb method) insertRelationData() (pyworkflow.mapper.sqlite.SqliteMapper method) insertText() (in module pwem.wizards.wizard) inspectObj() (in module pyworkflow.gui.project.utils) inspectPlugin() (in module scipion.install.inspect_plugins) INSTALL (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) install() (scipion.install.plugin_funcs.PluginInfo method) installBin() (scipion.install.plugin_funcs.PluginInfo method) installBinsDefault() (in module scipion.install.plugin_funcs) installDeepLearningToolkit() (in module xmipp3) INSTALLED (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) installed_item() (scipion.install.plugin_manager.PluginTree method) InstallHelper (class in scipion.install.funcs) installPipModule() (scipion.install.plugin_funcs.PluginInfo method)

installPluginMethods() (in module scipion.install.install_plugin) instanceCreated() (in module pyworkflow.utils.profiler) instanceDestroyed() (in module pyworkflow.utils.profiler) Integer (class in pyworkflow.object) INTEGER (pyworkflow.config.VarTypes attribute) interactiveSelStep() (xmipp3.protocols.protocol_classes_2d_mapping.XmippProtCL2DMap method) INTERP_METHOD_BSPLINE (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery attribute) INTERP_METHOD_LINEAR (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery attribute) INTERP_METHOD_NEAREST (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery attribute) interpMethodsDict (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery attribute) intersectStep() (xmipp3.protocols.protocol_consensus_classes.XmippProtConsensusClasses method) INTERVAL (pyworkflow.utils.log.STATUS attribute) IntParam (class in pyworkflow.protocol.params) invert() (pwem.emlib.image.image_handler.ImageHandler method) (pwem.objects.data.Transform method) invert_array() (in module xmipp3.protocols.protocol_movie_gain) invertImage() (in module pyworkflow.gui.gui) (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) invertStack() (pwem.emlib.image.image_handler.ImageHandler method) invertStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles method) (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) invertY() (pwem.objects.data.Coordinate method) is_class_private_name() (in module pyworkflow.utils.echo) is_classmethod() (in module pyworkflow.utils.echo) is_disabled() (scipion.install.plugin_manager.PluginTree method) is_enabled() (scipion.install.plugin_manager.PluginTree method) is_window_closed() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) (xmipp3.protocols.protocol_classes_2d_mapping.ScatterImageMarker method) isAborted() (pyworkflow.protocol.protocol.Step method) isActive() (pyworkflow.protocol.protocol.Step method) isAFinalProtocol() (in module pyworkflow.gui.project.utils) isAmplitudeCorrected() (pwem.objects.data.SetOfImages method) isAtEnd() (pyworkflow.gui.text.Text method) isBase() (pyworkflow.protocol.protocol.Protocol class method) isBeta() (pyworkflow.protocol.protocol.Protocol class method) isBlacklisted() (pwem.protocols.protocol_import.base.ProtImportFiles method) (pwem.protocols.protocol_import.micrographs.ProtImportMicBase method) isCentos() (pyworkflow.utils.utils.OS class method) isChild() (pyworkflow.protocol.protocol.Protocol method) isClosed() (pyworkflow.gui.plotter.Plotter method) isCompatible() (pwem.convert.headers.Ccp4Header class method) isCompressed() (pwem.objects.data.Movie method) isCondaInstallation() (pyworkflow.config.Config class method) isContinued() (pyworkflow.protocol.protocol.Protocol method) isDefault() (scipion.install.funcs.Target method) isDir() (pyworkflow.gui.browser.FileInfo method) isDisabled() (pwem.protocols.protocol_tests.ProtTests class method) (pyworkflow.protocol.protocol.Protocol class method) isDiscarded() (xmipp3.utils.Point method) isEerMovie() (in module xmipp3.convert.convert) isElf() (in module scipion.install.change_rpath) (in module scipion.install.find_deps) isEmpty() (in module pwem.emlib.metadata.utils) (pyworkflow.object.CsvList method) (pyworkflow.object.List method) (pyworkflow.object.Set method) (pyworkflow.project.config.MenuConfig method) (scipion.install.funcs.CommandDef method) (xmipp3.base.XmippSet method) isEnabled() (pyworkflow.object.Object method) isExpanded() (pyworkflow.project.config.NodeConfig method) isExpert() (pyworkflow.protocol.params.FormElement method) isFailed() (pyworkflow.protocol.protocol.Step method) isFileFinished() (in module pyworkflow.utils.path) isFinished() (pyworkflow.protocol.protocol.Step method) isImageFile() (pwem.emlib.image.image_handler.ImageHandler class method) isImportant() (pyworkflow.protocol.params.FormElement method) isInFile() (in module pyworkflow.utils.utils) isInReadOnlyFolder() (pyworkflow.project.project.Project method) isInstalled() (pyworkflow.protocol.package.Package method) (pyworkflow.protocol.protocol.Protocol class method) (scipion.install.plugin_funcs.PluginInfo method) isInStreaming() (pyworkflow.protocol.protocol.Protocol method) isInteractive() (pyworkflow.protocol.protocol.Step method) isItemEnabled() (pyworkflow.object.Set static method) isLaunched() (pyworkflow.protocol.protocol.Step method) isLink() (pyworkflow.gui.browser.FileInfo method) (pyworkflow.project.manager.ProjectInfo method) (pyworkflow.project.project.Project method) isMask() (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeParticles method) isModuleAFolder() (in module pyworkflow.utils.reflection) isModuleLoaded() (in module pyworkflow.utils.reflection) isMoveIn() (pwem.viewers.viewer_coordinates.MainWindow method) isMultiPointer() (pyworkflow.gui.form.ParamWidget method) isNew() (pyworkflow.protocol.protocol.Step method) isNewDev() (pyworkflow.protocol.protocol.Protocol class method) isOddX() (pwem.objects.data.SetOfImages method) isOnWindows() (pwem.viewers.viewer_chimera.Chimera class method) isPhaseFlipped() (pwem.objects.data.SetOfImages method) isPlugin() (scipion.install.plugin_manager.PluginBrowser method) isPointer() (pyworkflow.object.Object method) (pyworkflow.protocol.params.DeprecatedParam method) isPower2() (in module pyworkflow.utils.utils) isProcessAlive() (in module pyworkflow.utils.process) isProtocolUpToDate() (in module pyworkflow.protocol.protocol) isQueueMandatory() (pyworkflow.protocol.hosts.HostConfig method) isReadOnly() (pyworkflow.project.project.Project method) isRenderable() (pwem.viewers.showj.ColumnProperties method) isRoot() (pyworkflow.utils.graph.Node method) isRunning() (pyworkflow.protocol.protocol.Step method) isSameFunction() (in module pyworkflow.utils.reflection) isSaved() (pyworkflow.protocol.protocol.Step method) isScheduled() (pyworkflow.protocol.protocol.Step method) isScipionRunning() (pyworkflow.config.Config class method) isSelected() (pyworkflow.gui.form.ScalarTreeProvider method) (pyworkflow.gui.form.SubclassesTreeProvider method) (pyworkflow.project.config.NodeConfig method) (xmipp3.protocols.protocol_classes_2d_mapping.XmippProtCL2DMap method) (xmipp3.utils.Point method) isSortingAscending() (pyworkflow.gui.tree.TreeProvider method) isStandardImage() (in module pyworkflow.gui.browser) isStreamClosed() (pyworkflow.object.Set method) isStreamOpen() (pyworkflow.object.Set method) isStructExtensionValid() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) isUbuntu() (pyworkflow.utils.utils.OS class method) isUpdated() (pyworkflow.protocol.protocol.Protocol class method) isVisible() (pyworkflow.project.config.NodeConfig method) isWaiting() (pyworkflow.protocol.protocol.Step method) isWSL() (pyworkflow.utils.utils.OS class method) isXmippCudaPresent() (in module xmipp3.base) Item (class in pyworkflow.gui.canvas) ITEM_PREFIX (pyworkflow.object.List attribute) ITEM_TYPE (pwem.objects.data.SetOfAtomStructs attribute) (pwem.objects.data.SetOfClasses attribute) (pwem.objects.data.SetOfClasses2D attribute) (pwem.objects.data.SetOfClasses3D attribute) (pwem.objects.data.SetOfClassesVol attribute) (pwem.objects.data.SetOfCoordinates attribute) (pwem.objects.data.SetOfCTF attribute) (pwem.objects.data.SetOfData attribute) (pwem.objects.data.SetOfDefocusGroup attribute) (pwem.objects.data.SetOfFSCs attribute) (pwem.objects.data.SetOfImages attribute) (pwem.objects.data.SetOfMicrographs attribute) (pwem.objects.data.SetOfMovieParticles attribute) (pwem.objects.data.SetOfMovies attribute) (pwem.objects.data.SetOfNormalModes attribute) (pwem.objects.data.SetOfParticles attribute) (pwem.objects.data.SetOfSequences attribute) (pwem.objects.data.SetOfVolumes attribute) (pwem.objects.data_flexhub.SetOfAtomStructFlex attribute) (pwem.objects.data_flexhub.SetOfClassesFlex attribute) (pwem.objects.data_flexhub.SetOfClassesStructFlex attribute) (pwem.objects.data_flexhub.SetOfParticlesFlex attribute) (pwem.objects.data_flexhub.SetOfVolumesFlex attribute) (pwem.objects.data_tiltpairs.CoordinatesTiltPair attribute) (pwem.objects.data_tiltpairs.MicrographsTiltPair attribute) (pwem.objects.data_tiltpairs.ParticlesTiltPair attribute) (pwem.objects.data_tiltpairs.SetOfAngles attribute) (pwem.objects.data_tiltpairs.TiltPairSet attribute) (pyworkflow.object.Set attribute) itemConfig() (pyworkflow.gui.tree.BoundTree method) itemId (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) iterAll() (xmipp3.utils.Data method) iterAllParams() (pyworkflow.protocol.params.Form method) iterBigFile() (in module pyworkflow.utils.path) iterChildren() (pyworkflow.utils.graph.Node method) iterChildrenBreadth() (pyworkflow.utils.graph.Node method) iterClassItems() (pwem.objects.data.SetOfClasses method) iterColumns() (pyworkflow.utils.dataset.Table method) iterCoordinates() (pwem.objects.data.SetOfCoordinates method) iterDefinitionAttributes() (pyworkflow.protocol.protocol.Protocol method) iterDefinitionSections() (pyworkflow.protocol.protocol.Protocol method) iterFiles() (pwem.protocols.protocol_import.base.ProtImportFiles method) iterInputAttributes() (pyworkflow.protocol.protocol.Protocol method) iterInputPointers() (pyworkflow.protocol.protocol.Protocol method) iterItems() (pwem.objects.data.SetOfClasses method) (pwem.objects.data.SetOfImages method) (pyworkflow.object.Set method) iterMdRows() (in module xmipp3.base) iterMicrographCoordinates() (pwem.objects.data.SetOfCoordinates method) iterMicrographs() (pwem.objects.data.SetOfCoordinates method) iterNewInputFiles() (pwem.protocols.protocol_import.images.ProtImportImages method) (pwem.protocols.protocol_import.micrographs.ProtImportMovies method) iterOutputAttributes() (pyworkflow.protocol.protocol.Protocol method) iterParams() (pyworkflow.protocol.params.ElementGroup method) (pyworkflow.protocol.params.Form method) iterPointerParams() (pyworkflow.protocol.params.Form method) iterRepresentatives() (pwem.objects.data.SetOfClasses method) iterRows() (in module pwem.emlib.metadata.utils) (pyworkflow.utils.dataset.Table method) itersBoolValues() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) iterSections() (pyworkflow.protocol.params.Form method) iterSelectedObjects() (pyworkflow.gui.tree.BoundTree method) itersFloatValues() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) itersStringValues() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) iterSubclasses() (pyworkflow.project.project.Project method)

J

JAVA_HOME (pwem.Config attribute) JAVA_MAX_MEMORY (pwem.Config attribute) join() (in module pyworkflow.config) (pyworkflow.config.Config.Root method)

joinBlocks() (in module pwem.emlib.metadata.utils) joinExt() (in module pyworkflow.utils.path) joinSetOfParticlesStep() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) justPredict() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method)

K

keepColumns() (in module pwem.emlib.metadata.utils) KendersomBaseClassify (class in xmipp3.protocols.protocol_kerdensom) KEYSYM (class in pyworkflow.utils.properties)

KickoffView (class in scipion.scripts.kickoff) KickoffWindow (class in scipion.scripts.kickoff) killWithChilds() (in module pyworkflow.utils.process)

L

Label (class in pyworkflow.project.config) label2Python() (in module pwem.emlib.metadata.utils) LABEL_ALIG_PART (pyworkflow.utils.properties.Message attribute) LABEL_AMPLITUDE (pyworkflow.utils.properties.Message attribute) LABEL_ANALYZE (pyworkflow.utils.properties.Message attribute) LABEL_APPLY_TRANSFORM (pyworkflow.utils.properties.Message attribute) LABEL_BIB_BTN (pyworkflow.utils.properties.Message attribute) LABEL_BLOCK_SELECTION (pyworkflow.utils.properties.Message attribute) LABEL_BROWSE (pyworkflow.utils.properties.Message attribute) LABEL_BUTTON_CANCEL (pyworkflow.utils.properties.Message attribute) LABEL_BUTTON_CLOSE (pyworkflow.utils.properties.Message attribute) LABEL_BUTTON_EXEC (pyworkflow.utils.properties.Message attribute) LABEL_BUTTON_HELP (pyworkflow.utils.properties.Message attribute) LABEL_BUTTON_OK (pyworkflow.utils.properties.Message attribute) LABEL_BUTTON_RETURN (pyworkflow.utils.properties.Message attribute) LABEL_BUTTON_SAVE (pyworkflow.utils.properties.Message attribute) LABEL_BUTTON_VIS (pyworkflow.utils.properties.Message attribute) LABEL_BUTTON_WIZ (pyworkflow.utils.properties.Message attribute) LABEL_CHECKSTACK (pyworkflow.utils.properties.Message attribute) LABEL_CITE (pyworkflow.utils.properties.Message attribute) LABEL_COLS (pyworkflow.utils.properties.Message attribute) LABEL_COMMENT (pyworkflow.utils.properties.Message attribute) LABEL_CONTINUE (pyworkflow.utils.properties.Message attribute) LABEL_CONTINUE_WORKFLOW (pyworkflow.utils.properties.Message attribute) LABEL_COPY (pyworkflow.utils.properties.Message attribute) LABEL_COPYFILES (pyworkflow.utils.properties.Message attribute) LABEL_CREATE_PROJECT (pyworkflow.utils.properties.Message attribute) LABEL_CREATED (pyworkflow.utils.properties.Message attribute) LABEL_CTF_ESTI (pyworkflow.utils.properties.Message attribute) LABEL_DATA (pyworkflow.utils.properties.Message attribute) LABEL_DB (pyworkflow.utils.properties.Message attribute) LABEL_DEFAULT (pyworkflow.utils.properties.Message attribute) LABEL_DELETE (pyworkflow.utils.properties.Message attribute) LABEL_DELETE_FORM (pyworkflow.utils.properties.Message attribute) LABEL_DELETE_PROJECT (pyworkflow.utils.properties.Message attribute) LABEL_DISABLE (pyworkflow.utils.properties.Message attribute) LABEL_DISPLAY_TABLE_CONFIG (pyworkflow.utils.properties.Message attribute) LABEL_DUPLICATE (pyworkflow.utils.properties.Message attribute) LABEL_EDIT (pyworkflow.utils.properties.Message attribute) LABEL_ENABLE (pyworkflow.utils.properties.Message attribute) LABEL_EXECUTION (pyworkflow.utils.properties.Message attribute) LABEL_EXPERT (pyworkflow.utils.properties.Message attribute) LABEL_EXPERT_ADVANCE (pyworkflow.utils.properties.Message attribute) LABEL_EXPERT_EXPERT (pyworkflow.utils.properties.Message attribute) LABEL_EXPERT_NORMAL (pyworkflow.utils.properties.Message attribute) LABEL_EXPORT (pyworkflow.utils.properties.Message attribute) LABEL_EXPORT_UPLOAD (pyworkflow.utils.properties.Message attribute) LABEL_FOUND_ERROR (pyworkflow.utils.properties.Message attribute) LABEL_HELP (pyworkflow.utils.properties.Message attribute) LABEL_HOST (pyworkflow.utils.properties.Message attribute) LABEL_IMPORT_PROJECT (pyworkflow.utils.properties.Message attribute) LABEL_INPUT (pyworkflow.utils.properties.Message attribute) LABEL_INPUT_MIC (pyworkflow.utils.properties.Message attribute) LABEL_INPUT_MOVS (pyworkflow.utils.properties.Message attribute) LABEL_INPUT_PART (pyworkflow.utils.properties.Message attribute) LABEL_INPUT_VOLS (pyworkflow.utils.properties.Message attribute) LABEL_INSPECTOR (pyworkflow.utils.properties.Message attribute) LABEL_LABEL (pyworkflow.utils.properties.Message attribute) LABEL_LABEL_SELECTION (pyworkflow.utils.properties.Message attribute) LABEL_LAUNCHED (pyworkflow.utils.properties.Message attribute) LABEL_LOGS (pyworkflow.utils.properties.Message attribute) LABEL_LOGS_ERROR (pyworkflow.utils.properties.Message attribute) LABEL_LOGS_OUTPUT (pyworkflow.utils.properties.Message attribute) LABEL_LOGS_SCIPION (pyworkflow.utils.properties.Message attribute) LABEL_MAGNI_RATE (pyworkflow.utils.properties.Message attribute) LABEL_METHODS (pyworkflow.utils.properties.Message attribute) LABEL_MIRRORY (pyworkflow.utils.properties.Message attribute) LABEL_MODIFIED (pyworkflow.utils.properties.Message attribute) LABEL_MPI (pyworkflow.utils.properties.Message attribute) LABEL_NEW (pyworkflow.utils.properties.Message attribute) LABEL_OBJCREATED (pyworkflow.utils.properties.Message attribute) LABEL_OBJINFO (pyworkflow.utils.properties.Message attribute) LABEL_OBJLABEL (pyworkflow.utils.properties.Message attribute) LABEL_OBJSUMMARY (pyworkflow.utils.properties.Message attribute) LABEL_ONLY_SHIFTS (pyworkflow.utils.properties.Message attribute) LABEL_OPT_COMMENT (pyworkflow.utils.properties.Message attribute) LABEL_OUTPUT (pyworkflow.utils.properties.Message attribute) LABEL_PARALLEL (pyworkflow.utils.properties.Message attribute) LABEL_PARAM_NO (pyworkflow.utils.properties.Message attribute) LABEL_PARAM_YES (pyworkflow.utils.properties.Message attribute) LABEL_PASTE (pyworkflow.utils.properties.Message attribute) LABEL_PATTERN (pyworkflow.utils.properties.Message attribute) LABEL_PATTERNT (pyworkflow.utils.properties.Message attribute) LABEL_PATTERNU (pyworkflow.utils.properties.Message attribute) LABEL_PICK_GAUSS (pyworkflow.utils.properties.Message attribute) LABEL_PROJECT (pyworkflow.utils.properties.Message attribute) LABEL_PROJECTS (pyworkflow.utils.properties.Message attribute) LABEL_PROTTREE_NONE (pyworkflow.utils.properties.Message attribute) LABEL_QUEUE (pyworkflow.utils.properties.Message attribute) LABEL_QUEUE_NO (pyworkflow.utils.properties.Message attribute) LABEL_QUEUE_YES (pyworkflow.utils.properties.Message attribute) LABEL_REFRESH (pyworkflow.utils.properties.Message attribute) LABEL_RENAME (pyworkflow.utils.properties.Message attribute) LABEL_RENAME_PROJECT (pyworkflow.utils.properties.Message attribute) LABEL_RENDER (pyworkflow.utils.properties.Message attribute) LABEL_RESET_WORKFLOW (pyworkflow.utils.properties.Message attribute) LABEL_RESLICE (pyworkflow.utils.properties.Message attribute) LABEL_RESTART_WORKFLOW (pyworkflow.utils.properties.Message attribute) LABEL_ROWS (pyworkflow.utils.properties.Message attribute) LABEL_RUN_MODE_RESTART (pyworkflow.utils.properties.Message attribute) LABEL_RUN_MODE_RESUME (pyworkflow.utils.properties.Message attribute) LABEL_RUNMODE (pyworkflow.utils.properties.Message attribute) LABEL_RUNNAME (pyworkflow.utils.properties.Message attribute) LABEL_SAMP_MODE (pyworkflow.utils.properties.Message attribute) LABEL_SAMP_MODE_1 (pyworkflow.utils.properties.Message attribute) LABEL_SAMP_MODE_2 (pyworkflow.utils.properties.Message attribute) LABEL_SAMP_RATE (pyworkflow.utils.properties.Message attribute) LABEL_SAVE_OUTPUT (pyworkflow.utils.properties.Message attribute) LABEL_SAVED_FORM (pyworkflow.utils.properties.Message attribute) LABEL_SCANNED (pyworkflow.utils.properties.Message attribute) LABEL_SCIPION_THREADS (pyworkflow.utils.properties.Message attribute) LABEL_SELECT_ALL (pyworkflow.utils.properties.Message attribute) LABEL_SELECT_FROM (pyworkflow.utils.properties.Message attribute) LABEL_SELECT_TO (pyworkflow.utils.properties.Message attribute) LABEL_SMALLTREE (pyworkflow.utils.properties.Message attribute)

LABEL_SPH_ABERRATION (pyworkflow.utils.properties.Message attribute) LABEL_STEPS (pyworkflow.utils.properties.Message attribute) LABEL_STOP (pyworkflow.utils.properties.Message attribute) LABEL_STOP_FORM (pyworkflow.utils.properties.Message attribute) LABEL_STOP_WORKFLOW (pyworkflow.utils.properties.Message attribute) LABEL_SUMMARY (pyworkflow.utils.properties.Message attribute) LABEL_THREADS (pyworkflow.utils.properties.Message attribute) LABEL_THRESHOLD (pyworkflow.utils.properties.Message attribute) LABEL_TREE (pyworkflow.utils.properties.Message attribute) LABEL_VISIBLE (pyworkflow.utils.properties.Message attribute) LABEL_VOLTAGE (pyworkflow.utils.properties.Message attribute) LABEL_VOLUME_SELECTION (pyworkflow.utils.properties.Message attribute) LABEL_WAIT_FOR (pyworkflow.utils.properties.Message attribute) LABEL_WORKFLOW (pyworkflow.utils.properties.Message attribute) LABEL_WRAP (pyworkflow.utils.properties.Message attribute) LabelData (class in xmipp3.programs) LabelParam (class in pyworkflow.protocol.params) labelsColorMode() (pyworkflow.project.config.ProjectSettings method) LabelsDialog (class in pyworkflow.gui.project.labels) LabelSlider (class in pyworkflow.gui.widgets) LabelsList (class in pyworkflow.project.config) LabelsTreeProvider (class in pyworkflow.gui.project.labels) laplacianStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) LAST_ROUND (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) lastRoundStep() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) lastValue (pyworkflow.gui.browser.FileBrowserWindow attribute) launch() (in module pyworkflow.protocol.launch) launchGUI() (in module scipion.scripts.kickoff) launchParticlePickGUIStep() (xmipp3.protocols.protocol_particle_pick.XmippProtParticlePicking method) (xmipp3.protocols.protocol_particle_pick_pairs.XmippProtParticlePickingPairs method) launchPluginManager() (in module scipion.guiplugin) launchProtocol() (pyworkflow.project.project.Project method) (pyworkflow.tests.tests.BaseTest class method) launchSupervisedPickerGUI() (in module pwem.viewers.showj) launchTemplate() (in module scipion.scripts.kickoff) launchTemplates() (in module scipion.guiplugin) launchTiltPairPickerGUI() (in module pwem.viewers.showj) launchWorkflow() (pyworkflow.project.project.Project method) LazyDict (class in pyworkflow.utils.utils) LE (class in pyworkflow.protocol.params) leave() (pyworkflow.gui.tooltip.ToolTip method) LEFT (pyworkflow.gui.canvas.Item attribute) LEFT_CLICK (pyworkflow.constants.TK attribute) LEFT_DOUBLE_CLICK (pyworkflow.constants.TK attribute) legacyCheck() (pyworkflow.protocol.protocol.Protocol method) LegacyProtocol (class in pyworkflow.protocol.protocol) legend() (pyworkflow.gui.plotter.Plotter method) LevelFilter (class in pyworkflow.utils.log) LevelTree (class in pyworkflow.gui.graph) LevelTreeLayout (class in pyworkflow.gui.graph_layout) libDeps() (in module scipion.install.find_deps) lift() (pyworkflow.gui.canvas.Item method) (pyworkflow.gui.canvas.TextItem method) LIGHTBULB (pyworkflow.utils.properties.Icon attribute) lighter() (in module pyworkflow.utils.utils) lightgreen (pyworkflow.constants.StrColors attribute) Line (class in pyworkflow.protocol.params) LineWidget (class in pyworkflow.gui.form) Link (class in scipion.install.funcs) linkToWebSite() (scipion.install.plugin_manager.PluginBrowser method) LinuxHandler (class in pyworkflow.gui.project.utils) List (class in pyworkflow.object) listAllPlugins() (in module scipion.install.inspect_plugins) listDatasets() (in module pyworkflow.apps.pw_sync_data) ListDialog (class in pyworkflow.gui.dialog) listProjects() (pyworkflow.project.manager.Manager method) listTables() (pyworkflow.utils.dataset.DataSet method) ListTreeProvider (class in pyworkflow.gui.tree) ListTreeProviderString (class in pyworkflow.gui.tree) ListTreeProviderTemplate (class in pyworkflow.gui.tree) load() (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig class method) (pyworkflow.object.Set method) (pyworkflow.project.config.ProjectSettings class method) (pyworkflow.project.project.Project method) (pyworkflow.protocol.hosts.HostConfig class method) loadAcquisitionInfo() (pwem.protocols.protocol_import.dataimport.ScipionImport method) (pwem.protocols.protocol_import.images.ProtImportImages method) (pwem.protocols.protocol_import.micrographs.ProtImportMicBase method) (xmipp3.convert.dataimport.XmippImport method) loadAllProperties() (pyworkflow.object.Set method) loadContent() (pyworkflow.template.Template method) (pyworkflow.webservices.workflowhub.WHTemplate method) loadCoordinates() (pwem.viewers.viewer_coordinates.MainWindow method) loadCoords() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) loadCustomLoggingConfig() (pyworkflow.utils.log.LoggingConfigurator class method) loadFromMd() (pwem.objects.data.FSC method) loadInputs() (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) loadMappers() (pyworkflow.protocol.protocol.Protocol method) loadMeanAccuracy() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) loadMicSetFromFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) loadPlugins() (scipion.install.plugin_manager.PluginBrowser method) loadProject() (pyworkflow.gui.project.project.ProjectWindow method) (pyworkflow.project.manager.Manager method) loadProperty() (pyworkflow.object.Set method) loadProtocols() (pyworkflow.project.project.Project method) loadSetFromDb() (in module pwem.utils) loadSprites() (pyworkflow.utils.properties.Sprite class method) loadSteps() (pyworkflow.protocol.protocol.Protocol method) loadTrainedParams() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) loadWorkflow() (scipion.scripts.tutorial.Tutorial method) (scipion.scripts.tutorial.TutorialBetagal method) (scipion.scripts.tutorial.TutorialIntro method) LOCAL_ALIGNMENT (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes attribute) LOCAL_SEARCH (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry attribute) localAssignment() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) LOCALFILE (xmipp3.protocols.protocol_deep_center_predict.XmippProtDeepCenterPredict attribute) LocalResolutionViewer (class in pwem.viewers.viewer_localres) LocalTemplate (class in pyworkflow.template) locationToXmipp() (in module xmipp3.convert.convert) (pwem.emlib.image.image_handler.ImageHandler class method) lock (pwem.wizards.wizards_3d.callbacks.DraggablePoint attribute) LoggingConfigurator (class in pyworkflow.utils.log) LOW_RESOL (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes attribute) lower() (pyworkflow.gui.canvas.Item method) (pyworkflow.gui.canvas.TextItem method) LT (class in pyworkflow.protocol.params)

M

MacHandler (class in pyworkflow.gui.project.utils) magenta (pyworkflow.constants.StrColors attribute) magenta() (in module pyworkflow.utils.utils) (in module scipion.install.funcs) (in module scipion.scripts.config) magentaB() (in module pyworkflow.utils.utils) magentaStr() (in module pyworkflow.utils.utils) magnitude() (in module pwem.viewers.plotter) mailTo() (pyworkflow.gui.text.TaggedText static method) main() (in module pyworkflow.apps.pw_plot) (in module pyworkflow.apps.pw_sync_data) (in module scipion.install.change_rpath) (in module scipion.install.find_deps) (in module scipion.install.plugin_manager) (in module scipion.scripts.config) (in module scipion.scripts.kickoff) (pyworkflow.apps.pw_run_tests.Tester method) MAIN_COLOR (pyworkflow.constants.Color attribute) MainWindow (class in pwem.viewers.viewer_coordinates) make_request() (in module pyworkflow.webservices.workflowhub) makeBigger() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.MaskPreviewDialog method) (pwem.wizards.wizard.MaskRadiiPreviewDialog method) makeEerFilename() (in module xmipp3.convert.convert) makeFilePath() (in module pyworkflow.utils.path) makePath() (in module pyworkflow.utils.path) makePathsAndClean() (pyworkflow.protocol.protocol.Protocol method) makeResidueValuesDic() (in module pwem.viewers.viewer_localres) makeSmaller() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.MaskPreviewDialog method) (pwem.wizards.wizard.MaskRadiiPreviewDialog method) makeTmpPath() (in module pyworkflow.utils.path) makeWorkingDir() (pyworkflow.protocol.protocol.Protocol method) manageLabels() (pyworkflow.gui.project.project.ProjectWindow method) manageMaskVals() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.DownsampleDialog method) (pwem.wizards.wizard.MaskPreviewDialog method) (pwem.wizards.wizard.MaskRadiiPreviewDialog method) Manager (class in pyworkflow.project.manager) Mapper (class in pyworkflow.mapper.mapper) mapVolsWithColorkey() (in module pwem.viewers.viewer_chimera) Mask (class in pwem.objects.data) MASK_CLASSNAME (xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMaskParticles attribute) (xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMaskVolumes attribute) MASK_FILE (xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMaskParticles attribute) (xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMaskVolumes attribute) MASKDIR (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) MASKNAME (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) MaskPreview (class in pyworkflow.gui.matplotlib_image) MaskPreviewDialog (class in pwem.wizards.wizard) MaskRadiiPreviewDialog (class in pwem.wizards.wizard) MaskRadiiWizard (class in pwem.wizards.wizard) MaskRadiusWizard (class in pwem.wizards.wizard) maskStep() (xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMask method) MaskStructureWizard (class in pwem.wizards.wizards_3d.mask_structure_wizard) MaskVolumeWizard (class in pwem.wizards.wizards_3d.mask_volume_wizard) match_orientation() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) matchHyperText() (pyworkflow.gui.text.TaggedText method) matchingBfactorLocalResolution() (xmipp3.protocols.protocol_resolution_bfactor.XmippProtbfactorResolution method) matmul_serie() (in module xmipp3.utils) Matrix (class in pwem.objects.data) matrixFromGeometry() (in module xmipp3.convert.convert) MAX_PREVIEW_FILE_SIZE (pwem.Config attribute) maxId() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) maximizeWindow() (pyworkflow.gui.project.utils.LinuxHandler method) (pyworkflow.gui.project.utils.MacHandler method) (pyworkflow.gui.project.utils.OSHandler method) (pyworkflow.gui.project.utils.WindowsHandler method) md5sum() (in module pyworkflow.apps.pw_sync_data) MdFileHandler (class in pwem.viewers.filehandlers) mds() (in module xmipp3.protocols.protocol_structure_map_zernike3d) mdToCTFModel() (in module xmipp3.convert.convert) meanDoseList (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis attribute) meanGlobal (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis attribute) medianDifferences (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis attribute) medianDoseTemporal (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis attribute) MenuConfig (class in pyworkflow.project.config) mergeStep() (xmipp3.protocols.protocol_consensus_classes.XmippProtConsensusClasses method) Message (class in pyworkflow.utils.properties) MESSAGE_ASK_SINGLE_ALL (pyworkflow.utils.properties.Message attribute) MESSAGE_CONTINUE_FORM (pyworkflow.utils.properties.Message attribute) MESSAGE_CONTINUE_WORKFLOW (pyworkflow.utils.properties.Message attribute) MESSAGE_CONTINUE_WORKFLOW_WITH_RESULTS (pyworkflow.utils.properties.Message attribute) MESSAGE_DELETE_PROJECT (pyworkflow.utils.properties.Message attribute) MESSAGE_RESTART_FORM (pyworkflow.utils.properties.Message attribute) MESSAGE_RESTART_WORKFLOW (pyworkflow.utils.properties.Message attribute) MESSAGE_RESTART_WORKFLOW_WITH_RESULTS (pyworkflow.utils.properties.Message attribute) MessageDialog (class in pyworkflow.gui.dialog) MessageView (class in pyworkflow.viewer) METHOD_FOURIER (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery attribute) method_name() (in module pyworkflow.utils.echo) METHOD_REAL_SPACE (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery attribute) METHOD_SHEARS (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery attribute) methods() (pyworkflow.protocol.protocol.Protocol method) (xmipp3.protocols.protocol_preprocess.geometrical_mask.XmippGeometricalMask2D method) (xmipp3.protocols.protocol_preprocess.geometrical_mask.XmippGeometricalMask3D method) METRICS (xmipp3.protocols.protocol_consensus_classes.XmippProtConsensusClasses attribute) MIC_NAME (pwem.objects.data.Micrograph attribute) Micrograph (class in pwem.objects.data) micrograph (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) micrographId (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) MicrographsTiltPair (class in pwem.objects.data_tiltpairs) MicrographsView (class in pwem.viewers.views) micrographToCTFParam() (in module xmipp3.convert.convert) micrographToRow() (in module xmipp3.convert.convert) minms (pyworkflow.utils.profiler.Timer attribute) missingPaths() (in module pyworkflow.utils.path) MissingProjectDbException missingTables() (pyworkflow.mapper.sqlite.SqliteFlatDb method) mkdir() (in module scipion.install.funcs) MODE_AUTOMATIC (pwem.viewers.views.CoordinatesObjectView attribute) MODEL_TARGET_OPTIONS (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc attribute) modeParallel() (pyworkflow.protocol.protocol.Protocol method) modeSerial() (pyworkflow.protocol.protocol.Protocol method) ModificationNotAllowedException modifyFontSize() (pyworkflow.gui.text.TextFileViewer method) module pwem pwem.bibtex pwem.constants pwem.convert pwem.convert.atom_struct pwem.convert.headers pwem.convert.pdb_list pwem.convert.sequence pwem.convert.symmetry pwem.convert.transformations pwem.convert.trigonometry pwem.convert.utils pwem.emlib pwem.emlib.image pwem.emlib.image.image_handler pwem.emlib.image.image_readers pwem.emlib.lib pwem.emlib.metadata pwem.emlib.metadata.utils pwem.objects pwem.objects.data pwem.objects.data_flexhub pwem.objects.data_tiltpairs pwem.protocols pwem.protocols.parallel pwem.protocols.protocol pwem.protocols.protocol_2d pwem.protocols.protocol_3d pwem.protocols.protocol_align_movies pwem.protocols.protocol_alignment_assign pwem.protocols.protocol_alignment_invertHand pwem.protocols.protocol_base_flexhub pwem.protocols.protocol_batch pwem.protocols.protocol_boxsize_checkpoint pwem.protocols.protocol_boxsize_parameters pwem.protocols.protocol_classes_selector pwem.protocols.protocol_create_stream_data pwem.protocols.protocol_ctf_assign pwem.protocols.protocol_export pwem.protocols.protocol_export.protocol_export_DB pwem.protocols.protocol_extract_coordinates pwem.protocols.protocol_import pwem.protocols.protocol_import.base pwem.protocols.protocol_import.coordinates pwem.protocols.protocol_import.ctfs pwem.protocols.protocol_import.dataimport pwem.protocols.protocol_import.images pwem.protocols.protocol_import.masks pwem.protocols.protocol_import.micrographs pwem.protocols.protocol_import.particles pwem.protocols.protocol_import.sequence pwem.protocols.protocol_import.volumes pwem.protocols.protocol_mathematical_operator pwem.protocols.protocol_micrographs pwem.protocols.protocol_movie_eraser pwem.protocols.protocol_movies pwem.protocols.protocol_origin_sampling_volume pwem.protocols.protocol_particles pwem.protocols.protocol_particles_picking pwem.protocols.protocol_pdf_report pwem.protocols.protocol_projection_edit pwem.protocols.protocol_set_editor pwem.protocols.protocol_set_filter pwem.protocols.protocol_sets pwem.protocols.protocol_tests pwem.protocols.protocol_tiltpairs pwem.protocols.protocol_tools pwem.protocols.protocol_wait pwem.utils pwem.viewers pwem.viewers.filehandlers pwem.viewers.plotter pwem.viewers.showj pwem.viewers.viewer_angular_dist pwem.viewers.viewer_base pwem.viewers.viewer_chimera pwem.viewers.viewer_coordinates pwem.viewers.viewer_fsc pwem.viewers.viewer_localres pwem.viewers.viewer_pdf pwem.viewers.viewer_sequence pwem.viewers.viewer_vmd pwem.viewers.viewer_volumes pwem.viewers.viewers_data pwem.viewers.views pwem.wizards pwem.wizards.wizard pwem.wizards.wizards pwem.wizards.wizards_3d pwem.wizards.wizards_3d.callbacks pwem.wizards.wizards_3d.mask_structure_wizard pwem.wizards.wizards_3d.mask_volume_wizard pyworkflow pyworkflow.apps pyworkflow.apps.pw_manager pyworkflow.apps.pw_plot pyworkflow.apps.pw_project pyworkflow.apps.pw_protocol_list pyworkflow.apps.pw_protocol_run pyworkflow.apps.pw_run_tests pyworkflow.apps.pw_schedule_run pyworkflow.apps.pw_sleep pyworkflow.apps.pw_sync_data pyworkflow.apps.pw_viewer pyworkflow.config pyworkflow.constants pyworkflow.exceptions pyworkflow.gui pyworkflow.gui.browser pyworkflow.gui.canvas pyworkflow.gui.dialog pyworkflow.gui.form pyworkflow.gui.graph pyworkflow.gui.graph_layout pyworkflow.gui.gui pyworkflow.gui.matplotlib_image pyworkflow.gui.plotter pyworkflow.gui.project pyworkflow.gui.project.base pyworkflow.gui.project.constants pyworkflow.gui.project.labels pyworkflow.gui.project.project pyworkflow.gui.project.searchprotocol pyworkflow.gui.project.searchrun pyworkflow.gui.project.steps pyworkflow.gui.project.utils pyworkflow.gui.project.variables pyworkflow.gui.project.viewdata pyworkflow.gui.project.viewprojects pyworkflow.gui.project.viewprotocols pyworkflow.gui.project.viewprotocols_extra pyworkflow.gui.text pyworkflow.gui.tooltip pyworkflow.gui.tree pyworkflow.gui.widgets pyworkflow.mapper pyworkflow.mapper.mapper pyworkflow.mapper.sqlite pyworkflow.mapper.sqlite_db pyworkflow.object pyworkflow.plugin pyworkflow.project pyworkflow.project.config pyworkflow.project.manager pyworkflow.project.project pyworkflow.protocol pyworkflow.protocol.bibtex pyworkflow.protocol.constants pyworkflow.protocol.executor pyworkflow.protocol.hosts pyworkflow.protocol.launch pyworkflow.protocol.package pyworkflow.protocol.params pyworkflow.protocol.protocol pyworkflow.template pyworkflow.tests pyworkflow.tests.test_utils pyworkflow.tests.tests pyworkflow.utils pyworkflow.utils.dataset pyworkflow.utils.echo pyworkflow.utils.graph pyworkflow.utils.log pyworkflow.utils.path pyworkflow.utils.process pyworkflow.utils.profiler pyworkflow.utils.progressbar pyworkflow.utils.properties pyworkflow.utils.reflection pyworkflow.utils.utils pyworkflow.utils.which pyworkflow.viewer pyworkflow.webservices pyworkflow.webservices.config pyworkflow.webservices.notifier pyworkflow.webservices.repository pyworkflow.webservices.workflowhub pyworkflow.wizard scipion scipion.constants scipion.guiplugin scipion.install scipion.install.change_rpath scipion.install.clean scipion.install.find_deps scipion.install.funcs scipion.install.inspect_plugins scipion.install.install_plugin scipion.install.plugin_funcs scipion.install.plugin_manager scipion.install.update_manager scipion.scripts scipion.scripts.config scipion.scripts.fontbrowser scipion.scripts.kickoff scipion.scripts.tutorial scipion.utils xmipp3 xmipp3.base xmipp3.bibtex xmipp3.constants xmipp3.convert xmipp3.convert.convert xmipp3.convert.dataimport xmipp3.convert.io_coordinates xmipp3.programs xmipp3.protocols xmipp3.protocols.protocol_align_volume xmipp3.protocols.protocol_align_volume_and_particles xmipp3.protocols.protocol_analyze_local_ctf xmipp3.protocols.protocol_angular_graph_consistency xmipp3.protocols.protocol_apply_alignment xmipp3.protocols.protocol_apply_tilt_to_ctf xmipp3.protocols.protocol_apply_transformation_matrix xmipp3.protocols.protocol_apply_zernike3d xmipp3.protocols.protocol_assignment_tilt_pair xmipp3.protocols.protocol_break_symmetry xmipp3.protocols.protocol_center_particles xmipp3.protocols.protocol_cl2d xmipp3.protocols.protocol_cl2d_align xmipp3.protocols.protocol_cl2d_clustering xmipp3.protocols.protocol_classes_2d_mapping xmipp3.protocols.protocol_classify_pca xmipp3.protocols.protocol_classify_pca_streaming xmipp3.protocols.protocol_compare_angles xmipp3.protocols.protocol_compare_reprojections xmipp3.protocols.protocol_consensus_classes xmipp3.protocols.protocol_consensus_local_ctf xmipp3.protocols.protocol_convert_pdb xmipp3.protocols.protocol_core_analysis xmipp3.protocols.protocol_create_gallery xmipp3.protocols.protocol_ctf_consensus xmipp3.protocols.protocol_ctf_correct_wiener2d xmipp3.protocols.protocol_ctf_defocus_group xmipp3.protocols.protocol_ctf_micrographs xmipp3.protocols.protocol_deep_center xmipp3.protocols.protocol_deep_center_predict xmipp3.protocols.protocol_deep_hand xmipp3.protocols.protocol_deep_micrograph_screen xmipp3.protocols.protocol_denoise_particles xmipp3.protocols.protocol_eliminate_empty_images xmipp3.protocols.protocol_enrich xmipp3.protocols.protocol_extract_asymmetric_unit xmipp3.protocols.protocol_extract_particles xmipp3.protocols.protocol_extract_particles_movies xmipp3.protocols.protocol_extract_particles_pairs xmipp3.protocols.protocol_flexalign xmipp3.protocols.protocol_generate_reprojections xmipp3.protocols.protocol_helical_parameters xmipp3.protocols.protocol_kerdensom xmipp3.protocols.protocol_local_ctf xmipp3.protocols.protocol_mics_defocus_balancer xmipp3.protocols.protocol_ml2d xmipp3.protocols.protocol_movie_alignment_consensus xmipp3.protocols.protocol_movie_dose_analysis xmipp3.protocols.protocol_movie_gain xmipp3.protocols.protocol_movie_max_shift xmipp3.protocols.protocol_movie_split_frames xmipp3.protocols.protocol_multiple_fscs xmipp3.protocols.protocol_multireference_alignability xmipp3.protocols.protocol_normalize_strain xmipp3.protocols.protocol_particle_pick xmipp3.protocols.protocol_particle_pick_automatic xmipp3.protocols.protocol_particle_pick_consensus xmipp3.protocols.protocol_particle_pick_pairs xmipp3.protocols.protocol_particle_pick_remove_duplicates xmipp3.protocols.protocol_phantom_create xmipp3.protocols.protocol_pick_noise xmipp3.protocols.protocol_postProcessing_deepPostProcessing xmipp3.protocols.protocol_preprocess xmipp3.protocols.protocol_preprocess.geometrical_mask xmipp3.protocols.protocol_preprocess.protocol_add_noise xmipp3.protocols.protocol_preprocess.protocol_create_mask2d xmipp3.protocols.protocol_preprocess.protocol_create_mask3d xmipp3.protocols.protocol_preprocess.protocol_crop_resize xmipp3.protocols.protocol_preprocess.protocol_filter xmipp3.protocols.protocol_preprocess.protocol_image_operate xmipp3.protocols.protocol_preprocess.protocol_mask xmipp3.protocols.protocol_preprocess.protocol_movie_resize xmipp3.protocols.protocol_preprocess.protocol_preprocess xmipp3.protocols.protocol_preprocess.protocol_process xmipp3.protocols.protocol_preprocess_micrographs xmipp3.protocols.protocol_projmatch xmipp3.protocols.protocol_projmatch.projmatch_form xmipp3.protocols.protocol_projmatch.projmatch_initialize xmipp3.protocols.protocol_projmatch.projmatch_steps xmipp3.protocols.protocol_projmatch.protocol_projmatch xmipp3.protocols.protocol_random_conical_tilt xmipp3.protocols.protocol_ransac xmipp3.protocols.protocol_reconstruct_fourier xmipp3.protocols.protocol_reconstruct_highres xmipp3.protocols.protocol_reconstruct_significant xmipp3.protocols.protocol_reconstruct_swarm xmipp3.protocols.protocol_resolution3d xmipp3.protocols.protocol_resolution_bfactor xmipp3.protocols.protocol_resolution_deepres xmipp3.protocols.protocol_resolution_directional xmipp3.protocols.protocol_resolution_fso xmipp3.protocols.protocol_resolution_monogenic_signal xmipp3.protocols.protocol_rotate_volume xmipp3.protocols.protocol_rotational_symmetry xmipp3.protocols.protocol_screen_deepConsensus xmipp3.protocols.protocol_screen_deeplearning xmipp3.protocols.protocol_screen_particles xmipp3.protocols.protocol_shift_particles xmipp3.protocols.protocol_shift_volume xmipp3.protocols.protocol_simulate_ctf xmipp3.protocols.protocol_structure_map xmipp3.protocols.protocol_structure_map_zernike3d xmipp3.protocols.protocol_subtract_projection xmipp3.protocols.protocol_tilt_analysis xmipp3.protocols.protocol_trigger_data xmipp3.protocols.protocol_validate_fscq xmipp3.protocols.protocol_validate_nontilt xmipp3.protocols.protocol_validate_overfitting xmipp3.protocols.protocol_volume_adjust_sub xmipp3.protocols.protocol_volume_consensus xmipp3.protocols.protocol_volume_deform_zernike3d xmipp3.protocols.protocol_volume_local_adjust xmipp3.protocols.protocol_volume_local_sharpening xmipp3.protocols.protocol_volume_strain xmipp3.protocols.protocol_write_testC xmipp3.protocols.protocol_write_testP xmipp3.utils xmipp3.version xmipp3.viewers.plotter xmipp3.viewers.viewer

MonoResStep() (xmipp3.protocols.protocol_resolution_directional.XmippProtMonoDir method) (xmipp3.protocols.protocol_volume_local_sharpening.XmippProtLocSharp method) motion() (pyworkflow.gui.tooltip.ToolTip method) move() (pyworkflow.gui.canvas.Connector method) (pyworkflow.gui.canvas.Item method) (pyworkflow.gui.canvas.TextItem method) (pyworkflow.gui.project.viewprotocols.RunBox method) move_start() (pyworkflow.gui.canvas.Canvas method) moveFile() (in module pyworkflow.utils.path) moveItemDown() (pyworkflow.gui.tree.Tree method) moveItemUp() (pyworkflow.gui.tree.Tree method) moveParticle() (pwem.viewers.viewer_coordinates.MainWindow method) moveParticleInsideUnitCell() (in module pwem.convert.symmetry) (pwem.convert.symmetry.SymmetryHelper class method) moveParticlesInsideUnitCell() (in module pwem.convert.symmetry) moveSelectionDown() (pyworkflow.gui.tree.Tree method) moveSelectionUp() (pyworkflow.gui.tree.Tree method) moveTo() (pyworkflow.gui.canvas.Canvas method) (pyworkflow.gui.canvas.Item method) (pyworkflow.gui.project.viewprotocols.RunBox method) moveToUCStep() (pwem.protocols.protocol_projection_edit.ProtProjectionEditor method) moveTree() (in module pyworkflow.utils.path) Movie (class in pwem.objects.data) MovieAlignment (class in pwem.objects.data) MovieParticle (class in pwem.objects.data) MPI_BINDIR (pwem.Config attribute) MPI_LIBDIR (pwem.Config attribute) mrc_convert() (xmipp3.protocols.protocol_resolution_bfactor.XmippProtbfactorResolution method) (xmipp3.protocols.protocol_resolution_fso.XmippProtFSO method) MRCImageReader (class in pwem.emlib.image.image_readers) multipleItemsSelected() (pyworkflow.gui.canvas.Canvas method) multiply() (pyworkflow.object.Scalar method) MultiPointerParam (class in pyworkflow.protocol.params) MultiPointerTreeProvider (class in pyworkflow.gui.form) MultiPointerVar (class in pyworkflow.gui.form) MySocketServer (class in pwem.viewers.showj)

N

name() (in module pyworkflow.utils.echo) nearCoordinates() (pwem.viewers.viewer_coordinates.MainWindow method) needRefresh() (pyworkflow.project.project.Project method) needsGPU() (pyworkflow.protocol.protocol.Step method) neighbourhoodDirectionStep() (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) NET_TEMPLATE (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) networkReadyToPredict() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) NEW (pyworkflow.utils.properties.Icon attribute) new() (scipion.install.funcs.CommandDef method) newProtocol() (pyworkflow.project.project.Project method) (pyworkflow.tests.tests.BaseTest class method) nextSearchIndex() (pyworkflow.gui.text.TextFileViewer method) NO_ALIGNMENT (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes attribute) NO_COLOR (pyworkflow.config.Config attribute) NO_FLIP (xmipp3.protocols.protocol_flexalign.XmippProtFlexAlign attribute) NO_IMAGE_128 (pyworkflow.utils.properties.Icon attribute) NO_INFO_LOGS (pyworkflow.utils.properties.Message attribute) NO_INFO_METHODS (pyworkflow.utils.properties.Message attribute) NO_INFO_SUMMARY (pyworkflow.utils.properties.Message attribute) NO_ROTATION (xmipp3.protocols.protocol_flexalign.XmippProtFlexAlign attribute) NO_SAVE_SETTINGS (pyworkflow.utils.properties.Message attribute) NO_VIEWER_FOUND (pyworkflow.utils.properties.Message attribute) noAssignment() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) NOBAR (pyworkflow.utils.progressbar.ProgressBar attribute) Node (class in pyworkflow.utils.graph) NodeConfig (class in pyworkflow.project.config) NodeConfigList (class in pyworkflow.project.config) NonEmptyBoolCondition (class in pyworkflow.protocol.params) NonEmptyCondition (class in pyworkflow.protocol.params)

NoOutputGenerated NORM_NEW (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles attribute) NORM_OLD (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles attribute) NORM_RAMP (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles attribute) NORMAL (xmipp3.utils.Point attribute) NORMALIZATION_AUTO (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc attribute) NORMALIZATION_MASK (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc attribute) NORMALIZATION_OPTIONS (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc attribute) NORMALIZATION_STATS (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc attribute) normalize() (xmipp3.protocols.protocol_normalize_strain.XmippProtNormalizeStrain method) normalize_array() (in module xmipp3.utils) normalizeGainStep() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) normalizeStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles method) (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) NormalMode (class in pwem.objects.data) notifyWorkflow() (pyworkflow.webservices.notifier.ProjectWorkflowNotifier method) notOne() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) NUCLEOTIDES (pwem.objects.data.Alphabet attribute) NUCLEOTIDES_ALPHABET (pwem.objects.data.Alphabet attribute) numberOfSteps (pyworkflow.protocol.protocol.Protocol property) numberTests (pyworkflow.tests.tests.GTestResult attribute) NumericListParam (class in pyworkflow.protocol.params) NumericListValidator (class in pyworkflow.protocol.params) NumericRangeParam (class in pyworkflow.protocol.params) NumericRangeValidator (class in pyworkflow.protocol.params) nVols (xmipp3.protocols.protocol_align_volume.XmippProtAlignVolume attribute) (xmipp3.protocols.protocol_align_volume_and_particles.XmippProtAlignVolumeParticles attribute)

O

Object (class in pyworkflow.object) object (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData attribute) ObjectBrowser (class in pyworkflow.gui.browser) objectKey() (pyworkflow.gui.form.ScalarTreeProvider method) (pyworkflow.gui.form.SubclassesTreeProvider method) objectToRow() (in module xmipp3.convert.convert) ObjectTreeProvider (class in pyworkflow.gui.tree) ObjectView (class in pwem.viewers.views) objectView() (pwem.viewers.viewer_base.EmProtocolViewer method) ObjectWrap() (in module pyworkflow.object) OBJID (pyworkflow.utils.progressbar.ProgressBar attribute) Octahedral (class in pwem.convert.symmetry) on_motion() (pwem.wizards.wizards_3d.callbacks.DraggablePoint method) on_press() (pwem.wizards.wizards_3d.callbacks.DraggablePoint method) on_release() (pwem.wizards.wizards_3d.callbacks.DraggablePoint method) (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) onAbout() (pyworkflow.gui.project.base.ProjectBaseWindow method) onBoxSizeSlider() (pwem.viewers.viewer_coordinates.MainWindow method) onBrowseFiles() (pyworkflow.gui.project.project.ProjectManagerWindow method) (pyworkflow.gui.project.project.ProjectWindow method) onButton1Release() (pyworkflow.gui.canvas.Canvas method) onClick() (pyworkflow.gui.canvas.Canvas method) (pyworkflow.gui.text.Text method) onClickPress() (pwem.viewers.viewer_coordinates.MainWindow method) onClickRelease() (pwem.viewers.viewer_coordinates.MainWindow method) onClose() (pyworkflow.gui.browser.FileBrowser method) onConfiguration() (pyworkflow.gui.project.base.ProjectBaseWindow method) onContactSupport() (pyworkflow.gui.project.base.ProjectBaseWindow method) onControlClick() (pyworkflow.gui.canvas.Canvas method) onDebugMode() (pyworkflow.gui.project.project.ProjectWindow method) onDoubleClick() (pyworkflow.gui.canvas.Canvas method) onDrag() (pwem.viewers.viewer_coordinates.MainWindow method) (pyworkflow.gui.canvas.Canvas method) onDragActivate() (pwem.viewers.viewer_coordinates.MainWindow method) onExit() (pyworkflow.gui.project.base.ProjectBaseWindow method) (scipion.install.plugin_manager.PluginManagerWindow method) onFitActivate() (pwem.viewers.viewer_coordinates.MainWindow method) onGeneral() (pyworkflow.gui.project.project.ProjectManagerWindow method) onHelp() (scipion.install.plugin_manager.PluginManagerWindow method) onHosts() (pyworkflow.gui.project.project.ProjectManagerWindow static method) onImportWorkflow() (pyworkflow.gui.project.project.ProjectWindow method) onLeave() (pyworkflow.gui.canvas.Canvas method) onLocateAProtocol() (pyworkflow.gui.project.project.ProjectWindow method) onMotion() (pwem.viewers.viewer_coordinates.MainWindow method) (pyworkflow.gui.canvas.Canvas method) onNotes() (pyworkflow.gui.project.project.ProjectWindow method) onOnlineHelp() (pyworkflow.gui.project.base.ProjectBaseWindow method) onParticlesWindowClosing() (pwem.viewers.viewer_coordinates.MainWindow method) onProtocols() (pyworkflow.gui.project.project.ProjectManagerWindow static method) onRemoveTemporaryFiles() (pyworkflow.gui.project.project.ProjectWindow method) onRightClick() (pyworkflow.gui.canvas.Canvas method) (pyworkflow.gui.text.Text method) onSearchWorkflow() (pyworkflow.gui.project.project.ProjectWindow method) onSelectAllProtocols() (pyworkflow.gui.project.project.ProjectWindow method) onSliderMapMove() (pwem.viewers.viewer_coordinates.MainWindow method) onSliderRelease() (pwem.viewers.viewer_coordinates.MainWindow method) onTableClick() (pwem.viewers.viewer_coordinates.MainWindow method) onToggleColorMode() (pyworkflow.gui.project.project.ProjectWindow method) onUser() (pyworkflow.gui.project.project.ProjectManagerWindow static method) (scipion.install.plugin_manager.PluginManagerWindow method) onVariables() (scipion.install.plugin_manager.PluginManagerWindow method)

onZoomActivate() (pwem.viewers.viewer_coordinates.MainWindow method) onZoomImage() (pwem.viewers.viewer_coordinates.MainWindow method) open() (pwem.emlib.image.image_readers.ImageReadersRegistry class method) (pwem.emlib.image.image_readers.MRCImageReader class method) (pwem.emlib.image.image_readers.PILImageReader class method) (pwem.emlib.image.image_readers.STKImageReader class method) (pwem.emlib.image.image_readers.TiffImageReader class method) OPEN_CONNECTIONS (pyworkflow.mapper.sqlite_db.SqliteDb attribute) openedAsReadOnly() (pyworkflow.project.project.Project method) openFile() (pwem.viewers.viewer_coordinates.MainWindow method) (pyworkflow.gui.text.Text method) openLink() (pyworkflow.gui.text.TaggedText static method) openMd() (in module xmipp3.convert.convert) openPath() (pyworkflow.gui.text.Text method) openProject() (in module pyworkflow.apps.pw_project) (pyworkflow.gui.project.viewprojects.ProjectsView method) openTextFile() (in module pyworkflow.gui.text) openTextFileEditor() (in module pyworkflow.gui.text) openXmlReport() (pyworkflow.tests.tests.GTestResult method) Operation (class in scipion.install.plugin_manager) operationIndex() (scipion.install.plugin_manager.OperationList method) operationInformation() (scipion.install.plugin_manager.PluginBrowser method) OperationList (class in scipion.install.plugin_manager) operationStep() (xmipp3.protocols.protocol_preprocess.protocol_image_operate.XmippProtImageOperateParticles method) (xmipp3.protocols.protocol_preprocess.protocol_image_operate.XmippProtImageOperateVolumes method) opticalFlowAlignmentStep() (xmipp3.protocols.protocol_enrich.XmippProtEnrich method) OrderedObject (class in pyworkflow.object) ORIGIN (pwem.convert.headers.Ccp4Header attribute) ORIGINAL_CLASS_NAME_ATTRIBUTE (pyworkflow.mapper.mapper.Mapper attribute) originResampled() (pwem.objects.data.Image method) OS (class in pyworkflow.gui.project.utils) (class in pyworkflow.utils.utils) OSHandler (class in pyworkflow.gui.project.utils) otsu() (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) OutOfChainsError OUTPUT_MASK_NAME (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeParticles attribute) OUTPUT_NAME (pwem.protocols.protocol_alignment_assign.ProtAlignmentAssign attribute) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates attribute) (pwem.protocols.protocol_tiltpairs.ProtImportMicrographsTiltPairs attribute) OUTPUT_NAME1 (xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb attribute) OUTPUT_NAME2 (xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb attribute) OUTPUT_NAME3 (xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb attribute) OUTPUT_NAME4 (xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb attribute) OUTPUT_PARTICLES_NAME (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeParticles attribute) OUTPUT_PREFIX (pwem.protocols.protocol_particles_picking.ProtParticlePicking attribute) OUTPUT_SUFFIX (xmipp3.protocols.protocol_structure_map.XmippProtStructureMap attribute) (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D attribute) OUTPUTARG (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability attribute) outputCoordinates (pwem.protocols.protocol_particles_picking.ProtParticlePickingOutput attribute) outputCTF (pwem.protocols.protocol_micrographs.ProtCTFMicOutputs attribute) outputMask (pwem.protocols.protocol_import.masks.ImportMaskOutput attribute) outputMicrographs (pwem.protocols.protocol_import.micrographs.ImportMicsOutput attribute) outputMovies (pwem.protocols.protocol_import.micrographs.ImportMoviesOutput attribute) outputName (xmipp3.protocols.protocol_movie_alignment_consensus.XmippProtConsensusMovieAlignment attribute) (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking attribute) (xmipp3.protocols.protocol_particle_pick_remove_duplicates.XmippProtPickingRemoveDuplicates attribute) outputParticles (pwem.protocols.protocol_particles.ProtExtractParticlesOutput attribute) outputsToDefine (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint attribute) (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters attribute) OutputText (class in pyworkflow.gui.text) outputVolume (pwem.protocols.protocol_import.volumes.ImportVolumeOutputs attribute) outputVolumes (pwem.protocols.protocol_import.volumes.ImportVolumeOutputs attribute) Oval (class in pyworkflow.gui.canvas)

P

Package (class in pyworkflow.protocol.package) packageNames (scipion.install.update_manager.UpdateManager attribute) paint() (pyworkflow.gui.canvas.Cable method) (pyworkflow.gui.canvas.Edge method) (pyworkflow.gui.canvas.Oval method) (pyworkflow.gui.canvas.Rectangle method) (pyworkflow.gui.canvas.TextItem method) (pyworkflow.gui.graph.LevelTree method) paintPlug() (pyworkflow.gui.canvas.Connector method) (pyworkflow.gui.canvas.RoundConnector method) (pyworkflow.gui.canvas.SquareConnector method) paintPlugs() (pyworkflow.gui.canvas.Cable method) paintSocket() (pyworkflow.gui.canvas.Connector method) (pyworkflow.gui.canvas.Item method) (pyworkflow.gui.canvas.RoundConnector method) (pyworkflow.gui.canvas.SquareConnector method) paintSockets() (pyworkflow.gui.canvas.Item method) PARALLEL_BATCH_SIZE (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis attribute) (xmipp3.protocols.protocol_tilt_analysis.XmippProtTiltAnalysis attribute) Param (class in pyworkflow.protocol.params) PARAM1 (pwem.protocols.protocol_mathematical_operator.ProtMathematicalOperator attribute) PARAM2 (pwem.protocols.protocol_mathematical_operator.ProtMathematicalOperator attribute) PARAM_FILE_NAME (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery attribute) ParamWidget (class in pyworkflow.gui.form) parseArgs() (in module pyworkflow.apps.pw_schedule_run) parseBibTex() (in module pyworkflow.utils.utils) parseContent() (pyworkflow.template.Template method) parseHyperText() (in module pyworkflow.utils.utils) parseTopRankParam() (pwem.protocols.protocol_set_filter.ProtSetFilter method) partiallyCleaningFolder() (in module pwem.convert.atom_struct) Particle (class in pwem.objects.data) ParticleFileHandler (class in pwem.viewers.filehandlers) ParticleFlex (class in pwem.objects.data_flexhub) ParticleMaskRadiusWizard (class in pwem.wizards.wizard) Particles (xmipp3.protocols.protocol_align_volume_and_particles.AlignVolPartOutputs attribute) PARTICLES (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections attribute) PARTICLES_TEMPLATE (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) ParticlesMaskRadiiWizard (class in pwem.wizards.wizard) ParticlesTiltPair (class in pwem.objects.data_tiltpairs) particleToRow() (in module xmipp3.convert.convert) PATH (pyworkflow.config.VarTypes attribute) PathData (class in xmipp3.utils) PathParam (class in pyworkflow.protocol.params) pcaTraining() (xmipp3.protocols.protocol_classify_pca.XmippProtClassifyPca method) (xmipp3.protocols.protocol_classify_pca_streaming.XmippProtClassifyPcaStreaming method) PDB (pwem.convert.atom_struct.AtomicStructHandler attribute) PDB_REF (pwem.convert.pdb_list.PDBList attribute) pdbDownloadStep() (pwem.protocols.protocol_import.volumes.ProtImportPdb method) (pwem.protocols.protocol_import.volumes.ProtImportSetOfAtomStructs method) PdbFile (class in pwem.objects.data) PDBList (class in pwem.convert.pdb_list) pdbToCif() (in module pwem.convert.atom_struct) PDBVolumeWizard (class in pwem.wizards.wizard) PDFReportViewer (class in pwem.viewers.viewer_pdf) phantomProject() (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) phaseFlipStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles method) pickingActivate() (pwem.viewers.viewer_coordinates.MainWindow method) pickMicrographListStep() (pwem.protocols.protocol_particles_picking.ProtParticlePickingAuto method) pickMicrographStep() (pwem.protocols.protocol_particles_picking.ProtParticlePickingAuto method) pickNoise() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) pickNoise_prepareInput() (in module xmipp3.protocols.protocol_pick_noise) pickNoiseStep() (xmipp3.protocols.protocol_pick_noise.XmippProtPickNoise method) PILImageReader (class in pwem.emlib.image.image_readers) pipInstall() (scipion.install.funcs.CondaCommandDef method) plot_sphere() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) plotAngularDistribution() (pwem.viewers.plotter.EmPlotter method) (pwem.viewers.viewer_angular_dist.AngularDistributionViewer static method) plotAngularDistribution3D() (pwem.viewers.plotter.EmPlotter method) plotAngularDistributionBase() (pwem.viewers.plotter.EmPlotter method) plotAngularDistributionFromMd() (pwem.viewers.plotter.EmPlotter method) plotAngularDistributionFromSet() (pwem.viewers.plotter.EmPlotter method) plotAngularDistributionHistogram() (pwem.viewers.plotter.EmPlotter method) PlotData (class in pwem.viewers.plotter) plotData() (pwem.viewers.plotter.EmPlotter method) plotDataBar() (pwem.viewers.plotter.EmPlotter method) plotDoseAnalysis() (in module xmipp3.protocols.protocol_movie_dose_analysis) plotDoseAnalysisDiff() (in module xmipp3.protocols.protocol_movie_dose_analysis) plotFsc() (pwem.viewers.viewer_fsc.FscViewer method) plotHist() (pwem.viewers.plotter.EmPlotter method) plotHistogram() (pwem.viewers.viewer_coordinates.MainWindow method) plotMatrix() (pwem.viewers.plotter.EmPlotter method) plotMd() (xmipp3.viewers.plotter.XmippPlotter method) plotMdAngularDistribution() (xmipp3.viewers.plotter.XmippPlotter method) plotMdFile() (xmipp3.viewers.plotter.XmippPlotter method) plotScatter() (pwem.viewers.plotter.EmPlotter method) (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) plotScatterMd() (xmipp3.viewers.plotter.XmippPlotter method) Plotter (class in pyworkflow.gui.plotter) Plugin (class in pwem) (class in pyworkflow.plugin) (class in xmipp3) PLUGIN (pyworkflow.utils.properties.PluginStates attribute) PLUGIN_AUTHORS (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginInformation attribute) plugin_callback() (pyworkflow.gui.gui.Window method) PLUGIN_CONFIG_PROTOCOLS (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig attribute) PLUGIN_DESCRIPTION (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginInformation attribute) PLUGIN_MANAGER (pyworkflow.constants.DOCSITEURLS attribute) PLUGIN_NAME (pyworkflow.utils.properties.PluginInformation attribute) PLUGIN_PACKAGE (pyworkflow.utils.properties.Icon attribute) PLUGIN_RELEASE_DATE (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginInformation attribute) PLUGIN_URL (pyworkflow.utils.properties.PluginInformation attribute) PLUGIN_VERSION (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginInformation attribute) PluginBrowser (class in scipion.install.plugin_manager) PluginHelp (class in scipion.install.plugin_manager) PluginInfo (class in scipion.install.plugin_funcs) PluginInformation (class in pyworkflow.utils.properties) PluginManager (class in scipion.install.plugin_manager) PluginManagerWindow (class in scipion.install.plugin_manager) PluginRepository (class in scipion.install.plugin_funcs) PluginStates (class in pyworkflow.utils.properties) PluginTree (class in scipion.install.plugin_manager) Point (class in xmipp3.utils) Pointer (class in pyworkflow.object) PointerList (class in pyworkflow.object) PointerParam (class in pyworkflow.protocol.params) PointerVar (class in pyworkflow.gui.form) pointsNone() (pyworkflow.object.Pointer method) populateTree() (in module pyworkflow.gui.project.viewdata) (pyworkflow.gui.project.viewprotocols.ProtocolsView method) postProcessing() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) postProcessMaskStep() (xmipp3.protocols.protocol_preprocess.protocol_create_mask2d.XmippProtCreateMask2D method) (xmipp3.protocols.protocol_preprocess.protocol_create_mask3d.XmippProtCreateMask3D method) PRE_PROC_MICs_PATH (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) PRECESSING (pyworkflow.utils.properties.PluginStates attribute) predict() (xmipp3.protocols.protocol_deep_center.XmippProtDeepCenter method) (xmipp3.protocols.protocol_deep_center_predict.XmippProtDeepCenterPredict method) (xmipp3.protocols.protocol_screen_deeplearning.XmippProtScreenDeepLearning method) PREDICT_BATCH_MAX (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) predictCNN() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) PREDICTING (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) predictionsOn() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) predictStep() (xmipp3.protocols.protocol_deep_hand.XmippProtDeepHand method) prefixAttribute() (in module xmipp3.convert.convert) prepareImages() (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase method) (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyClasses method) (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyParticles method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) prepareInput() (xmipp3.protocols.protocol_pick_noise.XmippProtPickNoise method) prepareMask() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) prepareOutput() (xmipp3.protocols.protocol_volume_strain.XmippProtVolumeStrain method) prepareReferences() (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) prepareReferenceStep() (xmipp3.protocols.protocol_multiple_fscs.XmippProtMultipleFSCs method) PREPROCESS_BATCH_MAX (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) PREPROCESSING (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) preprocessMicsStep() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) preprocessStep() (xmipp3.protocols.protocol_deep_hand.XmippProtDeepHand method) press_shift() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) PRETRAINED (xmipp3.protocols.protocol_deep_center_predict.XmippProtDeepCenterPredict attribute) prettyDate() (in module pyworkflow.utils.utils) prettyDelta() (in module pyworkflow.utils.utils) prettyDict() (in module pyworkflow.utils.utils) prettyLog() (in module pyworkflow.utils.utils) prettySize() (in module pyworkflow.utils.utils) prettyTime() (in module pyworkflow.utils.utils) prettyTimestamp() (in module pyworkflow.utils.utils) prettyXml() (in module pyworkflow.utils.utils) Preview (class in pyworkflow.gui.matplotlib_image) PreviewDialog (class in pwem.wizards.wizard) PREVIOUS (xmipp3.protocols.protocol_deep_center_predict.XmippProtDeepCenterPredict attribute) printAll() (pyworkflow.object.Object method) printBinInfoStr() (scipion.install.plugin_funcs.PluginInfo method) printColumns() (pwem.viewers.showj.ColumnsConfig method) printDict() (pwem.emlib.metadata.utils.Row method) printHelp() (scipion.install.funcs.Environment method) printInfo() (pyworkflow.plugin.Domain class method) printInstances() (in module pyworkflow.utils.profiler) printLastLogLines() (pyworkflow.tests.tests.BaseTest static method) printObjDict() (pyworkflow.object.Object method) printPluginInfoStr() (scipion.install.plugin_funcs.PluginRepository method) printPlugins() (in module scipion.install.inspect_plugins) printTests() (pyworkflow.apps.pw_run_tests.Tester method) printTraceBack() (in module pyworkflow.utils.utils) process() (pyworkflow.gui.dialog.FlashMessage method) processConversion() (xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb method) processImportDict() (pwem.protocols.protocol_import.images.ProtImportImages method) (pyworkflow.protocol.protocol.Protocol method) PROCESSING (pyworkflow.utils.properties.Icon attribute) processing_item() (scipion.install.plugin_manager.PluginTree method) processMicrographListStep() (xmipp3.protocols.protocol_tilt_analysis.XmippProtTiltAnalysis method) processMovieStep() (pwem.protocols.protocol_movies.ProtProcessMovies method) produceAlignedImagesStep() (xmipp3.base.ProjMatcher method) produceProjections() (xmipp3.protocols.protocol_generate_reprojections.XmippProtGenerateReprojections method) produceResiduals() (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) PRODUCTION (pyworkflow.utils.properties.Icon attribute) progInPath() (in module scipion.install.funcs) ProgramDb (class in xmipp3.programs) ProgramKeywordsRank (class in xmipp3.programs) ProgressBar (class in pyworkflow.utils.progressbar) Project (class in pyworkflow.project.project) ProjectBaseWindow (class in pyworkflow.gui.project.base) ProjectCreateWindow (class in pyworkflow.gui.project.viewprojects) ProjectDataView (class in pyworkflow.gui.project.viewdata) ProjectImportWindow (class in pyworkflow.gui.project.viewprojects) ProjectInfo (class in pyworkflow.project.manager) projectInitialVolume() (xmipp3.protocols.protocol_ransac.XmippProtRansac method) projectionLibraryStep() (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) (xmipp3.protocols.protocol_validate_nontilt.XmippProtValidateNonTilt method) projectionMatchingStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) (xmipp3.protocols.protocol_validate_nontilt.XmippProtValidateNonTilt method) projectionStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) ProjectManagerWindow (class in pyworkflow.gui.project.project) ProjectRunsTreeProvider (class in pyworkflow.gui.tree) ProjectSettings (class in pyworkflow.project.config) ProjectsView (class in pyworkflow.gui.project.viewprojects) ProjectTCPRequestHandler (class in pyworkflow.gui.project.project) ProjectTCPServer (class in pyworkflow.gui.project.project) ProjectWindow (class in pyworkflow.gui.project.project) ProjectWorkflowNotifier (class in pyworkflow.webservices.notifier) ProjMatcher (class in xmipp3.base) projMatchStep() (xmipp3.base.ProjMatcher method) (xmipp3.protocols.protocol_ransac.XmippProtRansac method) projMatchStepAdapted() (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) Prot2D (class in pwem.protocols.protocol_2d) Prot3D (class in pwem.protocols.protocol_3d) PROT_DISABLED (pyworkflow.utils.properties.Icon attribute) ProtAlign2D (class in pwem.protocols.protocol_2d) ProtAlignmentAssign (class in pwem.protocols.protocol_alignment_assign) ProtAlignmentInvertHand (class in pwem.protocols.protocol_alignment_invertHand) ProtAlignMovies (class in pwem.protocols.protocol_align_movies) ProtAlignVolume (class in pwem.protocols.protocol_3d) ProtAnalysis2D (class in pwem.protocols.protocol_2d) ProtAnalysis3D (class in pwem.protocols.protocol_3d) ProtAverageFrames (class in pwem.protocols.protocol_align_movies) ProtBoxSizeCheckpoint (class in pwem.protocols.protocol_boxsize_checkpoint) ProtBoxSizeParameters (class in pwem.protocols.protocol_boxsize_parameters) ProtClassesSelector (class in pwem.protocols.protocol_classes_selector) ProtClassify2D (class in pwem.protocols.protocol_2d) ProtClassify3D (class in pwem.protocols.protocol_3d) ProtCreateFSC (class in pwem.protocols.protocol_batch) ProtCreateMask (class in pwem.protocols.protocol_batch) ProtCreateMask2D (class in pwem.protocols.protocol_2d) ProtCreateMask3D (class in pwem.protocols.protocol_3d) ProtCreateStreamData (class in pwem.protocols.protocol_create_stream_data) ProtCrossSubSet (class in pwem.protocols.protocol_sets) ProtCTFAssign (class in pwem.protocols.protocol_ctf_assign) ProtCTFMicOutputs (class in pwem.protocols.protocol_micrographs) ProtCTFMicrographs (class in pwem.protocols.protocol_micrographs) PROTEIN_ALPHABET (pwem.objects.data.Alphabet attribute) ProtEvenClassify2D (class in pwem.protocols.protocol_2d) ProtExportDataBases (class in pwem.protocols.protocol_export.protocol_export_DB) ProtExtractCoords (class in pwem.protocols.protocol_extract_coordinates) ProtExtractMovieParticles (class in pwem.protocols.protocol_movies) ProtExtractParticles (class in pwem.protocols.protocol_particles) ProtExtractParticlesOutput (class in pwem.protocols.protocol_particles) ProtExtractParticlesPair (class in pwem.protocols.protocol_particles) ProtFilterParticles (class in pwem.protocols.protocol_particles) ProtFilterVolumes (class in pwem.protocols.protocol_3d) ProtFitting3D (class in pwem.protocols.protocol_3d) ProtFlexBase (class in pwem.protocols.protocol_base_flexhub) ProtImport (class in pwem.protocols.protocol_import.base) ProtImportAverages (class in pwem.protocols.protocol_import.particles) ProtImportBase (class in pyworkflow.protocol.protocol) ProtImportCoordinates (class in pwem.protocols.protocol_import.coordinates) ProtImportCoordinatesPairs (class in pwem.protocols.protocol_import.coordinates) ProtImportCTF (class in pwem.protocols.protocol_import.ctfs) ProtImportFiles (class in pwem.protocols.protocol_import.base) ProtImportImages (class in pwem.protocols.protocol_import.images) ProtImportMask (class in pwem.protocols.protocol_import.masks) ProtImportMicBase (class in pwem.protocols.protocol_import.micrographs) ProtImportMicrographs (class in pwem.protocols.protocol_import.micrographs) ProtImportMicrographsTiltPairs (class in pwem.protocols.protocol_tiltpairs) ProtImportMovies (class in pwem.protocols.protocol_import.micrographs) ProtImportParticles (class in pwem.protocols.protocol_import.particles) ProtImportPdb (class in pwem.protocols.protocol_import.volumes) ProtImportSequence (class in pwem.protocols.protocol_import.sequence) ProtImportSetOfAtomStructs (class in pwem.protocols.protocol_import.volumes) ProtImportVolumes (class in pwem.protocols.protocol_import.volumes) ProtInitialVolume (class in pwem.protocols.protocol_3d) ProtManualCheckpoint (class in pwem.protocols.protocol_tools) ProtMaskParticles (class in pwem.protocols.protocol_particles) ProtMaskVolumes (class in pwem.protocols.protocol_3d) ProtMathematicalOperator (class in pwem.protocols.protocol_mathematical_operator) ProtMicrographs (class in pwem.protocols.protocol_micrographs) ProtMovieAssignGain (class in pwem.protocols.protocol_movies) ProtMovieEraser (class in pwem.protocols.protocol_movie_eraser) Protocol (class in pyworkflow.protocol.protocol) ProtocolClassParam (class in pyworkflow.protocol.params) ProtocolClassTreeProvider (class in pyworkflow.gui.form) ProtocolConfig (class in pyworkflow.gui.project.viewprotocols_extra) ProtocolsView (class in pyworkflow.gui.project.viewprotocols) ProtocolTCPRequestHandler (class in pwem.viewers.showj) ProtocolTreeConfig (class in pyworkflow.gui.project.viewprotocols_extra) ProtocolTreeProvider (class in pyworkflow.gui.project.searchprotocol) ProtocolViewer (class in pyworkflow.viewer) ProtOperateParticles (class in pwem.protocols.protocol_particles) ProtOperateVolumes (class in pwem.protocols.protocol_3d) ProtOrigSampling (class in pwem.protocols.protocol_origin_sampling_volume) ProtParticlePicking (class in pwem.protocols.protocol_particles_picking) ProtParticlePickingAuto (class in pwem.protocols.protocol_particles_picking) ProtParticlePickingOutput (class in pwem.protocols.protocol_particles_picking) ProtParticles (class in pwem.protocols.protocol_particles) ProtPDFReport (class in pwem.protocols.protocol_pdf_report) ProtPickingConsensusOutput (class in xmipp3.protocols.protocol_particle_pick_consensus) ProtPickingDifference (class in pwem.protocols.protocol_particles_picking) ProtPreprocessMicrographs (class in pwem.protocols.protocol_micrographs) ProtPreprocessVolumes (class in pwem.protocols.protocol_3d) ProtProcessMovies (class in pwem.protocols.protocol_movies) ProtProcessParticles (class in pwem.protocols.protocol_particles) ProtProjectionEditor (class in pwem.protocols.protocol_projection_edit) ProtReconstruct3D (class in pwem.protocols.protocol_3d) ProtRefine3D (class in pwem.protocols.protocol_3d) ProtSetAggregate (class in pwem.protocols.protocol_sets) ProtSetEditor (class in pwem.protocols.protocol_set_editor) ProtSetFilter (class in pwem.protocols.protocol_set_filter) ProtSets (class in pwem.protocols.protocol_sets) ProtSplitSet (class in pwem.protocols.protocol_sets) ProtStreamingBase (class in pyworkflow.protocol.protocol) ProtStress (class in pwem.protocols.protocol_tests) ProtSubSet (class in pwem.protocols.protocol_sets) ProtSubSetByCoord (class in pwem.protocols.protocol_sets) ProtSubSetByMic (class in pwem.protocols.protocol_sets) ProtTestParallel (class in pwem.protocols.parallel) ProtTests (class in pwem.protocols.protocol_tests) ProtUnionSet (class in pwem.protocols.protocol_sets) ProtUserSubSet (class in pwem.protocols.protocol_batch) ProtWait (class in pwem.protocols.protocol_wait) prunePaths() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) PSD_LABELS (pwem.viewers.views.CtfView attribute) PsdPreview (class in pyworkflow.gui.matplotlib_image) PURPLE (pyworkflow.utils.properties.colorText attribute) pwem module pwem (scipion.install.update_manager.UpdateManager attribute) pwem.bibtex module pwem.constants module pwem.convert module pwem.convert.atom_struct module pwem.convert.headers module pwem.convert.pdb_list module pwem.convert.sequence module

pwem.convert.symmetry module pwem.convert.transformations module pwem.convert.trigonometry module pwem.convert.utils module pwem.emlib module pwem.emlib.image module pwem.emlib.image.image_handler module pwem.emlib.image.image_readers module pwem.emlib.lib module pwem.emlib.metadata module pwem.emlib.metadata.utils module pwem.objects module pwem.objects.data module pwem.objects.data_flexhub module pwem.objects.data_tiltpairs module pwem.protocols module pwem.protocols.parallel module pwem.protocols.protocol module pwem.protocols.protocol_2d module pwem.protocols.protocol_3d module pwem.protocols.protocol_align_movies module pwem.protocols.protocol_alignment_assign module pwem.protocols.protocol_alignment_invertHand module pwem.protocols.protocol_base_flexhub module pwem.protocols.protocol_batch module pwem.protocols.protocol_boxsize_checkpoint module pwem.protocols.protocol_boxsize_parameters module pwem.protocols.protocol_classes_selector module pwem.protocols.protocol_create_stream_data module pwem.protocols.protocol_ctf_assign module pwem.protocols.protocol_export module pwem.protocols.protocol_export.protocol_export_DB module pwem.protocols.protocol_extract_coordinates module pwem.protocols.protocol_import module pwem.protocols.protocol_import.base module pwem.protocols.protocol_import.coordinates module pwem.protocols.protocol_import.ctfs module pwem.protocols.protocol_import.dataimport module pwem.protocols.protocol_import.images module pwem.protocols.protocol_import.masks module pwem.protocols.protocol_import.micrographs module pwem.protocols.protocol_import.particles module pwem.protocols.protocol_import.sequence module pwem.protocols.protocol_import.volumes module pwem.protocols.protocol_mathematical_operator module pwem.protocols.protocol_micrographs module pwem.protocols.protocol_movie_eraser module pwem.protocols.protocol_movies module pwem.protocols.protocol_origin_sampling_volume module pwem.protocols.protocol_particles module pwem.protocols.protocol_particles_picking module pwem.protocols.protocol_pdf_report module pwem.protocols.protocol_projection_edit module pwem.protocols.protocol_set_editor module pwem.protocols.protocol_set_filter module pwem.protocols.protocol_sets module pwem.protocols.protocol_tests module pwem.protocols.protocol_tiltpairs module pwem.protocols.protocol_tools module pwem.protocols.protocol_wait module pwem.utils module pwem.viewers module pwem.viewers.filehandlers module pwem.viewers.plotter module pwem.viewers.showj module pwem.viewers.viewer_angular_dist module pwem.viewers.viewer_base module pwem.viewers.viewer_chimera module pwem.viewers.viewer_coordinates module pwem.viewers.viewer_fsc module pwem.viewers.viewer_localres module pwem.viewers.viewer_pdf module pwem.viewers.viewer_sequence module pwem.viewers.viewer_vmd module pwem.viewers.viewer_volumes module pwem.viewers.viewers_data module pwem.viewers.views module pwem.wizards module pwem.wizards.wizard module pwem.wizards.wizards module pwem.wizards.wizards_3d module pwem.wizards.wizards_3d.callbacks module pwem.wizards.wizards_3d.mask_structure_wizard module pwem.wizards.wizards_3d.mask_volume_wizard module PYTHON_FILE (pyworkflow.utils.properties.Icon attribute) PythonFormulaeWizard (class in pwem.wizards.wizards) PythonFormulaWizardX1 (class in pwem.wizards.wizards) PythonFormulaWizardX2 (class in pwem.wizards.wizards) PythonTopRankWizard (class in pwem.wizards.wizards) pyworkflow module pyworkflow (scipion.install.update_manager.UpdateManager attribute) pyworkflow.apps module pyworkflow.apps.pw_manager module pyworkflow.apps.pw_plot module pyworkflow.apps.pw_project module pyworkflow.apps.pw_protocol_list module pyworkflow.apps.pw_protocol_run module pyworkflow.apps.pw_run_tests module pyworkflow.apps.pw_schedule_run module pyworkflow.apps.pw_sleep module pyworkflow.apps.pw_sync_data module pyworkflow.apps.pw_viewer module pyworkflow.config module pyworkflow.constants module pyworkflow.exceptions module pyworkflow.gui module pyworkflow.gui.browser module pyworkflow.gui.canvas module pyworkflow.gui.dialog module pyworkflow.gui.form module pyworkflow.gui.graph module pyworkflow.gui.graph_layout module pyworkflow.gui.gui module pyworkflow.gui.matplotlib_image module pyworkflow.gui.plotter module pyworkflow.gui.project module pyworkflow.gui.project.base module pyworkflow.gui.project.constants module pyworkflow.gui.project.labels module pyworkflow.gui.project.project module pyworkflow.gui.project.searchprotocol module pyworkflow.gui.project.searchrun module pyworkflow.gui.project.steps module pyworkflow.gui.project.utils module pyworkflow.gui.project.variables module pyworkflow.gui.project.viewdata module pyworkflow.gui.project.viewprojects module pyworkflow.gui.project.viewprotocols module pyworkflow.gui.project.viewprotocols_extra module pyworkflow.gui.text module pyworkflow.gui.tooltip module pyworkflow.gui.tree module pyworkflow.gui.widgets module pyworkflow.mapper module pyworkflow.mapper.mapper module pyworkflow.mapper.sqlite module pyworkflow.mapper.sqlite_db module pyworkflow.object module pyworkflow.plugin module pyworkflow.project module pyworkflow.project.config module pyworkflow.project.manager module pyworkflow.project.project module pyworkflow.protocol module pyworkflow.protocol.bibtex module pyworkflow.protocol.constants module pyworkflow.protocol.executor module pyworkflow.protocol.hosts module pyworkflow.protocol.launch module pyworkflow.protocol.package module pyworkflow.protocol.params module pyworkflow.protocol.protocol module pyworkflow.template module pyworkflow.tests module pyworkflow.tests.test_utils module pyworkflow.tests.tests module pyworkflow.utils module pyworkflow.utils.dataset module pyworkflow.utils.echo module pyworkflow.utils.graph module pyworkflow.utils.log module pyworkflow.utils.path module pyworkflow.utils.process module pyworkflow.utils.profiler module pyworkflow.utils.progressbar module pyworkflow.utils.properties module pyworkflow.utils.reflection module pyworkflow.utils.utils module pyworkflow.utils.which module pyworkflow.viewer module pyworkflow.webservices module pyworkflow.webservices.config module pyworkflow.webservices.notifier module pyworkflow.webservices.repository module pyworkflow.webservices.workflowhub module pyworkflow.wizard module PyworkflowException

Q

qualifyParticles() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) QueueDialog (class in pyworkflow.gui.form)

QueueStepExecutor (class in pyworkflow.protocol.executor) QueueSystemConfig (class in pyworkflow.protocol.hosts)

R

radius (pyworkflow.gui.canvas.RoundConnector attribute) randomizeStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles method) (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) Range (class in pyworkflow.protocol.params) rangeStr() (pwem.objects.data.FramesRange method) rankingStep() (pwem.protocols.protocol_set_filter.ProtSetFilter method) ransacIterationStep() (xmipp3.protocols.protocol_ransac.XmippProtRansac method) RATIO (pyworkflow.utils.properties.Sprite attribute) read() (pwem.convert.atom_struct.AtomicStructHandler method) (pwem.emlib.image.image_handler.ImageHandler method) (pwem.emlib.image.image_readers.STKImageReader class method) (pwem.emlib.metadata.utils.RowMetaData method) (xmipp3.base.XmippSet method) read_clusters_from_txt() (xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering method) readAnglesFromMicrographs() (in module xmipp3.convert.convert) readAngularDistFile() (pwem.viewers.viewer_chimera.ChimeraAngDist method) readBinary() (pwem.emlib.image.image_readers.STKImageReader class method) readCoordinates() (in module xmipp3.convert.convert) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs method) readCoordsFromMics() (pwem.protocols.protocol_particles_picking.ProtParticlePickingAuto method) (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) readCTFModel() (in module xmipp3.convert.convert) readFile() (pyworkflow.gui.text.OutputText method) readFromFile() (pwem.emlib.metadata.utils.Row method) readFromMd() (pwem.emlib.metadata.utils.Row method) readFromPDBDatabase() (pwem.convert.atom_struct.AtomicStructHandler method) readHeader() (pwem.convert.headers.Ccp4Header method) (pwem.emlib.image.image_readers.STKImageReader class method) readImage() (in module xmipp3.utils) (pwem.emlib.image.image_readers.STKImageReader class method) readImages() (xmipp3.protocols.protocol_classes_2d_mapping.ScatterImageMarker method) readInfoField() (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) readLowLevel() (pwem.convert.atom_struct.AtomicStructHandler method) readMetaDataOutput() (xmipp3.protocols.protocol_resolution_monogenic_signal.XmippProtMonoRes method) readNumpy() (pwem.emlib.image.image_readers.STKImageReader class method) readOutputDict() (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) readPartsFromMics() (pwem.protocols.protocol_particles.ProtExtractParticles method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) readPosCoordinates() (in module xmipp3.convert.convert) readProperties() (in module pyworkflow.utils.utils) readSequenceFromFile() (pwem.convert.sequence.SequenceHandler method) readSequencesFromFile() (pwem.convert.sequence.SequenceHandler method) readSetOfClasses() (in module xmipp3.convert.convert) readSetOfClasses2D() (in module xmipp3.convert.convert) readSetOfClasses3D() (in module xmipp3.convert.convert) readSetOfClassesVol() (in module xmipp3.convert.convert) readSetOfCoordinates() (in module xmipp3.convert.convert) (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) readSetOfCoordsFromPosFnames() (in module xmipp3.convert.io_coordinates) readSetOfImages() (in module xmipp3.convert.convert) readSetOfMicrographs() (in module xmipp3.convert.convert) readSetOfMovieParticles() (in module xmipp3.convert.convert) readSetOfParticles() (in module xmipp3.convert.convert) readSetOfVolumes() (in module xmipp3.convert.convert) readShiftsMovieAlignment() (in module xmipp3.convert.convert) readStack() (pwem.objects.data.SetOfImages method) readyPreliminarPrediction() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) readyToExtractMicFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) readyToPredictMicFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) readyToPreprocessMics() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) readyToTrainMicFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) realignStep() (xmipp3.protocols.protocol_center_particles.XmippProtCenterParticles method) realPath() (pyworkflow.project.manager.ProjectInfo method) reconstruct() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) reconstructClass() (xmipp3.protocols.protocol_random_conical_tilt.XmippProtRCT method) reconstructionStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) (xmipp3.protocols.protocol_validate_overfitting.XmippProtValidateOverfitting method) reconstructNewVolumes() (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) reconstructStep() (xmipp3.protocols.protocol_ransac.XmippProtRansac method) (xmipp3.protocols.protocol_reconstruct_fourier.XmippProtReconstructFourier method) recoveryPointer() (pwem.viewers.viewer_coordinates.MainWindow method) Rectangle (class in pyworkflow.gui.canvas) red (pyworkflow.constants.StrColors attribute) RED (pyworkflow.utils.properties.colorText attribute) red() (in module pyworkflow.utils.utils) (in module scipion.install.funcs) (in module scipion.scripts.config) RED_COLOR (pyworkflow.constants.Color attribute) red_methods (xmipp3.protocols.protocol_classes_2d_mapping.XmippProtCL2DMap attribute) redB() (in module pyworkflow.utils.utils) redStr() (in module pyworkflow.utils.utils) reEstimateCtfStep() (pwem.protocols.protocol_micrographs.ProtCTFMicrographs method) ref (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) referenceIntersectionStep() (xmipp3.protocols.protocol_consensus_classes.XmippProtConsensusClasses method) refineDefocus() (xmipp3.protocols.protocol_local_ctf.XmippProtLocalCTF method) refresh() (pyworkflow.gui.dialog.ListDialog method) refreshAll() (pyworkflow.gui.text.TextFileViewer method) refreshData() (pyworkflow.gui.project.viewdata.ProjectDataView method) refreshDisplayedRuns() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) refreshInThreads() (pyworkflow.config.Config class method) refreshOutput() (pyworkflow.gui.text.TextFileViewer method) refreshPlugin() (pyworkflow.plugin.Domain class method) refreshRuns() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) RegexParam (class in pyworkflow.protocol.params) register() (pyworkflow.config.VariablesRegistry class method) registerConfig() (pwem.viewers.viewers_data.DataViewer class method) (pwem.viewers.viewers_data.RegistryViewerConfig class method) registerCoords() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs method) (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_particle_pick_pairs.XmippProtParticlePickingPairs method) registerEvenBoxSize() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) registerFileHandler() (pyworkflow.gui.browser.FileTreeProvider class method) registerHandlers() (pyworkflow.gui.browser.FileBrowserWindow method) registerObjectCommand() (pyworkflow.gui.project.project.ProjectWindow class method) registerOutput() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) (pwem.protocols.protocol_boxsize_parameters.ProtBoxSizeParameters method) registerParam() (pyworkflow.protocol.params.Form method) registerPlugin() (pyworkflow.plugin.Domain class method) registerPluginMenu() (pyworkflow.gui.gui.Window class method) RegistryViewerConfig (class in pwem.viewers.viewers_data) REJ_AND (xmipp3.protocols.protocol_movie_max_shift.XmippProtMovieMaxShift attribute) REJ_FRAME (xmipp3.protocols.protocol_movie_max_shift.XmippProtMovieMaxShift attribute) REJ_MAXZSCORE (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles attribute) REJ_MOVIE (xmipp3.protocols.protocol_movie_max_shift.XmippProtMovieMaxShift attribute) REJ_NONE (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles attribute) REJ_OR (xmipp3.protocols.protocol_movie_max_shift.XmippProtMovieMaxShift attribute) REJ_PERCENTAGE (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles attribute) REJ_PERCENTAGE_SSNR (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles attribute) REJ_TYPES (xmipp3.protocols.protocol_movie_max_shift.XmippProtMovieMaxShift attribute) REJ_VARGINI (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles attribute) REJ_VARIANCE (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles attribute) rejectByPopulation() (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyClasses method) rejectByVariance() (in module xmipp3.protocols.protocol_screen_particles) RelationParam (class in pyworkflow.protocol.params) RelationsTreeProvider (class in pyworkflow.gui.form) release_shift() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) reloadInstalledPlugin() (scipion.install.plugin_manager.PluginBrowser method) relocateSockets() (pyworkflow.gui.canvas.Item method) remove() (pyworkflow.gui.form.MultiPointerVar method) (pyworkflow.gui.form.PointerVar method) remove_outliers() (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) remove_projection_direction() (pwem.wizards.wizards_3d.callbacks.DraggablePoint method) removeBaseExt() (in module pyworkflow.utils.path) removeCoordinates() (pwem.viewers.viewer_coordinates.MainWindow method) removeDuplicatesStep() (xmipp3.protocols.protocol_particle_pick_remove_duplicates.XmippProtPickingRemoveDuplicates method) removeDustStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles method) (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) removeExt() (in module pyworkflow.utils.path) removeExtended() (pyworkflow.object.Pointer method) removeFileType() (pwem.emlib.image.image_handler.ImageHandler class method) removeHighlightFromLabel() (pyworkflow.gui.widgets.LabelSlider method) removeJobId() (pyworkflow.protocol.protocol.Protocol method) removeLabel() (pwem.emlib.metadata.utils.Row method) removeLastPoint() (xmipp3.utils.PathData method) removeNode() (pyworkflow.project.config.NodeConfigList method) (pyworkflow.project.config.ProjectSettings method) removeObject() (pyworkflow.gui.form.MultiPointerTreeProvider method) removeOperation() (scipion.install.plugin_manager.OperationList method) renameChain() (pwem.convert.atom_struct.AtomicStructHandler method) renameChains() (pwem.convert.atom_struct.AtomicStructHandler method)

renameGpuIds() (pyworkflow.protocol.executor.QueueStepExecutor method) renameProject() (pyworkflow.gui.project.viewprojects.ProjectsView method) (pyworkflow.project.manager.Manager method) RENDER_LABELS (pwem.viewers.views.MicrographsView attribute) renderLine() (in module pyworkflow.utils.path) renderTextFile() (in module pyworkflow.utils.path) renumberChain() (pwem.convert.atom_struct.AtomicStructHandler method) reorganizeGraph() (pyworkflow.gui.canvas.Canvas method) REP_SET_TYPE (pwem.objects.data_flexhub.SetOfClassesFlex attribute) (pwem.objects.data_flexhub.SetOfClassesStructFlex attribute) REP_TYPE (pwem.objects.data.Class3D attribute) (pwem.objects.data.SetOfClasses attribute) (pwem.objects.data.SetOfClasses2D attribute) (pwem.objects.data.SetOfClasses3D attribute) (pwem.objects.data.SetOfParticles attribute) (pwem.objects.data.SetOfVolumes attribute) (pwem.objects.data_flexhub.ClassFlex attribute) (pwem.objects.data_flexhub.ClassStructFlex attribute) (pwem.objects.data_flexhub.SetOfClassesFlex attribute) (pwem.objects.data_flexhub.SetOfClassesStructFlex attribute) (pwem.objects.data_flexhub.SetOfVolumesFlex attribute) REPLACE (pyworkflow.utils.utils.Environ attribute) replace() (in module scipion.install.change_rpath) replace_at_index() (xmipp3.protocols.protocol_extract_asymmetric_unit.XmippProtExtractUnit method) replaceBaseExt() (in module pyworkflow.utils.path) replaceEnvVariables() (pyworkflow.template.Template method) replaceExt() (in module pyworkflow.utils.path) replaceOcuppancyWithAttribute() (in module pwem.viewers.viewer_localres) reportError() (pyworkflow.tests.tests.GTestResult method) requiresGpu() (pyworkflow.protocol.protocol.Protocol method) reset() (pyworkflow.gui.text.HyperlinkManager method) resetMicrograph() (pwem.viewers.viewer_coordinates.MainWindow method) resetProtocol() (pyworkflow.project.project.Project method) resetWorkFlow() (pyworkflow.project.project.Project method) residualDatabase (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain attribute) resize() (pyworkflow.gui.form.FormWindow method) RESIZE_DIMENSIONS (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles attribute) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippResizeHelper attribute) RESIZE_FACTOR (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles attribute) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippResizeHelper attribute) RESIZE_PYRAMID (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippResizeHelper attribute) RESIZE_SAMPLINGRATE (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles attribute) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippResizeHelper attribute) resizeInputStep() (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes method) resizeRadious() (pwem.viewers.viewer_coordinates.MainWindow method) resizeStep() (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeParticles method) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeVolumes method) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippResizeHelper class method) (xmipp3.protocols.protocol_ransac.XmippProtRansac method) RESLICE_X_NEGATIVE (pyworkflow.utils.properties.Message attribute) RESLICE_X_POSITIVE (pyworkflow.utils.properties.Message attribute) RESLICE_Y_NEGATIVE (pyworkflow.utils.properties.Message attribute) RESLICE_Y_POSITIVE (pyworkflow.utils.properties.Message attribute) RESLICE_Z_NEGATIVE (pyworkflow.utils.properties.Message attribute) resolutionMonogenicSignalStep() (xmipp3.protocols.protocol_resolution_monogenic_signal.XmippProtMonoRes method) resolutionStep() (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes method) resolveTemplate() (in module scipion.scripts.kickoff) restoreMicrograph() (pwem.viewers.viewer_coordinates.MainWindow method) restoreStdoutAndErr() (in module pyworkflow.utils.log) resultCancel() (pyworkflow.gui.dialog.Dialog method) resultNo() (pyworkflow.gui.dialog.Dialog method) resultYes() (pyworkflow.gui.dialog.Dialog method) resumableStepGeneratorStep() (pyworkflow.protocol.protocol.ProtStreamingBase method) retrieve_pdb_file() (pwem.convert.pdb_list.PDBList method) retrievePreviousPassModel() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) retrievePreviousRunModel() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) retrieveTrainSets() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) retry() (in module pwem.convert.atom_struct) RETURN (pyworkflow.constants.TK attribute) (pyworkflow.utils.properties.KEYSYM attribute) rewriteClassBlockStep() (xmipp3.protocols.protocol_kerdensom.KendersomBaseClassify method) rgb_to_hex() (in module pyworkflow.utils.utils) RIGHT (pyworkflow.gui.canvas.Item attribute) rigidAlignmentMapping() (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) rigidRegistration() (in module xmipp3.protocols.protocol_structure_map_zernike3d) ROCKET (pyworkflow.utils.properties.Icon attribute) ROT_X_90_CLOCKWISE (pwem.objects.data.Transform attribute) ROT_X_90_COUNTERCLOCKWISE (pwem.objects.data.Transform attribute) ROT_Y_90_CLOCKWISE (pwem.objects.data.Transform attribute) ROT_Y_90_COUNTERCLOCKWISE (pwem.objects.data.Transform attribute) ROT_Z_90_CLOCKWISE (pwem.objects.data.Transform attribute) ROT_Z_90_COUNTERCLOCKWISE (pwem.objects.data.Transform attribute) rotateDiStep() (pwem.protocols.protocol_projection_edit.ProtProjectionEditor method) rotateIcosahedralStep() (pwem.protocols.protocol_projection_edit.ProtProjectionEditor method) rotateIcoStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) rotateStep() (pwem.protocols.protocol_projection_edit.ProtProjectionEditor method) (xmipp3.protocols.protocol_rotate_volume.XmippProtRotateVolume method) rotateTetraStep() (pwem.protocols.protocol_projection_edit.ProtProjectionEditor method) rotateVectorStep() (pwem.protocols.protocol_projection_edit.ProtProjectionEditor method) rotateVolume() (pwem.emlib.image.image_handler.ImageHandler method) rotation() (in module xmipp3.protocols.protocol_tilt_analysis) (in module xmipp3.utils) round_to_nearest() (in module pwem.utils) RoundConnector (class in pyworkflow.gui.canvas) RoundedTextBox (class in pyworkflow.gui.canvas) Row (class in pwem.emlib.metadata.utils) rowFromMd() (in module xmipp3.convert.convert) RowMetaData (class in pwem.emlib.metadata.utils) rowToAcquisition() (in module xmipp3.convert.convert) rowToAlignment() (in module xmipp3.convert.convert) rowToAlignmentEmtable() (in module xmipp3.protocols.protocol_classify_pca) rowToClass() (in module xmipp3.convert.convert) rowToCoordinate() (in module xmipp3.convert.convert) rowToCtfModel() (in module xmipp3.convert.convert) rowToImage() (in module xmipp3.convert.convert) rowToMicrograph() (in module xmipp3.convert.convert) rowToMovieParticle() (in module xmipp3.convert.convert) rowToObject() (in module xmipp3.convert.convert) rowToParticle() (in module xmipp3.convert.convert) rowToVolume() (in module xmipp3.convert.convert) run() (pyworkflow.protocol.executor.StepThread method) (pyworkflow.protocol.protocol.Protocol method) (pyworkflow.protocol.protocol.Step method) RUN_COLUMN (pyworkflow.gui.tree.ProjectRunsTreeProvider attribute) runAngularProjectLibraryStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) runAssignImagesToReferences() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) runBlocresStep() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) RunBox (class in pyworkflow.gui.project.viewprotocols) runCalculateFscStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) runClassificationSteps() (xmipp3.protocols.protocol_classify_pca_streaming.XmippProtClassifyPcaStreaming method) runCoarseSearch() (xmipp3.base.HelicalFinder method) runCommand() (in module pyworkflow.utils.process) runCreateOutputStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) runExecuteCtfGroupsStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) runFilterVolumeStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) runFineSearch() (xmipp3.base.HelicalFinder method) runInitAngularReferenceFileStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) RunIOTreeProvider (class in pyworkflow.gui.project.viewprotocols_extra) runJavaIJapp() (in module pwem.viewers.showj) runJob() (in module pyworkflow.utils.process) (pyworkflow.protocol.executor.QueueStepExecutor method) (pyworkflow.protocol.executor.StepExecutor method) (pyworkflow.protocol.protocol.Protocol method) RunJobStep (class in pyworkflow.protocol.protocol) runObjectCommand() (pyworkflow.gui.project.project.ProjectWindow method) runOperation() (scipion.install.plugin_manager.Operation method) runPCASteps() (xmipp3.protocols.protocol_classify_pca_streaming.XmippProtClassifyPcaStreaming method) runProgram() (in module pwem.utils) (pwem.viewers.viewer_chimera.Chimera class method) runProjectionMatching() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) runProtocol() (pyworkflow.protocol.protocol.Protocol method) runProtocolMain() (in module pyworkflow.protocol.protocol) runReconstructionStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) RUNS_CANVAS_NAME (pyworkflow.gui.project.viewprotocols.ProtocolsView attribute) RUNS_TREE (pyworkflow.utils.properties.Icon attribute) RunScheduler (class in pyworkflow.apps.pw_schedule_run) runSingleTest() (pyworkflow.apps.pw_run_tests.Tester method) runsKey() (pyworkflow.gui.tree.ProjectRunsTreeProvider method) runSteps() (pyworkflow.protocol.executor.StepExecutor method) (pyworkflow.protocol.executor.ThreadStepExecutor method) runStoreResolutionStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) RunsTreeProvider (class in pyworkflow.gui.project.searchrun) runSymmetrize() (xmipp3.base.HelicalFinder method) runTests() (pyworkflow.apps.pw_run_tests.Tester method) runTransformMaskStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) runVolumeConvertStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) runXmippProgram() (xmipp3.Plugin class method)

S

save() (pyworkflow.config.VariablesRegistry class method) (pyworkflow.gui.form.FormWindow method) saveConfig() (in module pyworkflow.gui.gui) saveCorrelation() (xmipp3.protocols.protocol_structure_map.XmippProtStructureMap method) (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) saveData() (pwem.viewers.views.TableView method) saveDeformation() (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) savefig() (pyworkflow.gui.plotter.Plotter method) saveFile() (pwem.convert.sequence.SequenceHandler method) saveFiles() (pwem.convert.sequence.SequenceHandler method) saveFileSequencesToAlign() (in module pwem.convert.sequence) saveProtocol() (pyworkflow.project.project.Project method) (pyworkflow.tests.tests.BaseTest class method) saveSettings() (pyworkflow.gui.project.project.ProjectWindow method) (pyworkflow.project.project.Project method) saveTrainedParams() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) Scalar (class in pyworkflow.object) ScalarTreeProvider (class in pyworkflow.gui.form) ScalarWithPointerVar (class in pyworkflow.gui.form) scale() (pwem.objects.data.Coordinate method) (pwem.objects.data.Transform method) scale2DStack() (pwem.emlib.image.image_handler.ImageHandler class method) scaleCoordinate() (pwem.objects.data.Particle method) scaleFourier() (pwem.emlib.image.image_handler.ImageHandler class method) scaleShifts() (pwem.objects.data.Transform method) scaleSplines() (pwem.emlib.image.image_handler.ImageHandler class method) scatter3DPlot() (pwem.viewers.plotter.EmPlotter method) ScatterImageMarker (class in xmipp3.protocols.protocol_classes_2d_mapping) schedule() (in module pyworkflow.protocol.launch) (pyworkflow.apps.pw_schedule_run.RunScheduler method) (pyworkflow.gui.form.FormWindow method) schedulePlot() (pyworkflow.gui.project.project.ProjectWindow method) scheduleProject() (in module scipion.scripts.kickoff) scheduleProtocol() (pyworkflow.project.project.Project method) scipion module scipion (scipion.install.update_manager.UpdateManager attribute) scipion.constants module scipion.guiplugin module scipion.install module scipion.install.change_rpath module scipion.install.clean module scipion.install.find_deps module scipion.install.funcs module scipion.install.inspect_plugins module scipion.install.install_plugin module scipion.install.plugin_funcs module scipion.install.plugin_manager module scipion.install.update_manager module scipion.scripts module scipion.scripts.config module scipion.scripts.fontbrowser module scipion.scripts.kickoff module scipion.scripts.tutorial module scipion.utils module SCIPION_BG_COLOR (pyworkflow.config.Config attribute) SCIPION_CANCEL_FASTCOPY (pyworkflow.config.Config attribute) SCIPION_CONFIG (pyworkflow.config.Config attribute) SCIPION_CONTRAST_COLOR (pyworkflow.config.Config attribute) SCIPION_CWD (pyworkflow.config.Config attribute) SCIPION_DEFAULT_EXECUTION_ACTION (pyworkflow.config.Config attribute) SCIPION_DOMAIN (pyworkflow.config.Config attribute) SCIPION_EM_NEW_FILE_CHECK_SEC (pwem.Config attribute) SCIPION_FONT_NAME (pyworkflow.config.Config attribute) SCIPION_FONT_SIZE (pyworkflow.config.Config attribute) SCIPION_GUI_CANCEL_AUTO_REFRESH (pyworkflow.config.Config attribute) SCIPION_GUI_REFRESH_IN_THREAD (pyworkflow.config.Config attribute) SCIPION_GUI_REFRESH_INITIAL_WAIT (pyworkflow.config.Config attribute) SCIPION_HOME (pyworkflow.config.Config attribute) SCIPION_HOME_DEFINED (pyworkflow.config.Config attribute) SCIPION_HOSTS (pyworkflow.config.Config attribute) SCIPION_ICON (pyworkflow.utils.properties.Icon attribute) SCIPION_ICON_PROJ (pyworkflow.utils.properties.Icon attribute) SCIPION_ICON_PROJS (pyworkflow.utils.properties.Icon attribute) SCIPION_ICON_PROT (pyworkflow.utils.properties.Icon attribute) SCIPION_ICON_ZOOM (pyworkflow.config.Config attribute) SCIPION_LOCAL_CONFIG (pyworkflow.config.Config attribute) SCIPION_LOG (pyworkflow.config.Config attribute) SCIPION_LOG_CONFIG (pyworkflow.config.Config attribute) SCIPION_LOG_FORMAT (pyworkflow.config.Config attribute) SCIPION_LOG_LEVEL (pyworkflow.config.Config attribute) SCIPION_LOGO_SMALL (pyworkflow.utils.properties.Icon attribute) SCIPION_LOGS (pyworkflow.config.Config attribute) SCIPION_MAIN_COLOR (pyworkflow.config.Config attribute) SCIPION_MAPPER_USE_TEMPLATE (pyworkflow.config.Config attribute) SCIPION_NOTES_ARGS (pyworkflow.config.Config attribute) SCIPION_NOTES_FILE (pyworkflow.config.Config attribute) SCIPION_NOTES_PROGRAM (pyworkflow.config.Config attribute) SCIPION_NOTIFY (pyworkflow.config.Config attribute) SCIPION_PLUGIN_JSON (pyworkflow.config.Config attribute) SCIPION_PLUGIN_REPO_URL (pyworkflow.config.Config attribute) SCIPION_PRIORITY_PACKAGE_LIST (pyworkflow.config.Config attribute) SCIPION_PROTOCOLS (pyworkflow.config.Config attribute) SCIPION_SCRATCH (pyworkflow.config.Config attribute) SCIPION_SHOW_TEXT_IN_TOOLBAR (pyworkflow.config.Config attribute) SCIPION_SOFTWARE (pyworkflow.config.Config attribute) SCIPION_SPRITES_FILE (pyworkflow.config.Config attribute) SCIPION_STEPS_CHECK_SEC (pyworkflow.config.Config attribute) SCIPION_SUPPORT_EMAIL (pyworkflow.config.Config attribute) SCIPION_TEST_NOSYNC (pyworkflow.config.Config attribute) SCIPION_TESTS (pyworkflow.config.Config attribute) SCIPION_TESTS_CMD (pyworkflow.config.Config attribute) SCIPION_TESTS_OUTPUT (pyworkflow.config.Config attribute) SCIPION_TEXT_EDITOR (pyworkflow.config.Config attribute) SCIPION_UPDATE_SET_ATTEMPT_WAIT (pyworkflow.config.Config attribute) SCIPION_UPDATE_SET_ATTEMPTS (pyworkflow.config.Config attribute) SCIPION_URL (pyworkflow.config.Config attribute) SCIPION_URL_SOFTWARE (pyworkflow.config.Config attribute) SCIPION_URL_TESTDATA (pyworkflow.config.Config attribute) SCIPION_USE_QUEUE (pyworkflow.config.Config attribute) SCIPION_USER_DATA (pyworkflow.config.Config attribute) ScipionImport (class in pwem.protocols.protocol_import.dataimport) scipionMMCIFIO (class in pwem.convert.atom_struct) scoreByGiniCoeff (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) scoreByVariance (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) scoreFinalVolumes() (xmipp3.protocols.protocol_ransac.XmippProtRansac method) scoreProtocols() (pyworkflow.gui.project.searchprotocol.SearchProtocolWindow method) scroll() (pyworkflow.gui.widgets.Scrollable method) Scrollable (class in pyworkflow.gui.widgets) scrollH() (pyworkflow.gui.widgets.Scrollable method) scrollV() (pyworkflow.gui.widgets.Scrollable method) search() (pyworkflow.gui.tree.Tree method) (pyworkflow.webservices.repository.WorkflowRepository method) SearchBaseWindow (class in pyworkflow.gui.dialog) searchEstimatedGainPath() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) searchPaths() (in module scipion.install.find_deps) SearchProtocolWindow (class in pyworkflow.gui.project.searchprotocol) SearchRunWindow (class in pyworkflow.gui.project.searchrun) Section (class in pyworkflow.protocol.params) SectionFrame (class in pyworkflow.gui.form) SectionWidget (class in pyworkflow.gui.form) seek() (pwem.emlib.image.image_readers.STKImageReader class method) SEG_AMIN (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes attribute) SEG_AUTO (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes attribute) SEG_DALTON (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes attribute) SEG_VOXEL (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes attribute) segmentStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) SELECT (pyworkflow.mapper.sqlite.SqliteObjectsDb attribute) SELECT_ALL (pyworkflow.utils.properties.Icon attribute) SELECT_RELATION (pyworkflow.mapper.sqlite.SqliteObjectsDb attribute) SELECT_RELATIONS (pyworkflow.mapper.sqlite.SqliteObjectsDb attribute) selectAll() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) selectAllBatch() (pyworkflow.mapper.sqlite.SqliteMapper method) selectAllObjects() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) SelectAttributeWizard (class in pwem.wizards.wizards) selectBy() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) selectByClass() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) selectById() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) selectCategories() (xmipp3.programs.ProgramDb method) SelectChainWizard (class in pwem.wizards.wizards) selectChild() (pyworkflow.gui.tree.Tree method) selectChildByIndex() (pyworkflow.gui.tree.Tree method) selectCmd() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteObjectsDb method) selectCoordinate() (pwem.viewers.viewer_coordinates.MainWindow method) selectCtfStep() (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method) SELECTED (xmipp3.utils.Point attribute) selectedText() (pyworkflow.gui.text.TextFileViewer method) selectFirst() (pyworkflow.mapper.mapper.Mapper method) selectionListener() (pyworkflow.gui.canvas.Oval method) (pyworkflow.gui.canvas.Rectangle method) selectItem() (pyworkflow.gui.canvas.Canvas method) selectLabels() (xmipp3.programs.ProgramDb method) selectMissingObjectsByAncestor() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) selectObjectById() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteObjectsDb method) selectObjectsBy() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteObjectsDb method) selectObjectsByAncestor() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) selectObjectsByParent() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) selectObjectsWhere() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteObjectsDb method) selectProgram() (xmipp3.programs.ProgramDb method) selectPrograms() (xmipp3.programs.ProgramDb method) selectRelationChilds() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) selectRelationParents() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) selectRelationsByCreator() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) selectRelationsByName() (pyworkflow.mapper.sqlite.SqliteObjectsDb method) SelectResidueWizard (class in pwem.wizards.wizards) SEQ_TYPE (pwem.objects.data.Alphabet attribute) Sequence (class in pwem.objects.data) sequenceDatabaseDownloadStep() (pwem.protocols.protocol_import.sequence.ProtImportSequence method) SequenceHandler (class in pwem.convert.sequence) sequenceLength() (in module pwem.convert.sequence) SequenceViewer (class in pwem.viewers.viewer_sequence) serve_forever() (pwem.viewers.showj.MySocketServer method) Set (class in pyworkflow.object) set() (pyworkflow.gui.form.BoolVar method) (pyworkflow.gui.form.ComboVar method) (pyworkflow.gui.form.MultiPointerVar method) (pyworkflow.gui.form.ParamWidget method) (pyworkflow.gui.form.PointerVar method) (pyworkflow.gui.form.ScalarWithPointerVar method) (pyworkflow.gui.form.SectionWidget method) (pyworkflow.gui.form.TextVar method) (pyworkflow.gui.widgets.AutoScrollbar method) (pyworkflow.object.Object method) (pyworkflow.object.Pointer method) (pyworkflow.protocol.params.DeprecatedParam method) (pyworkflow.utils.utils.Environ method) set_axes_equal() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) SET_DIFFERENCE (pwem.protocols.protocol_sets.ProtSubSet attribute) SET_INTERSECTION (pwem.protocols.protocol_sets.ProtSubSet attribute) setAborted() (pyworkflow.protocol.protocol.Protocol method) (pyworkflow.protocol.protocol.Step method) setAcquisition() (pwem.objects.data.Image method) (pwem.objects.data.SetOfImages method) setAddress() (pyworkflow.protocol.hosts.HostConfig method) setAlignment() (pwem.objects.data.Movie method) (pwem.objects.data.SetOfImages method) (pwem.objects.data_flexhub.AtomStructFlex method) (pwem.objects.data_flexhub.SetOfAtomStructFlex method) setAlignment2D() (pwem.objects.data.SetOfImages method) setAlignment3D() (pwem.objects.data.SetOfImages method) setAlignmentProj() (pwem.objects.data.SetOfImages method) setAmplitudeContrast() (pwem.objects.data.Acquisition method) setAngles() (pwem.objects.data_tiltpairs.Angles method) (pwem.objects.data_tiltpairs.CoordinatesTiltPair method) setAttr() (pwem.objects.data_flexhub.FlexInfo method) setAttribute() (in module xmipp3.protocols.protocol_ctf_consensus) (in module xmipp3.protocols.protocol_movie_alignment_consensus) (in module xmipp3.protocols.protocol_movie_dose_analysis) (in module xmipp3.protocols.protocol_tilt_analysis) setAttributesFromDict() (pyworkflow.object.Object method) setAttributeValue() (pyworkflow.object.Object method) setAvgSet() (pwem.objects.data.SetOfDefocusGroup method) setBackend() (pyworkflow.gui.plotter.Plotter class method) setBoxSize() (pwem.objects.data.SetOfCoordinates method) setBrowser() (pyworkflow.gui.browser.BrowserWindow method) setCancelCommand() (pyworkflow.protocol.hosts.QueueSystemConfig method) setCanvas() (pyworkflow.gui.graph.LevelTree method) setCellDimensions() (pwem.convert.headers.Ccp4Header method) setChangeCallback() (pyworkflow.gui.widgets.ComboBox method) setCheckCommand() (pyworkflow.protocol.hosts.QueueSystemConfig method) setClassesDict() (pyworkflow.object.Set method) setClassId() (pwem.objects.data.Particle method) (pwem.objects.data.Volume method) setCollectivity() (pwem.objects.data.NormalMode method) setColor() (pyworkflow.project.config.Label method) setColorMode() (pyworkflow.project.config.ProjectSettings method) setComment() (pyworkflow.gui.project.project.ProjectWindow method) (pyworkflow.project.project.Project method) setCommonFonts() (in module pyworkflow.gui.gui) setCoordinate() (pwem.objects.data.Particle method) setCoordinates() (pwem.objects.data.SetOfParticles method) setCoordsPair() (pwem.objects.data_tiltpairs.ParticlesTiltPair method) setCreationTime() (pyworkflow.project.config.ProjectSettings method) setCTF() (pwem.objects.data.Image method) setDark() (pwem.objects.data.SetOfMovies method) setData() (pwem.objects.data.FSC method) setDbPath() (pyworkflow.project.project.Project method) setDefault() (pyworkflow.protocol.params.Param method) (scipion.install.funcs.Environment method) (scipion.install.funcs.Target method) setDefaultLoggingContext() (in module pyworkflow.utils.log) setDefocusAngle() (pwem.objects.data.CTFModel method) setDefocusU() (pwem.objects.data.CTFModel method) setDefocusV() (pwem.objects.data.CTFModel method) setDescription() (pwem.objects.data.Sequence method) setDim() (pwem.objects.data.SetOfImages method) setDims() (pwem.convert.headers.Ccp4Header method) setDir() (pyworkflow.gui.browser.FileTreeProvider method) setDiscarded() (xmipp3.utils.Point method) setDomain() (pyworkflow.config.Config class method) setDoseInitial() (pwem.objects.data.Acquisition method) setDosePerFrame() (pwem.objects.data.Acquisition method) setDownsample() (pwem.objects.data.SetOfImages method) setEnabled() (pyworkflow.object.Object method) setExpanded() (pyworkflow.project.config.NodeConfig method) setExpert() (pyworkflow.protocol.params.FormElement method) setExtended() (pyworkflow.object.Pointer method) setExtendedParts() (pyworkflow.object.Pointer method) setFailed() (pyworkflow.protocol.protocol.Protocol method) (pyworkflow.protocol.protocol.Step method) setFakedRemotePluginInfo() (scipion.install.plugin_funcs.PluginInfo method) setFileName() (pwem.objects.data.EMFile method) (pwem.objects.data.Image method) setFinished() (pyworkflow.protocol.protocol.Step method) setFirstFrame() (pwem.objects.data.FramesRange method) setFirstFrameIndex() (pwem.objects.data.FramesRange method) setFitQuality() (pwem.objects.data.CTFModel method) setFlexInfo() (pwem.objects.data_flexhub.AtomStructFlex method) (pwem.objects.data_flexhub.ParticleFlex method) (pwem.objects.data_flexhub.SetOfAtomStructFlex method) (pwem.objects.data_flexhub.SetOfParticlesFlex method) (pwem.objects.data_flexhub.SetOfVolumesFlex method) (pwem.objects.data_flexhub.VolumeFlex method) setFont() (in module pyworkflow.gui.gui) setFrameId() (pwem.objects.data.MovieParticle method) setFramesRange() (pwem.objects.data.Movie method) (pwem.objects.data.SetOfMovies method) setFreq() (pwem.wizards.wizard.CtfDialog static method) setGain() (pwem.objects.data.SetOfMovies method) setGridSampling() (pwem.convert.headers.Ccp4Header method) setHalfMaps() (pwem.objects.data.Volume method) setHasCTF() (pwem.objects.data.SetOfImages method) setHeader() (pwem.convert.headers.Ccp4Header method) setHostConfig() (pyworkflow.protocol.protocol.Protocol method) setHostFullName() (pyworkflow.protocol.protocol.Protocol method) setHostName() (pyworkflow.protocol.hosts.HostConfig method) (pyworkflow.protocol.protocol.Protocol method) setHostPath() (pyworkflow.protocol.hosts.HostConfig method) setId() (pwem.objects.data.Sequence method) setImage() (pyworkflow.gui.widgets.Button method) setImages() (pwem.objects.data.SetOfClasses method) setImagesClass() (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) setImagesType() (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) setImportant() (pyworkflow.protocol.params.FormElement method) setIndex() (pwem.objects.data.Image method) (pyworkflow.gui.text.TextFileViewer method) (pyworkflow.protocol.protocol.Step method) setInputFscList() (pwem.protocols.protocol_batch.ProtCreateFSC method) setInputMics() (xmipp3.protocols.protocol_movie_max_shift.XmippProtMovieMaxShift method) setInputObj() (pwem.protocols.protocol_batch.ProtCreateFSC method) setInteractive() (pyworkflow.protocol.protocol.Step method) setIsAmplitudeCorrected() (pwem.objects.data.SetOfImages method) setISPG() (pwem.convert.headers.Ccp4Header method) setIsPhaseFlipped() (pwem.objects.data.SetOfImages method) setIsSubparticles() (pwem.objects.data.SetOfParticles method) setJobDoneRegex() (pyworkflow.protocol.hosts.QueueSystemConfig method) setJobId() (pyworkflow.protocol.protocol.Protocol method) setJobIds() (pyworkflow.protocol.protocol.Protocol method) setLabel() (pyworkflow.gui.matplotlib_image.Preview method) (pyworkflow.protocol.hosts.HostConfig method) (pyworkflow.utils.graph.Node method) setLabels() (pyworkflow.project.config.NodeConfig method) setLabelToRender() (pyworkflow.utils.dataset.Table method) setLastFrame() (pwem.objects.data.FramesRange method) setLifeTime() (pyworkflow.project.config.ProjectSettings method) setLocalPluginInfo() (scipion.install.plugin_funcs.PluginInfo method) setLocation() (pwem.objects.data.Image method) (pwem.objects.data_flexhub.AtomStructFlex method) setMagnification() (pwem.objects.data.Acquisition method) setMandatory() (pyworkflow.protocol.hosts.QueueSystemConfig method) setMapper() (pyworkflow.protocol.protocol.Protocol method) setMapperClass() (pyworkflow.object.Set method) setMatrix() (pwem.objects.data.Matrix method) (pwem.objects.data.Transform method) setMaxSet() (pwem.objects.data.SetOfDefocusGroup method) setMd() (xmipp3.base.XmippSet method) SetMdIterator (class in pwem.emlib.metadata.utils) setMemory() (pwem.viewers.views.DataView method) setMessage() (pyworkflow.gui.dialog.FloatingMessage method) setMicId() (pwem.objects.data.Coordinate method) (pwem.objects.data.Particle method) setMicName() (pwem.objects.data.Coordinate method) (pwem.objects.data.Micrograph method) setMicrograph() (pwem.objects.data.Coordinate method) (pwem.objects.data.CTFModel method) setMicrographs() (pwem.objects.data.SetOfCoordinates method) (pwem.objects.data.SetOfCTF method) setMicsPair() (pwem.objects.data_tiltpairs.CoordinatesTiltPair method) setMinSet() (pwem.objects.data.SetOfDefocusGroup method) setMode() (pwem.convert.headers.Ccp4Header method) setModeFile() (pwem.objects.data.NormalMode method) setMpiCommand() (pyworkflow.protocol.hosts.HostConfig method) setMRCSamplingRate() (in module pwem.convert.headers) (pwem.objects.data.Image method)

setName() (pyworkflow.object.Object method) (pyworkflow.project.config.Label method) (pyworkflow.protocol.hosts.QueueSystemConfig method) setNumberSlices() (pyworkflow.utils.dataset.DataSet method) setObjComment() (pyworkflow.object.Object method) setObjCreation() (pyworkflow.object.Object method) setObjId() (in module xmipp3.convert.convert) (pyworkflow.object.Object method) setObjLabel() (pyworkflow.object.Object method) setObjStatus() (scipion.install.plugin_manager.Operation method) SetOfAngles (class in pwem.objects.data_tiltpairs) SetOfAtomStructFlex (class in pwem.objects.data_flexhub) SetOfAtomStructs (class in pwem.objects.data) SetOfAverages (class in pwem.objects.data) SetOfClasses (class in pwem.objects.data) SetOfClasses2D (class in pwem.objects.data) SetOfClasses3D (class in pwem.objects.data) SetOfClassesFlex (class in pwem.objects.data_flexhub) SetOfClassesStructFlex (class in pwem.objects.data_flexhub) SetOfClassesVol (class in pwem.objects.data) SetOfCoordinates (class in pwem.objects.data) SetOfCTF (class in pwem.objects.data) SetOfData (class in pwem.objects.data) SetOfDefocusGroup (class in pwem.objects.data) SetOfDefocusGroups (class in pwem.objects.data) SetOfFSCs (class in pwem.objects.data) SetOfImages (class in pwem.objects.data) setOfImagesToMd() (in module xmipp3.convert.convert) SetOfMicrographs (class in pwem.objects.data) SetOfMicrographsBase (class in pwem.objects.data) setOfMicrographsToMd() (in module xmipp3.convert.convert) SetOfMovieParticles (class in pwem.objects.data) SetOfMovies (class in pwem.objects.data) SetOfNormalModes (class in pwem.objects.data) SetOfParticles (class in pwem.objects.data) SetOfParticlesFlex (class in pwem.objects.data_flexhub) setOfParticlesToMd() (in module xmipp3.convert.convert) SetOfPDBs (class in pwem.objects.data) SetOfPrincipalComponents (class in pwem.objects.data) SetOfSequences (class in pwem.objects.data) SetOfStats (class in pwem.objects.data) SetOfVolumes (class in pwem.objects.data) SetOfVolumesFlex (class in pwem.objects.data_flexhub) setOrigin() (pwem.convert.headers.Ccp4Header method) (pwem.objects.data.AtomStruct method) (pwem.objects.data.Image method) setParamFromVar() (pyworkflow.gui.form.FormWindow method) setParamValue() (pyworkflow.template.Template method) setParticleId() (pwem.objects.data.MovieParticle method) setPassword() (pyworkflow.protocol.hosts.HostConfig method) setPdb() (pwem.objects.data.SetOfNormalModes method) setPhaseShift() (pwem.objects.data.CTFModel method) setPickCallback() (xmipp3.protocols.protocol_classes_2d_mapping.ScatterImageMarker method) setPid() (pyworkflow.protocol.protocol.Protocol method) setPointer() (pyworkflow.object.Scalar method) setPointerClass() (pyworkflow.protocol.params.PointerParam method) setPosition() (pwem.objects.data.Coordinate method) (pyworkflow.project.config.NodeConfig method) setPrecision() (pyworkflow.object.Float class method) setPrepend() (pyworkflow.utils.utils.Environ method) setPrerequisites() (pyworkflow.protocol.protocol.Step method) setProgName() (pwem.objects.data_flexhub.FlexInfo method) setProject() (pyworkflow.protocol.protocol.Protocol method) (pyworkflow.viewer.Viewer method) setProperty() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) setProtocol() (pyworkflow.protocol.executor.StepExecutor method) (pyworkflow.viewer.ProtocolViewer method) setProtocolView() (pyworkflow.project.config.ProjectSettings method) setProvider() (pyworkflow.gui.tree.BoundTree method) setPsdFile() (pwem.objects.data.CTFModel method) setPsdFiles() (in module xmipp3.convert.convert) setPseudoAtoms() (pwem.objects.data.AtomStruct method) setQueueParams() (pyworkflow.protocol.protocol.Protocol method) setQueues() (pyworkflow.protocol.hosts.QueueSystemConfig method) setQueueSystem() (pyworkflow.protocol.hosts.HostConfig method) setRadius() (pwem.wizards.wizard.MaskPreviewDialog static method) setReadOnly() (pyworkflow.gui.text.Text method) (pyworkflow.project.config.ProjectSettings method) (pyworkflow.project.project.Project method) setRectangleSelector() (xmipp3.protocols.protocol_classes_2d_mapping.ScatterImageMarker method) setRefresh() (pyworkflow.gui.tree.ProjectRunsTreeProvider method) setRemotePluginInfo() (scipion.install.plugin_funcs.PluginInfo method) setRenderType() (pyworkflow.utils.dataset.Column method) setRepresentative() (pyworkflow.object.Set method) setResolution() (pwem.objects.data.CTFModel method) setRoi() (pwem.objects.data.MovieAlignment method) setRowId() (in module xmipp3.convert.convert) setRunning() (pyworkflow.protocol.protocol.Protocol method) (pyworkflow.protocol.protocol.Step method) setRunsView() (pyworkflow.project.config.ProjectSettings method) setSampling() (pwem.convert.headers.Ccp4Header method) setSamplingRate() (pwem.objects.data.Image method) (pwem.objects.data.SetOfImages method) (pwem.objects.data.SetOfMicrographsBase method) (pwem.objects.data_flexhub.AtomStructFlex method) (pwem.objects.data_flexhub.SetOfAtomStructFlex method) (pwem.protocols.protocol_import.micrographs.ProtImportMicBase method) (pwem.protocols.protocol_import.micrographs.ProtImportMovies method) (pwem.protocols.protocol_import.particles.ProtImportParticles method) setSaved() (pyworkflow.protocol.protocol.Step method) setScannedPixelSize() (pwem.objects.data.SetOfMicrographsBase method) setScipionConfig() (pyworkflow.protocol.hosts.HostConfig method) setScipionHome() (pyworkflow.protocol.hosts.HostConfig method) setScore() (pwem.objects.data.NormalMode method) setSecondaryAttributes() (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method) setSelected() (pyworkflow.gui.canvas.Item method) (pyworkflow.project.config.NodeConfig method) (xmipp3.utils.Point method) setSelectionButtons() (xmipp3.protocols.protocol_classes_2d_mapping.ScatterImageMarker method) setSeqName() (pwem.objects.data.Sequence method) setSequence() (pwem.objects.data.Sequence method) setShifts() (pwem.objects.data.Transform method) setShiftsInOrigin() (pwem.objects.data.Image method) setShiftsTuple() (pwem.objects.data.Transform method) setSliderCallback() (xmipp3.protocols.protocol_classes_2d_mapping.ScatterImageMarker method) setSortingParams() (pyworkflow.gui.tree.TreeProvider method) setSphericalAberration() (pwem.objects.data.Acquisition method) setStandardDefocus() (pwem.objects.data.CTFModel method) setStartAngstrom() (pwem.convert.headers.Ccp4Header method) setStartPixel() (pwem.convert.headers.Ccp4Header method) setState() (xmipp3.utils.Point method) setStatus() (pyworkflow.protocol.protocol.Step method) setStepsExecutor() (pyworkflow.protocol.protocol.Protocol method) setStore() (pyworkflow.object.Object method) setStreamState() (pyworkflow.object.Set method) setSubmitCommand() (pyworkflow.protocol.hosts.QueueSystemConfig method) setSubmitTemplate() (pyworkflow.protocol.hosts.QueueSystemConfig method) setText() (pyworkflow.gui.text.Text method) setTilted() (pwem.objects.data_tiltpairs.TiltPair method) (pwem.objects.data_tiltpairs.TiltPairSet method) SETTINGS (pyworkflow.utils.properties.Icon attribute) setToDefault() (pyworkflow.config.Variable method) setTransform() (pwem.objects.data.Image method) setUntilted() (pwem.objects.data_tiltpairs.TiltPair method) (pwem.objects.data_tiltpairs.TiltPairSet method) setupCommands() (pyworkflow.mapper.sqlite.SqliteFlatDb method) setupDefaultLogging() (pyworkflow.utils.log.LoggingConfigurator static method) setUpGUILogging() (pyworkflow.utils.log.LoggingConfigurator class method) setupLogging() (pyworkflow.utils.log.LoggingConfigurator class method) setUpProtocolRunLogging() (pyworkflow.utils.log.LoggingConfigurator class method) setUpProtocolSchedulingLog() (pyworkflow.utils.log.LoggingConfigurator class method) setupTestOutput() (in module pyworkflow.tests.tests) (pyworkflow.tests.tests.BaseTest class method) setupTestProject() (in module pyworkflow.tests.tests) setUserName() (pyworkflow.protocol.hosts.HostConfig method) setValue() (pwem.emlib.metadata.utils.Row method) (pwem.emlib.metadata.utils.RowMetaData method) (pwem.objects.data.Matrix method) (pyworkflow.config.Variable method) (pyworkflow.template.TemplateParam method) setValues() (pwem.viewers.showj.ColumnProperties method) setVar() (pwem.wizards.wizard.MaskRadiusWizard method) (pyworkflow.gui.form.FormWindow method) setVarFromParam() (pyworkflow.gui.form.FormWindow method) setVersion() (pyworkflow.mapper.sqlite_db.SqliteDb method) setVisible() (pyworkflow.project.config.NodeConfig method) setVisibleNodes() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) setVoltage() (pwem.objects.data.Acquisition method) setVolume() (pwem.objects.data.AtomStruct method) setVolumeName() (pyworkflow.utils.dataset.DataSet method) setWindowTitle() (pyworkflow.gui.matplotlib_image.Preview method) setWorkingDir() (pyworkflow.protocol.protocol.Protocol method) setWrongDefocus() (pwem.objects.data.CTFModel method) setX() (pwem.objects.data.Coordinate method) (pyworkflow.project.config.NodeConfig method) (xmipp3.utils.Point method) setXmippAttribute() (in module xmipp3.convert.convert) setXmippAttributes() (in module xmipp3.convert.convert) setY() (pwem.objects.data.Coordinate method) (pyworkflow.project.config.NodeConfig method) (xmipp3.utils.Point method) setZ() (xmipp3.utils.Point method) setZFlex() (pwem.objects.data_flexhub.AtomStructFlex method) (pwem.objects.data_flexhub.ParticleFlex method) (pwem.objects.data_flexhub.VolumeFlex method) setZRed() (pwem.objects.data_flexhub.AtomStructFlex method) (pwem.objects.data_flexhub.ParticleFlex method) (pwem.objects.data_flexhub.VolumeFlex method) sharpeningAndMonoResStep() (xmipp3.protocols.protocol_volume_local_sharpening.XmippProtLocSharp method) sharpenStep() (xmipp3.protocols.protocol_volume_local_sharpening.XmippProtLocSharp method) SHIFT (pyworkflow.utils.properties.KEYSYM attribute) shiftPressed() (pyworkflow.viewer.Viewer method) shiftStep() (xmipp3.protocols.protocol_shift_particles.XmippProtShiftParticles method) (xmipp3.protocols.protocol_shift_volume.XmippProtShiftVolume method) shiftX (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) shiftX() (pwem.objects.data.Coordinate method) shiftY (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) shiftY() (pwem.objects.data.Coordinate method) shiftZ (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) ShortCut (class in pyworkflow.gui.browser) show() (pwem.viewers.viewer_coordinates.CoordinateView method) (pwem.viewers.viewer_fsc.FscViewer method) (pwem.viewers.viewer_vmd.VmdView method) (pwem.viewers.views.CoordinatesObjectView method) (pwem.viewers.views.DataView method) (pwem.viewers.views.ObjectView method) (pwem.wizards.wizard.ColorScaleWizardBase method) (pwem.wizards.wizard.CtfWizard method) (pwem.wizards.wizard.DownsampleWizard method) (pwem.wizards.wizard.FilterWizard method) (pwem.wizards.wizard.GaussianWizard method) (pwem.wizards.wizard.MaskRadiiWizard method) (pwem.wizards.wizard.MaskRadiusWizard method) (pwem.wizards.wizard.PDBVolumeWizard method) (pwem.wizards.wizards.ChangeOriginSamplingWizard method) (pwem.wizards.wizards.GetStructureChainsWizard method) (pwem.wizards.wizards.ImportAcquisitionWizard method) (pwem.wizards.wizards.ImportCoordinatesBoxSizeWizard class method) (pwem.wizards.wizards.ImportOriginVolumeWizard method) (pwem.wizards.wizards.PythonFormulaeWizard method) (pwem.wizards.wizards.PythonFormulaWizardX1 method) (pwem.wizards.wizards.PythonFormulaWizardX2 method) (pwem.wizards.wizards.SelectAttributeWizard method) (pwem.wizards.wizards.SelectChainWizard method) (pwem.wizards.wizards.SelectResidueWizard method) (pyworkflow.gui.dialog.FloatingMessage method) (pyworkflow.gui.form.GroupWidget method) (pyworkflow.gui.form.LineWidget method) (pyworkflow.gui.form.ParamWidget method) (pyworkflow.gui.form.SectionWidget method) (pyworkflow.gui.gui.Window method) (pyworkflow.gui.plotter.Plotter method) (pyworkflow.viewer.CommandView method) (pyworkflow.viewer.MessageView method) (pyworkflow.viewer.TextView method) (pyworkflow.viewer.View method) (pyworkflow.wizard.Wizard method) showCircles() (pwem.viewers.viewer_coordinates.MainWindow method) showCoordinates() (pwem.viewers.viewer_coordinates.MainWindow method) showDir() (in module pyworkflow.apps.pw_viewer) showError() (in module pyworkflow.gui.dialog) (pyworkflow.gui.gui.Window method) showFile() (in module pyworkflow.apps.pw_viewer) showInfo() (in module pyworkflow.gui.dialog) (in module scipion.install.inspect_plugins) (pyworkflow.gui.gui.Window method) SHOWJ_TITLE (pyworkflow.utils.properties.Message attribute) showLegend() (pyworkflow.gui.plotter.Plotter method) showOperationList() (scipion.install.plugin_manager.PluginBrowser method) showPalette() (pwem.viewers.viewer_coordinates.MainWindow method) showParticles() (pwem.viewers.viewer_coordinates.MainWindow method) showPluginInfo() (in module scipion.install.inspect_plugins) showPluginInformation() (scipion.install.plugin_manager.PluginBrowser method) showPoint() (pwem.viewers.viewer_coordinates.MainWindow method) showProjectList() (in module pyworkflow.apps.pw_project) showProtocols() (in module scipion.install.inspect_plugins) showReferences() (in module scipion.install.inspect_plugins) showSquare() (pwem.viewers.viewer_coordinates.MainWindow method) showTextFileViewer() (in module pyworkflow.gui.text) showValues() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.MaskPreviewDialog method) showWarning() (in module pyworkflow.gui.dialog) (pyworkflow.gui.gui.Window method) significantStep() (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) (xmipp3.protocols.protocol_reconstruct_significant.XmippProtReconstructSignificant method) (xmipp3.protocols.protocol_validate_nontilt.XmippProtValidateNonTilt method) simulateStep() (xmipp3.protocols.protocol_simulate_ctf.XmippProtSimulateCTF method) sine() (pwem.convert.trigonometry.TrigonometricMemoization method) SingleFileDataSet (class in pyworkflow.utils.dataset) SIZE_COLORS (pyworkflow.gui.project.viewprotocols.ProtocolsView attribute) SIZE_COLUMN (pyworkflow.gui.browser.FileTreeProvider attribute) sizeColorMode() (pyworkflow.project.config.ProjectSettings method) skipProgram() (in module xmipp3.programs) sleepStep() (pwem.protocols.parallel.ProtTestParallel method) socketSeparation (pyworkflow.gui.canvas.Item attribute) sort() (xmipp3.base.XmippSet method) sortByColumn() (pyworkflow.gui.tree.Tree method) sortClassesStep() (xmipp3.protocols.protocol_cl2d.XmippProtCL2D method) sortEnabled() (pyworkflow.gui.tree.TreeProvider method) sortImages() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles method) sortImagesStep() (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles method) sortListByList() (in module pyworkflow.utils.utils) sortListByPluginName() (pyworkflow.template.TemplateList method) sortTree() (pyworkflow.gui.tree.BoundTree method) specialBehavoir() (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase method) (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyClasses method) (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyParticles method) split() (xmipp3.protocols.protocol_structure_map.XmippProtStructureMap method) (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) SPLIT_FIXED (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes attribute) SPLIT_STOCHASTIC (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes attribute) splitInputStep() (xmipp3.protocols.protocol_reconstruct_fourier.XmippProtReconstructFourier method) splitLongestSegment() (xmipp3.utils.PathData method) splitRange() (in module pwem.utils) splittingStep() (xmipp3.protocols.protocol_movie_split_frames.XmippProtSplitFrames method) Sprite (class in pyworkflow.utils.properties) SpriteImage (class in pyworkflow.utils.properties) SqlFileHandler (class in pyworkflow.gui.browser) SqliteDataSet (class in pyworkflow.utils.dataset) SqliteDb (class in pyworkflow.mapper.sqlite_db) SqliteFlatDb (class in pyworkflow.mapper.sqlite) SqliteFlatMapper (class in pyworkflow.mapper.sqlite) SqliteFlatMapperException SqliteMapper (class in pyworkflow.mapper.sqlite) SqliteObjectsDb (class in pyworkflow.mapper.sqlite) SquareConnector (class in pyworkflow.gui.canvas) srcMoved() (pyworkflow.gui.canvas.Cable method) SSNR_CHOICES (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles attribute) StackHandler (class in pwem.viewers.filehandlers) standardize() (pwem.objects.data.CTFModel method) START (pwem.convert.headers.Ccp4Header attribute) (pyworkflow.utils.log.STATUS attribute) start() (pyworkflow.utils.progressbar.ProgressBar method) startTest() (pyworkflow.tests.tests.GTestResult method) STATE_COLUMN (pyworkflow.gui.tree.ProjectRunsTreeProvider attribute) stats (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis attribute) STATUS (class in pyworkflow.utils.log) STATUS_ABORTED (pyworkflow.constants.Color attribute) STATUS_FAILED (pyworkflow.constants.Color attribute) STATUS_FINISHED (pyworkflow.constants.Color attribute) STATUS_INTERACTIVE (pyworkflow.constants.Color attribute) STATUS_LAUNCHED (pyworkflow.constants.Color attribute) STATUS_RUNNING (pyworkflow.constants.Color attribute) STATUS_SAVED (pyworkflow.constants.Color attribute) statusColorMode() (pyworkflow.project.config.ProjectSettings method) Step (class in pyworkflow.protocol.protocol) StepExecutor (class in pyworkflow.protocol.executor) stepsDone (pyworkflow.protocol.protocol.Protocol property) StepSet (class in pyworkflow.protocol.protocol) stepsExecutionMode (pwem.protocols.parallel.ProtTestParallel attribute) (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData attribute) (pwem.protocols.protocol_micrographs.ProtCTFMicrographs attribute) (pwem.protocols.protocol_movies.ProtProcessMovies attribute) (pyworkflow.protocol.protocol.Protocol attribute) (pyworkflow.protocol.protocol.ProtStreamingBase attribute) stepsGeneratorStep() (pyworkflow.protocol.protocol.ProtStreamingBase method) (xmipp3.protocols.protocol_classify_pca_streaming.XmippProtClassifyPcaStreaming method) StepsTreeProvider (class in pyworkflow.gui.project.steps) StepsWindow (class in pyworkflow.gui.project.steps) StepThread (class in pyworkflow.protocol.executor) stk_handler (pwem.emlib.image.image_readers.STKImageReader attribute) STKImageReader (class in pwem.emlib.image.image_readers) STOCHASTIC_ALIGNMENT (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes attribute) STOP (pyworkflow.utils.log.STATUS attribute) stop() (in module pyworkflow.protocol.launch) stopImport() (pwem.protocols.protocol_import.images.ProtImportImages method) stopProtocol() (pyworkflow.project.project.Project method) stopStreamingFileExists() (pwem.protocols.protocol_import.images.ProtImportImages method) stopWait() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) (pwem.protocols.protocol_tools.ProtManualCheckpoint method) (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) stopWorkFlow() (pyworkflow.project.project.Project method) store() (pyworkflow.mapper.mapper.Mapper method) storeResolutionStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) StrColors (class in pyworkflow.constants) STREAM_CLOSED (pyworkflow.object.Set attribute) STREAM_OPEN (pyworkflow.object.Set attribute) stressStep() (pwem.protocols.protocol_tests.ProtStress method) strId() (pyworkflow.object.Object method) String (class in pyworkflow.object) STRING (pyworkflow.config.VarTypes attribute) StringParam (class in pyworkflow.protocol.params) strToBoolean() (in module pyworkflow.utils.utils) strToDuration() (in module pyworkflow.utils.utils) STUDENT_NOISE (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoise attribute) SubclassesTreeProvider (class in pyworkflow.gui.form) substractBlocresStep() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) subtractionStep() (xmipp3.protocols.protocol_subtract_projection.XmippProtSubtractProjection method) (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolSubtraction method) SUCCESS (pyworkflow.utils.properties.PluginStates attribute) sum() (pyworkflow.object.Scalar method) summary() (pyworkflow.protocol.protocol.Protocol method) (xmipp3.protocols.protocol_preprocess.geometrical_mask.XmippGeometricalMask2D method) (xmipp3.protocols.protocol_preprocess.geometrical_mask.XmippGeometricalMask3D method) surrounding_values() (in module xmipp3.utils) swap() (pyworkflow.object.Scalar method) switchRunsView() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) switchView() (pyworkflow.gui.project.base.ProjectBaseWindow method) (scipion.scripts.kickoff.KickoffWindow method) SYM_CHOICES (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) symmetrize() (xmipp3.protocols.protocol_helical_parameters.XmippProtHelicalParameters method) (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry method) symmetrizeStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) SymmetryHelper (class in pwem.convert.symmetry) symmetryMatrices() (pwem.convert.symmetry.Cyclic method) (pwem.convert.symmetry.Dihedral method) (pwem.convert.symmetry.Octahedral method) (pwem.convert.symmetry.Tetrahedral method) SYMNAME (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) SYMNAMEORDER (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) SYMPLIFIED_STRUCT (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) (pwem.protocols.protocol_import.volumes.ProtImportPdb attribute)

T

Table (class in pyworkflow.utils.dataset) TableView (class in pwem.viewers.views) TAG_PROTOCOL (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig attribute) TAG_PROTOCOL_BETA (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig attribute) TAG_PROTOCOL_DISABLED (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig attribute) TAG_PROTOCOL_GROUP (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig attribute) TAG_PROTOCOL_NEW (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig attribute) TAG_PROTOCOL_UPDATED (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig attribute) TAG_SECTION (pyworkflow.gui.project.viewprotocols_extra.ProtocolTreeConfig attribute) TaggedText (class in pyworkflow.gui.text) TAGS (pyworkflow.utils.properties.Icon attribute) takeScreenShot() (pyworkflow.gui.form.FormWindow method) tangent() (pwem.convert.trigonometry.TrigonometricMemoization method) Target (class in scipion.install.funcs) Template (class in pyworkflow.template) TemplateList (class in pyworkflow.template) TemplateParam (class in pyworkflow.template) Tester (class in pyworkflow.apps.pw_run_tests) testFailed (pyworkflow.tests.tests.GTestResult attribute) testLog() (in module pwem.convert.atom_struct) testWriteStep() (xmipp3.protocols.protocol_write_testC.XmippProtWriteTestC method) (xmipp3.protocols.protocol_write_testP.XmippProtWriteTestP method) testWriteValidate() (xmipp3.protocols.protocol_write_testP.XmippProtWriteTestP method) Tetrahedral (class in pwem.convert.symmetry) TETRAHEDRAL_SYM_NAME (pwem.protocols.protocol_projection_edit.ProtProjectionEditor attribute) Text (class in pyworkflow.gui.text) TEXT_ALIG_PART (pyworkflow.utils.properties.Message attribute) TEXT_AMPLITUDE (pyworkflow.utils.properties.Message attribute) TEXT_HELP (pyworkflow.utils.properties.Message attribute) TEXT_MAGNI_RATE (pyworkflow.utils.properties.Message attribute) TEXT_NO_CTF_READY (pyworkflow.utils.properties.Message attribute) TEXT_NO_INPUT_MIC (pyworkflow.utils.properties.Message attribute) TEXT_NO_OUTPUT_CO (pyworkflow.utils.properties.Message attribute) TEXT_NO_OUTPUT_FILES (pyworkflow.utils.properties.Message attribute) TEXT_PATTERN (pyworkflow.utils.properties.Message attribute) TEXT_SAMP_MODE (pyworkflow.utils.properties.Message attribute) TEXT_SAMP_RATE (pyworkflow.utils.properties.Message attribute) TEXT_SPH_ABERRATION (pyworkflow.utils.properties.Message attribute) TEXT_VOLTAGE (pyworkflow.utils.properties.Message attribute) TextBox (class in pyworkflow.gui.canvas) TextCircle (class in pyworkflow.gui.canvas) TextFileHandler (class in pyworkflow.gui.browser) TextFileViewer (class in pyworkflow.gui.text) TextItem (class in pyworkflow.gui.canvas) TextParam (class in pyworkflow.protocol.params) TextVar (class in pyworkflow.gui.form) TextView (class in pyworkflow.viewer) textView() (pyworkflow.viewer.Viewer method) THREADS_MPIS_AND_GPUS (pyworkflow.constants.DOCSITEURLS attribute) ThreadStepExecutor (class in pyworkflow.protocol.executor) thresholdStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles method) (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes method) tic() (pyworkflow.tests.tests.GTestResult method) (pyworkflow.utils.utils.Timer method) TiffImageReader (class in pwem.emlib.image.image_readers) TIGHT_MODEL (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc attribute) tightLayout() (pyworkflow.gui.plotter.Plotter method) TiltPair (class in pwem.objects.data_tiltpairs) TiltPairSet (class in pwem.objects.data_tiltpairs) TIME_COLUMN (pyworkflow.gui.tree.ProjectRunsTreeProvider attribute) timeit() (in module pyworkflow.utils.utils) Timer (class in pyworkflow.utils.profiler) (class in pyworkflow.utils.utils) TITLE_ACTIVE_PROTOCOLS (pyworkflow.utils.properties.Message attribute) TITLE_BROWSE_DATA (pyworkflow.utils.properties.Message attribute) TITLE_COMMENT (pyworkflow.utils.properties.Message attribute) TITLE_CONTINUE_FORM (pyworkflow.utils.properties.Message attribute) TITLE_CONTINUE_WORKFLOW_FORM (pyworkflow.utils.properties.Message attribute) TITLE_CREATE_PROJECT (pyworkflow.utils.properties.Message attribute) TITLE_CREATE_PROJECT_NAME (pyworkflow.utils.properties.Message attribute) TITLE_DELETE_FORM (pyworkflow.utils.properties.Message attribute) TITLE_DELETE_PROJECT (pyworkflow.utils.properties.Message attribute) TITLE_EDIT_OBJECT (pyworkflow.utils.properties.Message attribute) TITLE_EXEC (pyworkflow.utils.properties.Message attribute) TITLE_INSPECTOR (pyworkflow.utils.properties.Message attribute) TITLE_LABEL (pyworkflow.utils.properties.Message attribute) TITLE_LAUNCHED (pyworkflow.utils.properties.Message attribute) TITLE_LAUNCHED_WORKFLOW_FAILED (pyworkflow.utils.properties.Message attribute) TITLE_LAUNCHED_WORKFLOW_FAILED_FORM (pyworkflow.utils.properties.Message attribute)

TITLE_NAME_RUN (pyworkflow.utils.properties.Message attribute) TITLE_PICK_GAUSS (pyworkflow.utils.properties.Message attribute) TITLE_RENAME_PROJECT (pyworkflow.utils.properties.Message attribute) TITLE_RESET_WORKFLOW (pyworkflow.utils.properties.Message attribute) TITLE_RESET_WORKFLOW_FORM (pyworkflow.utils.properties.Message attribute) TITLE_RESETED_WORKFLOW_FAILED (pyworkflow.utils.properties.Message attribute) TITLE_RESTART_FORM (pyworkflow.utils.properties.Message attribute) TITLE_RESTART_WORKFLOW_FORM (pyworkflow.utils.properties.Message attribute) TITLE_RUN (pyworkflow.utils.properties.Message attribute) TITLE_SAVE_OUTPUT (pyworkflow.utils.properties.Message attribute) TITLE_SAVED_FORM (pyworkflow.utils.properties.Message attribute) TITLE_STOP_FORM (pyworkflow.utils.properties.Message attribute) TITLE_STOP_WORKFLOW (pyworkflow.utils.properties.Message attribute) TITLE_STOP_WORKFLOW_FORM (pyworkflow.utils.properties.Message attribute) TITLE_STOPPED_WORKFLOW_FAILED (pyworkflow.utils.properties.Message attribute) TK (class in pyworkflow.constants) tkWindow() (pyworkflow.viewer.Viewer method) tmpCTF (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterParticles attribute) TO_EXTRACT_MICFNS (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) TO_INSTALL (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) to_spherical() (in module pwem.viewers.plotter) TO_TRAIN_MICFNS (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) TO_UPDATE (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) to_utc() (in module pyworkflow.utils.utils) toc() (pyworkflow.tests.tests.GTestResult method) (pyworkflow.utils.utils.Timer method) toCIF() (in module pwem.convert.atom_struct) toggleDataSelection() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) toggleDebug() (pyworkflow.config.Config static method) toggleDebugSQL() (pyworkflow.config.Config static method) toggleItemSelection() (pyworkflow.gui.project.viewdata.ProjectDataView method) ToolbarButton (class in pyworkflow.gui.dialog) ToolbarListDialog (class in pyworkflow.gui.dialog) ToolTip (class in pyworkflow.gui.tooltip) TOOLTIP_EXTERNAL (pyworkflow.utils.properties.Message attribute) TOOLTIP_REFRESH (pyworkflow.utils.properties.Message attribute) TOOLTIP_SEARCH (pyworkflow.utils.properties.Message attribute) TOOLTIP_SEARCH_NEXT (pyworkflow.utils.properties.Message attribute) TOOLTIP_SEARCH_PREVIOUS (pyworkflow.utils.properties.Message attribute) TOP (pyworkflow.gui.canvas.Item attribute) toPdb() (in module pwem.convert.atom_struct) toSeconds() (pyworkflow.object.String method) touch() (scipion.install.funcs.CommandDef method) toUrl() (pyworkflow.viewer.View method) trace() (in module pyworkflow.utils.utils) (pyworkflow.gui.form.ScalarWithPointerVar method) (pyworkflow.object.Object method) train() (xmipp3.protocols.protocol_deep_center.XmippProtDeepCenter method) (xmipp3.protocols.protocol_screen_deeplearning.XmippProtScreenDeepLearning method) TRAIN_BATCH_MAX (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) trainCNN() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) TRAINED_PARAMS_PATH (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) TRAINING (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) trainingOn() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) Transform (class in pwem.objects.data) transform() (pwem.convert.atom_struct.AtomicStructHandler method) transform2EvenNumber() (in module pwem.protocols.protocol_boxsize_checkpoint) (in module pwem.protocols.protocol_boxsize_parameters) transformGain() (xmipp3.protocols.protocol_flexalign.XmippProtFlexAlign method) transformMaskStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) transformStep() (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes method) translation_correction() (in module xmipp3.protocols.protocol_movie_gain) Tree (class in pyworkflow.gui.tree) TreeProvider (class in pyworkflow.gui.tree) TREEVIEW_CLOSE (pyworkflow.constants.TK attribute) TREEVIEW_OPEN (pyworkflow.constants.TK attribute) TrigonometricMemoization (class in pwem.convert.trigonometry) truncateMask() (pwem.emlib.image.image_handler.ImageHandler method) tryProcessMovie() (xmipp3.protocols.protocol_flexalign.XmippProtFlexAlign method) TupleParam (class in pyworkflow.protocol.params) Tutorial (class in scipion.scripts.tutorial) TutorialBetagal (class in scipion.scripts.tutorial) TutorialIntro (class in scipion.scripts.tutorial) TXT_FILE (pyworkflow.utils.properties.Icon attribute) TYPE (pwem.emlib.image.image_readers.STKImageReader attribute) TYPE_CTF (pwem.protocols.protocol_sets.ProtUnionSet attribute) TYPE_VOLUME (pwem.protocols.protocol_sets.ProtUnionSet attribute) TYPE_VOLUME_INDEX (pwem.protocols.protocol_sets.ProtUnionSet attribute)

U

UNAMBIGOUS_DNA_ALPHABET (pwem.objects.data.Alphabet attribute) UNAMBIGOUS_RNA_ALPHABET (pwem.objects.data.Alphabet attribute) uncheck_item() (scipion.install.plugin_manager.PluginTree method) UNCHECKED (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) UNDERLINE (pyworkflow.utils.properties.colorText attribute) UNIFORM_NOISE (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoise attribute) UNINSTALL (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) uninstallBins() (scipion.install.plugin_funcs.PluginInfo method) uninstallPip() (scipion.install.plugin_funcs.PluginInfo method) unique() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) unitCellPlanes() (pwem.convert.symmetry.Cyclic method) (pwem.convert.symmetry.Dihedral method) (pwem.convert.symmetry.Icosahedron method) (pwem.convert.symmetry.Octahedral method) (pwem.convert.symmetry.Tetrahedral method) update() (in module pyworkflow.apps.pw_sync_data) (pyworkflow.gui.tree.BoundTree method) (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.object.Set method) (pyworkflow.utils.progressbar.ProgressBar method) (pyworkflow.utils.utils.Environ method) UPDATE_CLASSES (xmipp3.protocols.protocol_classify_pca.XmippProtClassifyPca attribute) (xmipp3.protocols.protocol_classify_pca_streaming.XmippProtClassifyPcaStreaming attribute) update_item() (scipion.install.plugin_manager.PluginTree method) update_pdb() (pwem.convert.pdb_list.PDBList method) updateColor() (pyworkflow.gui.canvas.Edge method) updateCoords() (pyworkflow.gui.canvas.Cable method) updateCudaEnviron() (scipion.install.funcs.Environment method) UPDATED (pyworkflow.utils.properties.Icon attribute) updateData() (pyworkflow.gui.matplotlib_image.Preview method) updateDict() (pyworkflow.project.config.LabelsList method) (pyworkflow.project.config.NodeConfigList method) updateDst() (pyworkflow.gui.canvas.Edge method) updateEnviron() (in module xmipp3.protocols.protocol_classify_pca) (in module xmipp3.protocols.protocol_resolution_deepres) updateExpText() (pyworkflow.gui.widgets.ExplanationText method) updateFileName() (in module xmipp3.protocols.protocol_classify_pca_streaming) updateFilteredImage() (pwem.wizards.wizard.BandPassFilterDialog method) updateFreq() (pyworkflow.gui.matplotlib_image.PsdPreview method) updateFreqRing() (pwem.wizards.wizard.CtfDialog method) updateFrom() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) updateGainsOutput() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) updateImage() (pwem.viewers.viewer_coordinates.MainWindow method) updateItem() (pwem.emlib.metadata.utils.SetMdIterator method) (pwem.protocols.protocol_set_editor.ProtSetEditor method) updateLabelAndCommentVars() (pyworkflow.gui.form.FormWindow method) UpdateManager (class in scipion.install.update_manager) updateManagerParser() (in module scipion.install.update_manager)

updateMask() (pyworkflow.gui.matplotlib_image.MaskPreview method) updateMenu() (pyworkflow.gui.text.Text method) updateObject() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteObjectsDb method) updateOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) updateOutputSetOfClasses() (xmipp3.protocols.protocol_classify_pca_streaming.XmippProtClassifyPcaStreaming method) updateParticle() (pwem.viewers.viewer_coordinates.MainWindow method) updatePatch() (xmipp3.protocols.protocol_classes_2d_mapping.ScatterImageMarker method) updatePreOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) updateProgramCategory() (xmipp3.programs.ProgramDb method) updateProtocolLabel() (pyworkflow.gui.form.FormWindow method) updateProtocolParams() (pyworkflow.gui.form.FormWindow method) updateProtocolsTree() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) updateRelations() (xmipp3.protocols.protocol_mics_defocus_balancer.XmippProtMicDefocusSampler method) updateRow() (pyworkflow.utils.dataset.Table method) updateRunsGraph() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) updateRunsTree() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) updateRunsTreeSelection() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) updateScipion() (scipion.install.update_manager.UpdateManager class method) updateScrollRegion() (pyworkflow.gui.canvas.Canvas method) updateSize() (pwem.viewers.viewer_coordinates.MainWindow method) updateSliderInnerRadius() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.MaskRadiiPreviewDialog method) updateSliderOuterRadius() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.MaskRadiiPreviewDialog method) updateSliderRadius() (pwem.wizards.wizard.MaskPreviewDialog method) updateSrc() (pyworkflow.gui.canvas.Edge method) (pyworkflow.gui.canvas.Oval method) (pyworkflow.gui.canvas.Rectangle method) updateSteps() (pyworkflow.protocol.protocol.Protocol method) updateSubElement() (pwem.protocols.protocol_set_editor.ProtSetEditor method) updateTo() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) updateVolumes() (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) upKeyPress() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.MaskRadiiPreviewDialog method) upload() (in module pyworkflow.apps.pw_sync_data) (pyworkflow.webservices.repository.WorkflowRepository method) uploadTrainedParam() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) url (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) usage() (in module scipion.install.inspect_plugins) useQueue() (pyworkflow.protocol.protocol.Protocol method) useQueueForProtocol() (pyworkflow.protocol.protocol.Protocol method) useQueueForSteps() (pyworkflow.protocol.protocol.Protocol method) USER (pyworkflow.constants.DOCSITEURLS attribute) usesGpu() (pyworkflow.protocol.protocol.Protocol method) USING_INPUT_COORDS (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) USING_INPUT_MICS (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus attribute) usingExperimental (xmipp3.protocols.protocol_movie_dose_analysis.XmippProtMovieDoseAnalysis attribute) usingShowJ() (pwem.protocols.protocol_batch.ProtUserSubSet method) usingXmipp() (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method)

V

validate() (pwem.protocols.protocol_import.dataimport.ScipionImport method) (pyworkflow.gui.dialog.Dialog method) (pyworkflow.gui.dialog.EntryDialog method) (pyworkflow.gui.dialog.ListDialog method) (pyworkflow.gui.form.QueueDialog method) (pyworkflow.gui.project.labels.EditLabelDialog method) (pyworkflow.gui.project.variables.EditVariableDialog method) (pyworkflow.protocol.params.Param method) (pyworkflow.protocol.protocol.Protocol method) (pyworkflow.template.TemplateParam method) (xmipp3.convert.dataimport.XmippImport method) (xmipp3.protocols.protocol_preprocess.protocol_movie_resize.XmippProtMovieResize method) (xmipp3.protocols.protocol_structure_map_zernike3d.XmippProtStructureMapZernike3D method) (xmipp3.protocols.protocol_volume_deform_zernike3d.XmippProtVolumeDeformZernike3D method) validateClose() (pyworkflow.gui.dialog.Dialog method) validateDLtoolkit() (xmipp3.base.XmippProtocol method) validateInstallation() (pwem.protocols.protocol_pdf_report.ProtPDFReport class method) (pyworkflow.plugin.Plugin class method) (pyworkflow.protocol.protocol.Protocol class method) (pyworkflow.viewer.ProtocolViewer method) validateMicrographs() (pwem.protocols.protocol_import.dataimport.ScipionImport method) (xmipp3.convert.dataimport.XmippImport method) validatePackageVersion() (pyworkflow.protocol.protocol.Protocol class method) validateParams() (pyworkflow.protocol.params.Form method) validateParticles() (pwem.protocols.protocol_import.dataimport.ScipionImport method) (xmipp3.convert.dataimport.XmippImport method) validatePath() (pwem.protocols.protocol_import.images.ProtImportImages class method) validateXmippGpuBins() (in module xmipp3.utils) ValidationException Validations (class in pyworkflow.template) validationStep() (xmipp3.protocols.protocol_validate_nontilt.XmippProtValidateNonTilt method) Validator (class in pyworkflow.protocol.params) validBoolean() (pyworkflow.template.Validations static method) validColor() (in module pyworkflow.config) validDecimal() (pyworkflow.template.Validations static method) validInteger() (pyworkflow.template.Validations static method) validPath() (pyworkflow.template.Validations static method) validString() (pyworkflow.template.Validations static method) valueToList() (in module pyworkflow.utils.utils) VAR_CHOICES (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles attribute) VAR_COMMENT (pyworkflow.utils.properties.Message attribute) VAR_EXEC_HOST (pyworkflow.utils.properties.Message attribute) VAR_EXPERT (pyworkflow.utils.properties.Message attribute) VAR_MPI (pyworkflow.utils.properties.Message attribute)

VAR_QUEUE (pyworkflow.utils.properties.Message attribute) VAR_RUN_MODE (pyworkflow.utils.properties.Message attribute) VAR_RUN_NAME (pyworkflow.utils.properties.Message attribute) VAR_THREADS (pyworkflow.utils.properties.Message attribute) Variable (class in pyworkflow.config) variables() (pyworkflow.config.VariablesRegistry class method) VariablesDialog (class in pyworkflow.gui.project.variables) VariablesRegistry (class in pyworkflow.config) VariablesTreeProvider (class in pyworkflow.gui.project.variables) VariableWizard (class in pwem.wizards.wizard) VarTypes (class in pyworkflow.config) VERSION (pyworkflow.mapper.sqlite.SqliteFlatDb attribute) (pyworkflow.mapper.sqlite.SqliteObjectsDb attribute) verticalFlow (pyworkflow.gui.canvas.Item attribute) VerticalScrolledFrame (class in pyworkflow.gui.form) View (class in pyworkflow.viewer) VIEW_DATA (pyworkflow.utils.properties.Message attribute) VIEW_PROJECTS (pyworkflow.utils.properties.Message attribute) VIEW_PROTOCOLS (pyworkflow.utils.properties.Message attribute) VIEW_UPLOAD (pyworkflow.utils.properties.Message attribute) Viewer (class in pyworkflow.viewer) viewerProtImportVolumes (class in pwem.viewers.viewer_volumes) VIEWERS (pyworkflow.config.Config attribute) viewersLoaded() (pyworkflow.plugin.Domain class method) visualize() (pwem.viewers.viewer_fsc.FscViewer method) (pwem.viewers.viewer_pdf.PDFReportViewer method) (pwem.viewers.viewer_sequence.SequenceViewer method) (pwem.viewers.viewer_vmd.VmdViewer method) (pyworkflow.viewer.ProtocolViewer method) (pyworkflow.viewer.Viewer method) Vmd (class in pwem.viewers.viewer_vmd) VmdView (class in pwem.viewers.viewer_vmd) VmdViewer (class in pwem.viewers.viewer_vmd) VolFileHandler (class in pwem.viewers.filehandlers) Volume (class in pwem.objects.data) (xmipp3.protocols.protocol_align_volume_and_particles.AlignVolPartOutputs attribute) VOLUME (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections attribute) volumeAlignmentStep() (xmipp3.protocols.protocol_enrich.XmippProtEnrich method) volumeConvertStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) VolumeFlex (class in pwem.objects.data_flexhub) VolumeMask (class in pwem.objects.data) VolumeMaskRadiiWizard (class in pwem.wizards.wizard) VolumeMaskRadiusWizard (class in pwem.wizards.wizard) VOLUMENAME (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) volumeToRow() (in module xmipp3.convert.convert)

W

wait() (in module pyworkflow.tests.test_utils) WAIT_FOR (pyworkflow.constants.DOCSITEURLS attribute) waitForDebugger() (in module pyworkflow.utils.profiler) waitFreeInputCoords() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) waitFreeInputMics() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) WAITING (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) waitingHasFinished() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) (pwem.protocols.protocol_tools.ProtManualCheckpoint method) (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) waitingStep() (pwem.protocols.protocol_boxsize_checkpoint.ProtBoxSizeCheckpoint method) (pwem.protocols.protocol_tools.ProtManualCheckpoint method) warning() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.protocol.protocol.Protocol method) warnings() (pyworkflow.protocol.protocol.Protocol method) warnMessage() (pyworkflow.viewer.Viewer method) weakImport() (in module pyworkflow.utils.utils) WEB (xmipp3.protocols.protocol_validate_nontilt.XmippProtValidateNonTilt attribute) WEIGHT_INDEX (pyworkflow.gui.dialog.SearchBaseWindow attribute) weightEulerAngles() (pwem.viewers.plotter.EmPlotter method) weightParticles() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) which() (in module pyworkflow.utils.which) whichall() (in module pyworkflow.utils.which) WhichError whichgen() (in module pyworkflow.utils.which) white (pyworkflow.constants.StrColors attribute) white() (in module pyworkflow.utils.utils) (in module scipion.install.funcs) (in module scipion.scripts.config) whiteB() (in module pyworkflow.utils.utils) whiteList (pyworkflow.utils.profiler.Timer attribute) WHTemplate (class in pyworkflow.webservices.workflowhub) WIDE_MODEL (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc attribute) wienerStep() (xmipp3.protocols.protocol_ctf_correct_wiener2d.XmippProtCTFCorrectWiener2D method) Window (class in pyworkflow.gui.gui) window_coordinates2D() (in module xmipp3.protocols.protocol_tilt_analysis) WINDOW_OP_CROP (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippResizeHelper attribute) WINDOW_OP_WINDOW (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippResizeHelper attribute) WindowsHandler (class in pyworkflow.gui.project.utils) windowStep() (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeParticles method) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippProtCropResizeVolumes method) (xmipp3.protocols.protocol_preprocess.protocol_crop_resize.XmippResizeHelper class method) Wizard (class in pyworkflow.wizard) WLSfile2Windows() (pyworkflow.utils.utils.OS class method) WorkflowRepository (class in pyworkflow.webservices.repository) worksInStreaming() (pwem.protocols.protocol_import.base.ProtImportFiles class method) (pyworkflow.protocol.protocol.Protocol class method)

write() (pwem.convert.atom_struct.AtomicStructHandler method) (pwem.emlib.image.image_handler.ImageHandler method) (pwem.emlib.image.image_readers.ImageReader static method) (pwem.emlib.image.image_readers.ImageReadersRegistry class method) (pwem.emlib.image.image_readers.MRCImageReader class method) (pwem.emlib.image.image_readers.PILImageReader class method) (pwem.emlib.image.image_readers.TiffImageReader class method) (pwem.emlib.metadata.utils.RowMetaData method) (pwem.objects.data_tiltpairs.TiltPairSet method) (pyworkflow.object.Set method) (pyworkflow.project.config.ProjectSettings method) (xmipp3.base.XmippSet method) writeAsCif() (pwem.convert.atom_struct.AtomicStructHandler method) writeAsPdb() (pwem.convert.atom_struct.AtomicStructHandler method) writeBasic() (pyworkflow.protocol.hosts.HostConfig class method) writeCoordsConfig() (in module xmipp3.convert.convert) writeCoordsListToPosFname() (in module xmipp3.convert.io_coordinates) writeCoordsListToRawText() (in module xmipp3.convert.io_coordinates) writeCTFModel() (in module xmipp3.convert.convert) writeHeader() (pwem.convert.headers.Ccp4Header method) writeImageFromArray() (in module xmipp3.utils) writeInfoField() (xmipp3.protocols.protocol_angular_graph_consistency.XmippProtAngularGraphConsistency method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) writeMicCoordinates() (in module xmipp3.convert.convert) writeMovieMd() (in module xmipp3.convert.convert) writeOutputDict() (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) writePosFilesStep() (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) writeSetOfClasses2D() (in module xmipp3.convert.convert) writeSetOfClassesVol() (in module xmipp3.convert.convert) writeSetOfCoordinates() (in module xmipp3.convert.convert) writeSetOfCoordinatesWithState() (in module xmipp3.convert.convert) writeSetOfCTFs() (in module xmipp3.convert.convert) writeSetOfDefocusGroups() (in module xmipp3.convert.convert) writeSetOfImages() (in module xmipp3.convert.convert) writeSetOfMicrographs() (in module xmipp3.convert.convert) writeSetOfMicrographsPairs() (in module xmipp3.convert.convert) writeSetOfMovies() (in module xmipp3.convert.convert) writeSetOfParticles() (in module xmipp3.convert.convert) writeSetOfVolumes() (in module xmipp3.convert.convert) writeShiftsMovieAlignment() (in module xmipp3.convert.convert) writeStack() (pwem.objects.data.SetOfClasses2D method) (pwem.objects.data.SetOfImages method) writeToFile() (pwem.emlib.metadata.utils.Row method) writeToMd() (pwem.emlib.metadata.utils.Row method) writeZernikeFile() (xmipp3.protocols.protocol_apply_zernike3d.XmippApplyZernike3D method)

X

xcoor (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) xmipp3 module xmipp3.base module xmipp3.bibtex module xmipp3.constants module xmipp3.convert module xmipp3.convert.convert module xmipp3.convert.dataimport module xmipp3.convert.io_coordinates module xmipp3.programs module xmipp3.protocols module xmipp3.protocols.protocol_align_volume module xmipp3.protocols.protocol_align_volume_and_particles module xmipp3.protocols.protocol_analyze_local_ctf module xmipp3.protocols.protocol_angular_graph_consistency module xmipp3.protocols.protocol_apply_alignment module xmipp3.protocols.protocol_apply_tilt_to_ctf module xmipp3.protocols.protocol_apply_transformation_matrix module xmipp3.protocols.protocol_apply_zernike3d module xmipp3.protocols.protocol_assignment_tilt_pair module xmipp3.protocols.protocol_break_symmetry module xmipp3.protocols.protocol_center_particles module xmipp3.protocols.protocol_cl2d module xmipp3.protocols.protocol_cl2d_align module xmipp3.protocols.protocol_cl2d_clustering module xmipp3.protocols.protocol_classes_2d_mapping module xmipp3.protocols.protocol_classify_pca module xmipp3.protocols.protocol_classify_pca_streaming module xmipp3.protocols.protocol_compare_angles module xmipp3.protocols.protocol_compare_reprojections module xmipp3.protocols.protocol_consensus_classes module xmipp3.protocols.protocol_consensus_local_ctf module xmipp3.protocols.protocol_convert_pdb module xmipp3.protocols.protocol_core_analysis module xmipp3.protocols.protocol_create_gallery module xmipp3.protocols.protocol_ctf_consensus module xmipp3.protocols.protocol_ctf_correct_wiener2d module xmipp3.protocols.protocol_ctf_defocus_group module xmipp3.protocols.protocol_ctf_micrographs module xmipp3.protocols.protocol_deep_center module xmipp3.protocols.protocol_deep_center_predict module xmipp3.protocols.protocol_deep_hand module xmipp3.protocols.protocol_deep_micrograph_screen module xmipp3.protocols.protocol_denoise_particles module xmipp3.protocols.protocol_eliminate_empty_images module xmipp3.protocols.protocol_enrich module xmipp3.protocols.protocol_extract_asymmetric_unit module xmipp3.protocols.protocol_extract_particles module xmipp3.protocols.protocol_extract_particles_movies module xmipp3.protocols.protocol_extract_particles_pairs module xmipp3.protocols.protocol_flexalign module xmipp3.protocols.protocol_generate_reprojections module xmipp3.protocols.protocol_helical_parameters module xmipp3.protocols.protocol_kerdensom module xmipp3.protocols.protocol_local_ctf module xmipp3.protocols.protocol_mics_defocus_balancer module xmipp3.protocols.protocol_ml2d module xmipp3.protocols.protocol_movie_alignment_consensus module xmipp3.protocols.protocol_movie_dose_analysis module xmipp3.protocols.protocol_movie_gain module xmipp3.protocols.protocol_movie_max_shift module xmipp3.protocols.protocol_movie_split_frames module xmipp3.protocols.protocol_multiple_fscs module xmipp3.protocols.protocol_multireference_alignability module xmipp3.protocols.protocol_normalize_strain module xmipp3.protocols.protocol_particle_pick module xmipp3.protocols.protocol_particle_pick_automatic module xmipp3.protocols.protocol_particle_pick_consensus module xmipp3.protocols.protocol_particle_pick_pairs module xmipp3.protocols.protocol_particle_pick_remove_duplicates module xmipp3.protocols.protocol_phantom_create module xmipp3.protocols.protocol_pick_noise module xmipp3.protocols.protocol_postProcessing_deepPostProcessing module xmipp3.protocols.protocol_preprocess module xmipp3.protocols.protocol_preprocess.geometrical_mask module xmipp3.protocols.protocol_preprocess.protocol_add_noise module xmipp3.protocols.protocol_preprocess.protocol_create_mask2d module xmipp3.protocols.protocol_preprocess.protocol_create_mask3d module xmipp3.protocols.protocol_preprocess.protocol_crop_resize module xmipp3.protocols.protocol_preprocess.protocol_filter module xmipp3.protocols.protocol_preprocess.protocol_image_operate module xmipp3.protocols.protocol_preprocess.protocol_mask module xmipp3.protocols.protocol_preprocess.protocol_movie_resize module xmipp3.protocols.protocol_preprocess.protocol_preprocess module xmipp3.protocols.protocol_preprocess.protocol_process module xmipp3.protocols.protocol_preprocess_micrographs module xmipp3.protocols.protocol_projmatch module xmipp3.protocols.protocol_projmatch.projmatch_form module xmipp3.protocols.protocol_projmatch.projmatch_initialize module xmipp3.protocols.protocol_projmatch.projmatch_steps module xmipp3.protocols.protocol_projmatch.protocol_projmatch module xmipp3.protocols.protocol_random_conical_tilt module xmipp3.protocols.protocol_ransac module xmipp3.protocols.protocol_reconstruct_fourier module xmipp3.protocols.protocol_reconstruct_highres module xmipp3.protocols.protocol_reconstruct_significant module xmipp3.protocols.protocol_reconstruct_swarm module xmipp3.protocols.protocol_resolution3d module xmipp3.protocols.protocol_resolution_bfactor module xmipp3.protocols.protocol_resolution_deepres module xmipp3.protocols.protocol_resolution_directional module xmipp3.protocols.protocol_resolution_fso module

xmipp3.protocols.protocol_resolution_monogenic_signal module xmipp3.protocols.protocol_rotate_volume module xmipp3.protocols.protocol_rotational_symmetry module xmipp3.protocols.protocol_screen_deepConsensus module xmipp3.protocols.protocol_screen_deeplearning module xmipp3.protocols.protocol_screen_particles module xmipp3.protocols.protocol_shift_particles module xmipp3.protocols.protocol_shift_volume module xmipp3.protocols.protocol_simulate_ctf module xmipp3.protocols.protocol_structure_map module xmipp3.protocols.protocol_structure_map_zernike3d module xmipp3.protocols.protocol_subtract_projection module xmipp3.protocols.protocol_tilt_analysis module xmipp3.protocols.protocol_trigger_data module xmipp3.protocols.protocol_validate_fscq module xmipp3.protocols.protocol_validate_nontilt module xmipp3.protocols.protocol_validate_overfitting module xmipp3.protocols.protocol_volume_adjust_sub module xmipp3.protocols.protocol_volume_consensus module xmipp3.protocols.protocol_volume_deform_zernike3d module xmipp3.protocols.protocol_volume_local_adjust module xmipp3.protocols.protocol_volume_local_sharpening module xmipp3.protocols.protocol_volume_strain module xmipp3.protocols.protocol_write_testC module xmipp3.protocols.protocol_write_testP module xmipp3.utils module xmipp3.version module xmipp3.viewers.plotter module xmipp3.viewers.viewer module XMIPP_HOME (pwem.Config attribute) XmippApplyZernike3D (class in xmipp3.protocols.protocol_apply_zernike3d) XMIPPCOLUMNS (class in xmipp3.protocols.protocol_classify_pca) XmippFilterHelper (class in xmipp3.protocols.protocol_preprocess.protocol_filter) XmippGeometricalMask2D (class in xmipp3.protocols.protocol_preprocess.geometrical_mask) XmippGeometricalMask3D (class in xmipp3.protocols.protocol_preprocess.geometrical_mask) XMIPPImageReader (class in pwem.emlib.image.image_readers) XmippImport (class in xmipp3.convert.dataimport) XmippOperateHelper (class in xmipp3.protocols.protocol_preprocess.protocol_image_operate) XmippParticlePickingAutomatic (class in xmipp3.protocols.protocol_particle_pick_automatic) XmippPlotter (class in xmipp3.viewers.plotter) XmippPreprocessHelper (class in xmipp3.protocols.protocol_preprocess.protocol_preprocess) XmippProcessParticles (class in xmipp3.protocols.protocol_preprocess.protocol_process) XmippProcessVolumes (class in xmipp3.protocols.protocol_preprocess.protocol_process) XmippProtAddNoise (class in xmipp3.protocols.protocol_preprocess.protocol_add_noise) XmippProtAddNoiseParticles (class in xmipp3.protocols.protocol_preprocess.protocol_add_noise) XmippProtAddNoiseVolumes (class in xmipp3.protocols.protocol_preprocess.protocol_add_noise) XmippProtAlignVolume (class in xmipp3.protocols.protocol_align_volume) XmippProtAlignVolumeForWeb (class in xmipp3.protocols.protocol_align_volume) XmippProtAlignVolumeParticles (class in xmipp3.protocols.protocol_align_volume_and_particles) XmippProtAnalyzeLocalCTF (class in xmipp3.protocols.protocol_analyze_local_ctf) XmippProtAngBreakSymmetry (class in xmipp3.protocols.protocol_break_symmetry) XmippProtAngularGraphConsistency (class in xmipp3.protocols.protocol_angular_graph_consistency) XmippProtApplyAlignment (class in xmipp3.protocols.protocol_apply_alignment) XmippProtApplyTiltToCtf (class in xmipp3.protocols.protocol_apply_tilt_to_ctf) XmippProtApplyTransformationMatrix (class in xmipp3.protocols.protocol_apply_transformation_matrix) XmippProtAssignmentTiltPair (class in xmipp3.protocols.protocol_assignment_tilt_pair) XmippProtbfactorResolution (class in xmipp3.protocols.protocol_resolution_bfactor) XmippProtBoostParticles (class in xmipp3.protocols.protocol_subtract_projection) XmippProtCenterParticles (class in xmipp3.protocols.protocol_center_particles) XmippProtCL2D (class in xmipp3.protocols.protocol_cl2d) XmippProtCL2DAlign (class in xmipp3.protocols.protocol_cl2d_align) XmippProtCL2DClustering (class in xmipp3.protocols.protocol_cl2d_clustering) XmippProtCL2DMap (class in xmipp3.protocols.protocol_classes_2d_mapping) XmippProtClassifyPca (class in xmipp3.protocols.protocol_classify_pca) XmippProtClassifyPcaStreaming (class in xmipp3.protocols.protocol_classify_pca_streaming) XmippProtCompareAngles (class in xmipp3.protocols.protocol_compare_angles) XmippProtCompareReprojections (class in xmipp3.protocols.protocol_compare_reprojections) XmippProtConsensusClasses (class in xmipp3.protocols.protocol_consensus_classes) XmippProtConsensusLocalCTF (class in xmipp3.protocols.protocol_consensus_local_ctf) XmippProtConsensusMovieAlignment (class in xmipp3.protocols.protocol_movie_alignment_consensus) XmippProtConsensusPicking (class in xmipp3.protocols.protocol_particle_pick_consensus) XmippProtConvertPdb (class in xmipp3.protocols.protocol_convert_pdb) XmippProtCoreAnalysis (class in xmipp3.protocols.protocol_core_analysis) XmippProtCreateGallery (class in xmipp3.protocols.protocol_create_gallery) XmippProtCreateMask2D (class in xmipp3.protocols.protocol_preprocess.protocol_create_mask2d) XmippProtCreateMask3D (class in xmipp3.protocols.protocol_preprocess.protocol_create_mask3d) XmippProtCropResizeParticles (class in xmipp3.protocols.protocol_preprocess.protocol_crop_resize) XmippProtCropResizeVolumes (class in xmipp3.protocols.protocol_preprocess.protocol_crop_resize) XmippProtCTFConsensus (class in xmipp3.protocols.protocol_ctf_consensus) XmippProtCTFCorrectWiener2D (class in xmipp3.protocols.protocol_ctf_correct_wiener2d) XmippProtCTFDefocusGroup (class in xmipp3.protocols.protocol_ctf_defocus_group) XmippProtCTFMicrographs (class in xmipp3.protocols.protocol_ctf_micrographs) XmippProtDeepCenter (class in xmipp3.protocols.protocol_deep_center) XmippProtDeepCenterPredict (class in xmipp3.protocols.protocol_deep_center_predict) XmippProtDeepConsSubSet (class in xmipp3.protocols.protocol_screen_deepConsensus) XmippProtDeepHand (class in xmipp3.protocols.protocol_deep_hand) XmippProtDeepMicrographScreen (class in xmipp3.protocols.protocol_deep_micrograph_screen) XmippProtDeepRes (class in xmipp3.protocols.protocol_resolution_deepres) XmippProtDeepVolPostProc (class in xmipp3.protocols.protocol_postProcessing_deepPostProcessing) XmippProtDenoiseParticles (class in xmipp3.protocols.protocol_denoise_particles) XmippProtEliminateEmptyBase (class in xmipp3.protocols.protocol_eliminate_empty_images) XmippProtEliminateEmptyClasses (class in xmipp3.protocols.protocol_eliminate_empty_images) XmippProtEliminateEmptyParticles (class in xmipp3.protocols.protocol_eliminate_empty_images) XmippProtEnrich (class in xmipp3.protocols.protocol_enrich) XmippProtExtractMovieParticles (class in xmipp3.protocols.protocol_extract_particles_movies) XmippProtExtractParticles (class in xmipp3.protocols.protocol_extract_particles) XmippProtExtractParticlesPairs (class in xmipp3.protocols.protocol_extract_particles_pairs) XmippProtExtractUnit (class in xmipp3.protocols.protocol_extract_asymmetric_unit) XmippProtFilterParticles (class in xmipp3.protocols.protocol_preprocess.protocol_filter) XmippProtFilterVolumes (class in xmipp3.protocols.protocol_preprocess.protocol_filter) XmippProtFlexAlign (class in xmipp3.protocols.protocol_flexalign) XmippProtFSO (class in xmipp3.protocols.protocol_resolution_fso) XmippProtGenerateReprojections (class in xmipp3.protocols.protocol_generate_reprojections) XmippProtHelicalParameters (class in xmipp3.protocols.protocol_helical_parameters) XmippProtImageOperateParticles (class in xmipp3.protocols.protocol_preprocess.protocol_image_operate) XmippProtImageOperateVolumes (class in xmipp3.protocols.protocol_preprocess.protocol_image_operate) XmippProtKerdensom (class in xmipp3.protocols.protocol_kerdensom) XmippProtLocalCTF (class in xmipp3.protocols.protocol_local_ctf) XmippProtLocalVolAdj (class in xmipp3.protocols.protocol_volume_local_adjust) XmippProtLocSharp (class in xmipp3.protocols.protocol_volume_local_sharpening) XmippProtMask (class in xmipp3.protocols.protocol_preprocess.protocol_mask) XmippProtMaskParticles (class in xmipp3.protocols.protocol_preprocess.protocol_mask) XmippProtMaskVolumes (class in xmipp3.protocols.protocol_preprocess.protocol_mask) XmippProtMicDefocusSampler (class in xmipp3.protocols.protocol_mics_defocus_balancer) XmippProtML2D (class in xmipp3.protocols.protocol_ml2d) XmippProtMonoDir (class in xmipp3.protocols.protocol_resolution_directional) XmippProtMonoRes (class in xmipp3.protocols.protocol_resolution_monogenic_signal) XmippProtMovieDoseAnalysis (class in xmipp3.protocols.protocol_movie_dose_analysis) XmippProtMovieGain (class in xmipp3.protocols.protocol_movie_gain) XmippProtMovieMaxShift (class in xmipp3.protocols.protocol_movie_max_shift) XmippProtMovieResize (class in xmipp3.protocols.protocol_preprocess.protocol_movie_resize) XmippProtMultipleFSCs (class in xmipp3.protocols.protocol_multiple_fscs) XmippProtMultiRefAlignability (class in xmipp3.protocols.protocol_multireference_alignability) XmippProtNormalizeStrain (class in xmipp3.protocols.protocol_normalize_strain) XmippProtocol (class in xmipp3.base) XmippProtParticlePicking (class in xmipp3.protocols.protocol_particle_pick) XmippProtParticlePickingPairs (class in xmipp3.protocols.protocol_particle_pick_pairs) XmippProtPhantom (class in xmipp3.protocols.protocol_phantom_create) XmippProtPickingRemoveDuplicates (class in xmipp3.protocols.protocol_particle_pick_remove_duplicates) XmippProtPickNoise (class in xmipp3.protocols.protocol_pick_noise) XmippProtPreprocessMicrographs (class in xmipp3.protocols.protocol_preprocess_micrographs) XmippProtPreprocessParticles (class in xmipp3.protocols.protocol_preprocess.protocol_preprocess) XmippProtPreprocessVolumes (class in xmipp3.protocols.protocol_preprocess.protocol_preprocess) XmippProtProjMatch (class in xmipp3.protocols.protocol_projmatch.protocol_projmatch) XmippProtRansac (class in xmipp3.protocols.protocol_ransac) XmippProtRCT (class in xmipp3.protocols.protocol_random_conical_tilt) XmippProtReconstructFourier (class in xmipp3.protocols.protocol_reconstruct_fourier) XmippProtReconstructHighRes (class in xmipp3.protocols.protocol_reconstruct_highres) XmippProtReconstructSignificant (class in xmipp3.protocols.protocol_reconstruct_significant) XmippProtReconstructSwarm (class in xmipp3.protocols.protocol_reconstruct_swarm) XmippProtResolution3D (class in xmipp3.protocols.protocol_resolution3d) XmippProtRotateVolume (class in xmipp3.protocols.protocol_rotate_volume) XmippProtRotationalSymmetry (class in xmipp3.protocols.protocol_rotational_symmetry) XmippProtScreenDeepConsensus (class in xmipp3.protocols.protocol_screen_deepConsensus) XmippProtScreenDeepLearning (class in xmipp3.protocols.protocol_screen_deeplearning) XmippProtScreenParticles (class in xmipp3.protocols.protocol_screen_particles) XmippProtShiftParticles (class in xmipp3.protocols.protocol_shift_particles) XmippProtShiftVolume (class in xmipp3.protocols.protocol_shift_volume) XmippProtSimulateCTF (class in xmipp3.protocols.protocol_simulate_ctf) XmippProtSplitFrames (class in xmipp3.protocols.protocol_movie_split_frames) XmippProtStructureMap (class in xmipp3.protocols.protocol_structure_map) XmippProtStructureMapZernike3D (class in xmipp3.protocols.protocol_structure_map_zernike3d) XmippProtSubtractProjection (class in xmipp3.protocols.protocol_subtract_projection) XmippProtSubtractProjectionBase (class in xmipp3.protocols.protocol_subtract_projection) XmippProtTiltAnalysis (class in xmipp3.protocols.protocol_tilt_analysis) XmippProtTriggerData (class in xmipp3.protocols.protocol_trigger_data) XmippProtValFit (class in xmipp3.protocols.protocol_validate_fscq) XmippProtValidateNonTilt (class in xmipp3.protocols.protocol_validate_nontilt) XmippProtValidateOverfitting (class in xmipp3.protocols.protocol_validate_overfitting) XmippProtVolAdjBase (class in xmipp3.protocols.protocol_volume_adjust_sub) XmippProtVolAdjust (class in xmipp3.protocols.protocol_volume_adjust_sub) XmippProtVolConsensus (class in xmipp3.protocols.protocol_volume_consensus) XmippProtVolSubtraction (class in xmipp3.protocols.protocol_volume_adjust_sub) XmippProtVolumeDeformZernike3D (class in xmipp3.protocols.protocol_volume_deform_zernike3d) XmippProtVolumeStrain (class in xmipp3.protocols.protocol_volume_strain) XmippProtWriteTestC (class in xmipp3.protocols.protocol_write_testC) XmippProtWriteTestP (class in xmipp3.protocols.protocol_write_testP) XmippResizeHelper (class in xmipp3.protocols.protocol_preprocess.protocol_crop_resize) XmippSet (class in xmipp3.base) xmippToLocation() (in module xmipp3.convert.convert) XmippViewer (class in xmipp3.viewers.viewer) xml (pyworkflow.tests.tests.GTestResult attribute)

Y

ycoor (xmipp3.protocols.protocol_classify_pca.XMIPPCOLUMNS attribute) yellow (pyworkflow.constants.StrColors attribute) YELLOW (pyworkflow.utils.properties.colorText attribute) yellow() (in module pyworkflow.utils.utils) (in module scipion.install.funcs) (in module scipion.scripts.config)

yellowB() (in module pyworkflow.utils.utils) yellowStr() (in module pyworkflow.utils.utils) YesNoDialog (class in pyworkflow.gui.dialog)

Z

zoomerM() (pwem.viewers.viewer_coordinates.MainWindow method) (pyworkflow.gui.canvas.Canvas method)

zoomerP() (pwem.viewers.viewer_coordinates.MainWindow method) (pyworkflow.gui.canvas.Canvas method) ZSCORE_CHOICES (xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles attribute)