Index

A

accumDoses (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) Acquisition (class in pwem.objects.data) acquisitionParams (pyseg.protocols.protocol_picking.ProtPySegPicking attribute) acquisitions (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) acquisitionToRow() (in module cryosparc2.convert.convert) (in module relion.convert.convert_deprecated) (in module xmipp3.convert.convert) ACTION_BROWSE (pyworkflow.utils.properties.Icon attribute) ACTION_CLOSE (pyworkflow.utils.properties.Icon attribute) ACTION_CONTINUE (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_EDIT (pyworkflow.utils.properties.Icon attribute) ACTION_EXECUTE (pyworkflow.utils.properties.Icon attribute) ACTION_EXPORT (pyworkflow.utils.properties.Icon attribute) ACTION_EXPORT_UPLOAD (pyworkflow.utils.properties.Icon attribute) ACTION_FIND_NEXT (pyworkflow.utils.properties.Icon attribute) ACTION_FIND_PREVIOUS (pyworkflow.utils.properties.Icon attribute) ACTION_HELP (pyworkflow.utils.properties.Icon attribute) ACTION_IN (pyworkflow.utils.properties.Icon attribute) ACTION_LIST (pyworkflow.utils.properties.Icon attribute) ACTION_NEW (pyworkflow.utils.properties.Icon attribute) ACTION_OUT (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_STEPS (pyworkflow.utils.properties.Icon attribute) ACTION_STOP (pyworkflow.utils.properties.Icon attribute) ACTION_STOP_WORKFLOW (pyworkflow.utils.properties.Icon attribute) ACTION_TREE (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) activate() (pyworkflow.gui.plotter.Plotter method) adaptDynamoStep() (continuousflex.protocols.protocol_subtomogram_averaging.FlexProtSubtomogramAveraging method) adaptShifts() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) adaptTomboxStep() (continuousflex.protocols.protocol_subtomogram_averaging.FlexProtSubtomogramAveraging method) adaptXmippStep() (continuousflex.protocols.protocol_subtomogram_averaging.FlexProtSubtomogramAveraging method) add() (pyworkflow.gui.text.HyperlinkManager method) (relion.convert.convert31.OpticsGroups 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_extra_fields() (in module pwperformance.loggers.influxdb) ADD_MODEL_GENERAL (topaz.protocols.protocol_topaz_picking.TopazProtPicking attribute) ADD_MODEL_PRETRAINED (topaz.protocols.protocol_topaz_picking.TopazProtPicking attribute) ADD_MODEL_TRAIN_MODEL (topaz.protocols.protocol_topaz_training.TopazProtTraining attribute) ADD_MODEL_TRAIN_NEW (topaz.protocols.protocol_topaz_training.TopazProtTraining attribute) (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 (topaz.protocols.protocol_topaz_picking.TopazProtPicking attribute) (topaz.protocols.protocol_topaz_training.TopazProtTraining attribute) (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) addChainStep() (atomstructutils.protocols.protocol_operate.ProtAtomStrucOperate method) addChild() (pyworkflow.utils.graph.Node method) addChildNode() (spider.protocols.protocol_classify_base.SpiderProtClassifyCluster method) addCodeSpeedLogger() (in module pwperformance.main) addColumns() (relion.convert.convert31.OpticsGroups method) addCommand() (scipion.install.funcs.Target method) addComputeSectionParams() (in module cryosparc2.utils) addCoord() (topaz.convert.CsvCoordinateList method) addCryoloPackage() (sphire.Plugin class method) addCTF() (pwem.objects.data.DefocusGroup method) addCTFTomoSeriesToSetFromDefocusFile() (imod.protocols.protocol_base.ProtImodBase method) addDeepFinderPackage() (deepfinder.Plugin class method) addDefocus() (relion.convert.DefocusGroups.Group method) addDep() (scipion.install.funcs.Target method) addEntry() (relion.objects.CtfRefineMicInfo 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) (spider.wizards.SpiderFilterDialog 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) addImage() (spider.protocols.protocol_classify_base.DendroNode 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) addLandmark() (tomo.objects.LandmarkModel 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) addMic() (topaz.convert.CsvMicrographList method) addMicInfo() (relion.objects.CtfRefineGlobalInfo 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) addNotifier() (emfacilities.protocols.protocol_monitor.Monitor method) addObject() (emxlib.utils.EmxData method) (pyworkflow.gui.form.MultiPointerTreeProvider method) addPackage() (scipion.install.funcs.Environment method) addParallelSection() (pyworkflow.protocol.params.Form method) addParam() (pyworkflow.protocol.params.ElementGroup method) (pyworkflow.protocol.params.Form method) addParticle() (spider.protocols.protocol_projmatch.DefocusGroupInfo method) addPipModule() (scipion.install.funcs.Environment method) addPluginsVariables() (in module scipion.scripts.config) addPluginTemplates() (pyworkflow.template.TemplateList method) addPoint() (continuousflex.protocols.data.Data method) (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) addRandomSubset() (in module cryosparc2.convert.convert) addRow() (pyworkflow.utils.dataset.Table method) addScipionTemplates() (pyworkflow.template.TemplateList method) addSection() (pyworkflow.protocol.params.Form method) addSelectionListener() (pyworkflow.gui.canvas.Item method) addSocket() (pyworkflow.gui.canvas.Item method) addStatisticsTable() (xmipp3.viewers.viewer_validate_fscq.Statistics method) addStruct() (pwem.convert.atom_struct.AtomicStructHandler method) addSubElement() (pyworkflow.mapper.xmlmapper.XmlMapper method) addSubMenu() (pyworkflow.gui.project.viewprotocols.ProtocolConfig method) (pyworkflow.project.config.MenuConfig method) addSuccess() (pyworkflow.tests.tests.GTestResult method) addSummaryWarning() (pyworkflow.protocol.protocol.Protocol method) addSymmetry() (relion.protocols.protocol_base.ProtRelionBase method) (relion.protocols.protocol_initialmodel.ProtRelionInitialModel method) (reliontomo.protocols.protocol_base_tomo.ProtRelionBaseTomo method) addSymmetryParam() (in module cryosparc2.utils) addTarget() (scipion.install.funcs.Environment method) addTargetAlias() (scipion.install.funcs.Environment method) addTemplate() (pyworkflow.template.TemplateList method) addText() (pyworkflow.gui.text.Text method) addTi() (tomo.objects.TiltSeriesDict method) addToMd() (pwem.emlib.metadata.utils.Row method) addTopazPackage() (topaz.Plugin class method) addTs() (tomo.objects.TiltSeriesDict method) addValidator() (pyworkflow.protocol.params.Param method) addVariablesToSection() (in module scipion.scripts.config) addViewList() (pyworkflow.gui.project.base.ProjectBaseWindow 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) 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)

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) ALIGNMENT_LABELS (relion.convert.convert30.Reader attribute) (relion.convert.convert31.Reader attribute) alignmentToRow() (in module cryosparc2.convert.convert) (in module eman2.convert.convert) (in module emantomo.convert.convert) (in module relion.convert.convert_deprecated) (in module spider.convert) (in module xmipp3.convert.convert) alignMuscleSequences() (in module pwem.convert.sequence) alignParticlesStep() (spider.protocols.protocol_align_apsr.SpiderProtAlignAPSR method) (spider.protocols.protocol_align_pairwise.SpiderProtAlignPairwise method) (xmipp3.protocols.protocol_align_volume_and_particles.XmippProtAlignVolumeParticles method) alignSeq() (pwem.convert.sequence.SequenceHandler method) alignStep() (dynamo.protocols.protocol_subtomo_MRA.DynamoSubTomoMRA method) alignToReference() (xmipptomo.protocols.protocol_align_transform.XmippProtAlignTransform method) alignTsStep() (jjsoft.protocols.protocol_align_ts.ProtJjsoftAlignTs method) (jjsoft.protocols.protocol_motion_compensation.ProtJjsoftAlignReconstructTomogram method) alignTypeList (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) alignVolumeStep() (continuousflex.protocols.protocol_structure_mapping.FlexProtStructureMapping method) (xmipp3.protocols.protocol_align_volume.XmippProtAlignVolume method) (xmipp3.protocols.protocol_align_volume_and_particles.XmippProtAlignVolumeParticles method) ALL_PROTOCOLS (pyworkflow.gui.project.viewprotocols.ProtocolTreeConfig attribute) allCtfGroups() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) allDone() (tomo.objects.TiltSeriesDict method) allFree() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) allIters() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) allowsDelete() (imod.protocols.protocol_ctfEstimation_automatic.ProtImodAutomaticCtfEstimation method) (pwem.protocols.protocol.EMProtocol method) (pyworkflow.protocol.protocol.Protocol method) (tomo.protocols.protocol_ctf_validate.ProtCTFTomoSeriesValidate method) (tomo.protocols.protocol_ts_estimate_ctf.ProtTsEstimateCTF method) allowsGpu() (pyworkflow.protocol.protocol.Protocol method) allowsRenderable() (pwem.viewers.showj.ColumnProperties method) allRefs() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) alphabetToIndex() (in module pwem.convert.sequence) ANALYSISTMPFILE (phenix.viewers.viewer_refinement_base.PhenixProtRefinementBaseViewer attribute) 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) Angles (class in pwem.objects.data_tiltpairs) ANGLES_FROM_FILENAME (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) ANGLES_FROM_HEADER (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) ANGLES_FROM_MDOC (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) ANGLES_FROM_RANGE (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) ANGLES_FROM_TLT (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) anglesDifference() (in module xmipp3.protocols.protocol_ctf_consensus) angularAccuracyStep() (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) angularDistance() (xmipp3.protocols.protocol_deep_align.XmippProtDeepAlign method) angularProjectLibraryStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) animate() (emfacilities.viewers.viewer_monitors.CtfMonitorPlotter method) (emfacilities.viewers.viewer_monitors.MovieGainMonitorPlotter method) (emfacilities.viewers.viewer_monitors.SystemMonitorPlotter method) animateModesStep() (continuousflex.protocols.protocol_nma.FlexProtNMA 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.objects.data.SetOfImages method) (pyworkflow.object.PointerList method) (pyworkflow.object.Set method) (tomo.objects.TiltSeriesBase method) (xmipp3.base.XmippSet method) appendCutOnFreqList() (tomo.objects.CTFTomo method) appendDefocusAngleList() (tomo.objects.CTFTomo method) appendDefocusUList() (tomo.objects.CTFTomo method) appendDefocusVList() (tomo.objects.CTFTomo method) appendFromClasses() (pwem.objects.data.SetOfClasses method) (pwem.objects.data.SetOfImages method) appendFromImages() (pwem.objects.data.SetOfImages method) appendJson() (in module emantomo.convert.convert) appendPhaseShiftList() (tomo.objects.CTFTomo method) appion (module) appion.bibtex (module) appion.constants (module) appion.convert (module) appion.convert.convert (module) appion.convert.dataimport (module) appion.protocols (module) appion.protocols.protocol_dogpicker (module) appion.wizards (module) apply() (pyworkflow.gui.dialog.Dialog method) (pyworkflow.gui.dialog.EditObjectDialog method) (pyworkflow.gui.dialog.EntryDialog method) (pyworkflow.gui.dialog.FileBrowseDialog method) (pyworkflow.gui.dialog.ListDialog method) (pyworkflow.gui.form.QueueDialog method) (pyworkflow.gui.project.labels.EditLabelDialog method) apply_noise_and_ctf() (continuousflex.protocols.protocol_image_synthesize.FlexProtSynthesizeImages method) (continuousflex.protocols.protocol_subtomogrmas_synthesize.FlexProtSynthesizeSubtomo method) applyAlignment() (continuousflex.protocols.protocol_apply_volumeset_alignment.FlexProtApplyVolSetAlignment method) applyAlignmentStep() (xmipp3.protocols.protocol_apply_alignment.XmippProtApplyAlignment method) (xmipptomo.protocols.protocol_applyAlignmentTS.XmippProtApplyTransformationMatrixTS method) (xmipptomo.protocols.protocol_apply_alignment_subtomo.XmippProtApplyTransformSubtomo method) applyAlignStep() (xmipptomo.protocols.protocol_subtraction_subtomo.XmippProtSubtractionSubtomo method) applyOperations() (scipion.install.plugin_manager.OperationList method) applyTransform() (in module xmipp3.utils) (pwem.emlib.image.image_handler.ImageHandler static method) (tomo.objects.TiltSeries method) applyTransformationStep() (atomstructutils.protocols.protocol_convertsymmetry.ProtAtomStrucConvertSymmetry method) applyWorkflowStep() (dynamo.protocols.protocol_model_workflow.DynamoModelWorkflow 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_LEFT (pyworkflow.utils.properties.Icon attribute) ARROW_UP (pyworkflow.utils.properties.Icon attribute) ask() (in module pyworkflow.apps.pw_sync_data) askColor() (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) assignParamValue() (cryosparc2.protocols.protocol_cryosparc2d.ProtCryo2D method) assignPdbStep() (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) assignStep() (localrec.protocols.protocol_localized_set_origin.ProtLocalOrigSampling method) (pwem.protocols.protocol_origin_sampling_volume.ProtOrigSampling method) assignTransformationMatricesStep() (imod.protocols.protocol_importSetOfTM.ProtImodImportTransformationMatrix method) (tomo.protocols.protocol_assignTransformationTS.ProtAssignTransformationMatrixTiltSeries method) ATOM (xmipp3.viewers.viewer_validate_fscq.XmippProtValFitViewer attribute) AtomicStructHandler (class in pwem.convert.atom_struct) AtomStruct (class in pwem.objects.data) atomstructutils (module) atomstructutils.bibtex (module) atomstructutils.constants (module) atomstructutils.protocols (module) atomstructutils.protocols.protocol_average_subunits (module) atomstructutils.protocols.protocol_convertsymmetry (module) atomstructutils.protocols.protocol_operate (module) atomstructutils.viewers (module) atomstructutils.viewers.viewer (module) atomstructutils.viewers.viewer_protocol_convertsymmetry (module) atomstructutils.wizards (module) atsas (module) atsas.bibtex (module) atsas.constants (module) atsas.protocols (module) atsas.protocols.protocol_pdb_to_saxs (module) atsas.viewers (module) atsas.viewers.viewer (module) AtsasProtConvertPdbToSAXS (class in atsas.protocols.protocol_pdb_to_saxs) AtsasViewer (class in atsas.viewers.viewer) attractionGeneralStep() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) attractionSplitStep() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) 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) averageClasses() (xmipp3.protocols.protocol_classification_gpuCorr_full.XmippProtStrGpuCrrCL2D method) averageMovie() (pwem.protocols.protocol_align_movies.ProtAlignMovies method) AverageSubTomogram (class in tomo.objects) averagingStep() (continuousflex.protocols.protocol_batch_cluster_vol.FlexBatchProtNMAClusterVol method) awakeStep() (pwem.protocols.parallel.ProtTestParallel method) AXIS_X (imod.protocols.protocol_tomoProjection.ProtImodTomoProjection attribute) AXIS_Y (imod.protocols.protocol_tomoProjection.ProtImodTomoProjection attribute) AXIS_Z (imod.protocols.protocol_tomoProjection.ProtImodTomoProjection attribute)

B

backend (pyworkflow.gui.plotter.Plotter attribute) bamfordlab (module) bamfordlab.bibtex (module) bamfordlab.constants (module) bamfordlab.protocols (module) bamfordlab.protocols.protocol_ethan_picking (module) bamfordlab.wizards (module) BandPassFilterDialog (class in pwem.wizards.wizard) bar1Free (emfacilities.protocols.pynvml.c_nvmlBAR1Memory_t attribute) bar1Total (emfacilities.protocols.pynvml.c_nvmlBAR1Memory_t attribute) bar1Used (emfacilities.protocols.pynvml.c_nvmlBAR1Memory_t attribute) BaseTest (class in pyworkflow.tests.tests) BasicLayout (class in pyworkflow.gui.graph_layout) BatchProtocol (class in pwem.protocols.protocol_batch) BEGIN (pyworkflow.utils.utils.Environ attribute) Benchmark (class in pwperformance.main) BfactorWindow (class in xmipp3.viewers.viewer_resolution3d) 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) binTomosStep() (dynamo.protocols.protocol_bin_tomograms.DynamoBinTomograms 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.utils.properties.colorText attribute) blue (pyworkflow.utils.utils.StrColors 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) bm4d() (in module continuousflex.protocols.utilities.bm4d) body() (imod.viewers.views_tkinter_tree.ImodListDialog method) (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.FileBrowseDialog 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) (tomo.viewers.views_tkinter_tree.CtfEstimationListDialog method) (xmipptomo.viewers.monotomo_tree_provider.MonoTomoListDialog method)

BOLD (pyworkflow.utils.properties.colorText attribute) Boolean (class in pyworkflow.object) BooleanParam (class in pyworkflow.protocol.params) BoolVar (class in pyworkflow.gui.form) BOTTOM (pyworkflow.gui.canvas.Item attribute) BOTTOM_LEFT_CORNER() (in module tomo.constants) BoundTree (class in pyworkflow.gui.tree) boxSizeEstimated (sphire.protocols.protocol_cryolo_picking.SphireProtCRYOLOPicking attribute) boxsizeStep() (xmipp3.protocols.protocol_particle_boxsize.XmippProtParticleBoxsize method) breakSymmetryStep() (xmipp3.protocols.protocol_break_symmetry.XmippProtAngBreakSymmetry method) bridgeChipInfo (emfacilities.protocols.pynvml.c_nvmlBridgeChipHierarchy_t attribute) bridgeCount (emfacilities.protocols.pynvml.c_nvmlBridgeChipHierarchy_t attribute) BrowserWindow (class in pyworkflow.gui.browser) BRUSH (pyworkflow.utils.properties.Icon attribute) bsoft (module) bsoft.bibtex (module) bsoft.constants (module) bsoft.convert (module) bsoft.protocols (module) bsoft.protocols.protocol_bfilter (module) bsoft.protocols.protocol_blocres (module) bsoft.protocols.protocol_particle_pick (module) bsoft.viewers (module) bsoft.viewers.bsoft_viewers (module) bsoft.wizards (module) BsoftColorScaleWizard (class in bsoft.wizards) BsoftFilterDialog (class in bsoft.wizards) BsoftFilterParticlesWizard (class in bsoft.wizards) BsoftPlotter (class in bsoft.viewers.bsoft_viewers) BsoftProtBfilter (class in bsoft.protocols.protocol_bfilter) BsoftProtBlocres (class in bsoft.protocols.protocol_blocres) BsoftProtParticlePicking (class in bsoft.protocols.protocol_particle_pick) BsoftViewer (class in bsoft.viewers.bsoft_viewers) BsoftViewerBlocres (class in bsoft.viewers.bsoft_viewers) BsoftVolumeView (class in bsoft.viewers.bsoft_viewers) BSPLINE (localrec.protocols.protocol_localized_stitch.ProtLocalizedStich attribute) BufferingInfluxHandler (class in pwperformance.loggers.influxdb) buildDendrogram() (spider.protocols.protocol_classify_base.SpiderProtClassifyCluster method) buildRunCommand() (in module pyworkflow.utils.process) buildSearchList() (pyworkflow.gui.text.TextFileViewer method) bus (emfacilities.protocols.pynvml.nvmlPciInfo_t attribute) busId (emfacilities.protocols.pynvml.nvmlPciInfo_t attribute) Button (class in pyworkflow.gui.widgets) BUTTON_CANCEL (pyworkflow.utils.properties.Icon attribute) BUTTON_CLOSE (pyworkflow.utils.properties.Icon attribute) BUTTON_PC (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)

C

c_nvmlAccountingStats_t (class in emfacilities.protocols.pynvml) c_nvmlBAR1Memory_t (class in emfacilities.protocols.pynvml) c_nvmlBridgeChipHierarchy_t (class in emfacilities.protocols.pynvml) c_nvmlBridgeChipInfo_t (class in emfacilities.protocols.pynvml) c_nvmlDevice_t (in module emfacilities.protocols.pynvml) c_nvmlEccErrorCounts_t (class in emfacilities.protocols.pynvml) c_nvmlEventData_t (class in emfacilities.protocols.pynvml) c_nvmlEventSet_t (in module emfacilities.protocols.pynvml) c_nvmlHwbcEntry_t (class in emfacilities.protocols.pynvml) c_nvmlLedState_t (class in emfacilities.protocols.pynvml) c_nvmlMemory_t (class in emfacilities.protocols.pynvml) c_nvmlProcessInfo_t (class in emfacilities.protocols.pynvml) c_nvmlPSUInfo_t (class in emfacilities.protocols.pynvml) c_nvmlSample_t (class in emfacilities.protocols.pynvml) c_nvmlUnit_t (in module emfacilities.protocols.pynvml) c_nvmlUnitFanInfo_t (class in emfacilities.protocols.pynvml) c_nvmlUnitFanSpeeds_t (class in emfacilities.protocols.pynvml) c_nvmlUnitInfo_t (class in emfacilities.protocols.pynvml) c_nvmlUtilization_t (class in emfacilities.protocols.pynvml) c_nvmlValue_t (class in emfacilities.protocols.pynvml) c_nvmlViolationTime_t (class in emfacilities.protocols.pynvml) Cable (class in pyworkflow.gui.canvas) calcFrameMotion() (motioncorr.protocols.protocol_motioncorr.ProtMotionCorr method) calculateAngStep() (xmipp3.protocols.protocol_reconstruct_heterogeneous.XmippProtReconstructHeterogeneous method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) calculateAutodownsampling() (xmipp3.protocols.protocol_ctf_micrographs.XmippProtCTFMicrographs method) calculateAverage() (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) calculateConsensusStep() (tomo3D.protocols.protocol_particle_pick_consensus.ProtTomoConsensusPicking method) (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking method) calculateCoorConsensusStep() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) calculateDefocusUDeviation() (tomo.objects.CTFTomoSeries method) calculateDefocusVDeviation() (tomo.objects.CTFTomoSeries 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) calculateNewSamplingRate() (in module cryosparc2.utils) calculatePhaseShift() (in module eman2.convert.convert) (in module emantomo.convert.convert) calculateRotationAngleFromTM() (in module imod.utils) (in module xmipptomo.utils) calculateSpectraStep() (xmipp3.protocols.protocol_rotational_spectra.XmippProtRotSpectra method) calculateStrain() (xmipp3.protocols.protocol_volume_strain.XmippProtVolumeStrain method) call_BFlow() (jjsoft.protocols.protocol_denoise_tomogram.ProtJjsoftProtDenoiseTomogram method) call_EED() (jjsoft.protocols.protocol_denoise_tomogram.ProtJjsoftProtDenoiseTomogram method) cancel() (pyworkflow.gui.dialog.Dialog method) CANCEL_SELECTED_OPERATION (pyworkflow.utils.properties.Message attribute) Canvas (class in pyworkflow.gui.canvas) capcaStep() (spider.protocols.protocol_ca_pca.SpiderProtCAPCA method) cause (emfacilities.protocols.pynvml.c_nvmlLedState_t attribute) cc() (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify method) CCCHAINFILE (phenix.viewers.viewer_validation_cryoem.PhenixProtRunValidationCryoEMViewer attribute) CCCHAINFILE2 (phenix.viewers.viewer_validation_cryoem.PhenixProtRunValidationCryoEMViewer attribute) ccp4 (module) ccp4.bibtex (module) ccp4.constants (module) ccp4.convert (module) ccp4.protocols (module) ccp4.protocols.protocol_coot (module) ccp4.protocols.protocol_refmac (module) ccp4.protocols.refmac_template_map2mtz (module) ccp4.protocols.refmac_template_refine (module) ccp4.viewers (module) ccp4.viewers.viewer_coot (module) ccp4.viewers.viewer_refmac (module) Ccp4Header (class in pwem.convert.headers) CCP4ProtRunRefmac (class in ccp4.protocols.protocol_refmac) CCP4ProtRunRefmacViewer (class in ccp4.viewers.viewer_refmac) CCRESIDUESFILE (phenix.viewers.viewer_validation_cryoem.PhenixProtRunValidationCryoEMViewer attribute) CCRESIDUESFILE2 (phenix.viewers.viewer_validation_cryoem.PhenixProtRunValidationCryoEMViewer attribute) CENTER_GRAVITY() (in module tomo.constants) centerAveragesStep() (relion.protocols.protocol_center_averages.ProtRelionCenterAverages method) centerFirstHarmonicStep() (xmipp3.protocols.protocol_rotational_spectra.XmippProtRotSpectra method) centerOfMass() (pwem.convert.atom_struct.AtomicStructHandler method) centerStep() (xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles method) centerWindows() (in module pyworkflow.gui.gui) CHANGE_LABELS (relion.protocols.protocol_base.ProtRelionBase attribute) (relion.protocols.protocol_classify3d.ProtRelionClassify3D attribute) (relion.protocols.protocol_initialmodel.ProtRelionInitialModel attribute) (relion.protocols.protocol_refine3d.ProtRelionRefine3D attribute) 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) (tomo.viewers.views_tkinter_tree.CTFEstimationTree method) checkAttraction() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) checkBackgroundStep() (xmipp3.protocols.protocol_volume_local_sharpening.XmippProtLocSharp method) checkBinaries() (ccp4.Plugin class method) checkConf() (in module scipion.scripts.config) checkContinueClassification() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) CHECKED (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) (tomo.viewers.views_tkinter_tree.CTFSerieStates attribute) checkIfInputIsCompareReprojection() (xmipp3.protocols.protocol_deep_denoising.XmippProtDeepDenoising method) checkIfNewMics() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) checkIfParentsFinished() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) checkInfoField() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) checkInputTomoSetsSize() (cryocare.utils.CryocareUtils static method) checkLabelInFile() (pwem.convert.atom_struct.AtomicStructHandler method) checkLib() (in module scipion.install.funcs) checkMaskFormat() (in module pyseg.utils) checkNewThumbsReady() (emfacilities.protocols.report_html.ReportHtml method) checkNotify() (in module scipion.scripts.config) checkOutput() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) checkOutputsStep() (xmipp3.protocols.protocol_metaprotocol_discrete_heterogeneity_scheduler.XmippMetaProtDiscreteHeterogeneityScheduler method) (xmipp3.protocols.protocol_metaprotocol_golden_highres.XmippMetaProtGoldenHighRes method) checkPaths() (in module scipion.scripts.config) checkPid() (pyworkflow.project.project.Project method) checkPlugin() (in module pyworkflow.utils.reflection) checkPositionTiltSeriesInList() (imod.protocols.protocol_excludeViews.ProtImodExcludeViews method) checkRead() (pwem.convert.atom_struct.AtomicStructHandler method) checkRejectedCriteria() (xmipp3.protocols.protocol_ctf_micrographs.XmippProtCTFMicrographs method) checkSplit() (xmipp3.protocols.protocol_classification_gpuCorr_full.XmippProtStrGpuCrrCL2D method) checkSummaryWarnings() (pyworkflow.protocol.protocol.Protocol method) Chimera (class in pwem.viewers.viewer_chimera) chimera (module) chimera.bibtex (module) chimera.constants (module) chimera.convert (module) chimera.editList (module) chimera.getchimera (module) chimera.protocols (module) chimera.protocols.protocol_base (module) chimera.protocols.protocol_contacts (module) chimera.protocols.protocol_fit (module) chimera.protocols.protocol_modeller_search (module) chimera.protocols.protocol_operate (module) chimera.protocols.protocol_restore (module) chimera.protocols.protocol_subtraction_maps (module) chimera.utils (module) chimera.viewers (module) chimera.viewers.viewer (module) chimera.viewers.viewer_contacts (module) chimera.wizards (module) CHIMERA_FILTERS (chimera.protocols.protocol_subtraction_maps.ChimeraSubtractionMaps attribute) ChimeraAngDist (class in pwem.viewers.viewer_chimera) chimeraClashesStep() (chimera.protocols.protocol_contacts.ChimeraProtContacts method) ChimeraClientView (class in pwem.viewers.viewer_chimera) ChimeraDataView (class in pwem.viewers.viewer_chimera) ChimeraHandler (class in pwem.viewers.filehandlers) ChimeraModelFromTemplate (class in chimera.protocols.protocol_modeller_search) ChimeraModelFromTemplateViewer (class in chimera.viewers.viewer) ChimeraProtBase (class in chimera.protocols.protocol_base) ChimeraProtContacts (class in chimera.protocols.protocol_contacts) ChimeraProtContactsViewer (class in chimera.viewers.viewer_contacts) ChimeraProtOperate (class in chimera.protocols.protocol_operate) ChimeraProtOperateViewer (class in chimera.viewers.viewer) ChimeraProtRestore (class in chimera.protocols.protocol_restore) ChimeraProtRigidFit (class in chimera.protocols.protocol_fit) ChimeraProtRigidFitViewer (class in chimera.viewers.viewer) ChimeraRestoreViewer (class in chimera.viewers.viewer) ChimeraSubtractionMaps (class in chimera.protocols.protocol_subtraction_maps) ChimeraSubtractionMapsViewer (class in chimera.viewers.viewer) ChimeraView (class in pwem.viewers.viewer_chimera) ChimeraViewer (class in pwem.viewers.viewer_chimera) ChimeraViewerBase (class in chimera.viewers.viewer) 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_editor.ProtSetEditor attribute) (pwem.protocols.protocol_set_filter.ProtSetFilter attribute) CHOICE_LABEL (pwem.protocols.protocol_set_editor.ProtSetEditor attribute) (pwem.protocols.protocol_set_filter.ProtSetFilter attribute) CHOICE_RANKED (pwem.protocols.protocol_set_filter.ProtSetFilter attribute) CHOICE_ROTATE_ICOSAHEDRAL (pwem.protocols.protocol_set_editor.ProtSetEditor attribute) CHOICE_ROTATE_VECTOR (pwem.protocols.protocol_set_editor.ProtSetEditor attribute) choices (emantomo.protocols.protocol_tomo_reconstruction.EmanProtTomoReconstruction attribute) chooseTemplate() (in module scipion.scripts.kickoff) CIF (pwem.convert.atom_struct.AtomicStructHandler attribute) cifToPdb() (in module pwem.convert.atom_struct) cistem (module) cistem.bibtex (module) cistem.constants (module) cistem.convert (module) cistem.convert.convert (module) cistem.convert.dataimport (module) cistem.protocols (module) cistem.protocols.program_ctffind (module) cistem.protocols.protocol_ctffind (module) cistem.protocols.protocol_picking (module) cistem.protocols.protocol_refine2d (module) cistem.protocols.protocol_ts_ctffind (module) cistem.protocols.protocol_unblur (module) cistem.viewers (module) cistem.wizards (module) CistemCTFWizard (class in cistem.wizards) CistemProtCTFFind (class in cistem.protocols.protocol_ctffind) CistemProtFindParticles (class in cistem.protocols.protocol_picking) CistemProtRefine2D (class in cistem.protocols.protocol_refine2d) CistemProtTsCtffind (class in cistem.protocols.protocol_ts_ctffind) CistemProtUnblur (class in cistem.protocols.protocol_unblur) citations() (pyworkflow.protocol.protocol.Protocol method) claasesTable (reliontomo.protocols.protocol_base_tomo.ProtRelionBaseTomo attribute) CLASHESFILE (phenix.viewers.viewer_validation_cryoem.PhenixProtRunValidationCryoEMViewer attribute) Class2D (class in pwem.objects.data) class2DToRow() (in module xmipp3.convert.convert) Class3D (class in pwem.objects.data) CLASS_LABEL (relion.protocols.protocol_base.ProtRelionBase attribute) CLASS_MAP (pyworkflow.mapper.sqlite.SqliteFlatDb attribute) Classes3DView (class in pwem.viewers.views) ClassesLoader (class in relion.convert) (class in reliontomo.convert) ClassesSubTomogramsView (class in tomo.viewers.views) ClassesView (class in pwem.viewers.views) classifyGroupsStep() (xmipp3.protocols.protocol_solid_angles.XmippProtSolidAngles method) (xmipp3.protocols.protocol_split_volume_hierarchical_cluster.XmippProtSplitVolumeHierarchical method) classifyItems() (pwem.objects.data.SetOfClasses method) classifyOneGroup() (xmipp3.protocols.protocol_solid_angles.XmippProtSolidAngles method) (xmipp3.protocols.protocol_split_volume_hierarchical_cluster.XmippProtSplitVolumeHierarchical method) classifyParticles() (xmipp3.protocols.protocol_reconstruct_heterogeneous.XmippProtReconstructHeterogeneous method) classifyStep() (spider.protocols.protocol_classify_base.SpiderProtClassify method) (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) (xmipp3.protocols.protocol_classification_gpuCorr_full.XmippProtStrGpuCrrCL2D method) (xmipp3.protocols.protocol_classification_gpuCorr_semi.XmippProtStrGpuCrrSimple method) classifyWholeSetStep() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) ClassSubTomogram (class in tomo.objects) ClassVol (class in pwem.objects.data) cleanDirectory() (xmipp3.protocols.protocol_reconstruct_heterogeneous.XmippProtReconstructHeterogeneous method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes 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) cleaningPath() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) cleaningStep() (xmipp3.protocols.protocol_split_volume_hierarchical_cluster.XmippProtSplitVolumeHierarchical 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) cleanVolume() (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) cleanVolumeStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) cleanWorkingDir() (pyworkflow.protocol.protocol.Protocol method) clear() (continuousflex.protocols.data.Data method) (emxlib.utils.EmxData method) (emxlib.utils.EmxObject method) (pyworkflow.gui.canvas.Canvas 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) clearIntermediateResults() (in module cryosparc2.utils) clearJob() (in module cryosparc2.utils) 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) (pyworkflow.object.Object method) (tomo.objects.CTFTomoSeries method) (tomo.objects.ClassSubTomogram method) (tomo.objects.TiltSeriesBase method) close() (cistem.convert.convert.FrealignParFile method) (emfacilities.protocols.transport.Connect method) (gautomatch.convert.CoordStarWriter method) (gctf.convert.convert.CoordinatesWriter method) (pwem.objects.data.Class2D method) (pwem.objects.data.Class3D method) (pwem.objects.data.ClassVol 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) (relion.objects.CtfRefineGlobalInfo method) (scipion.install.plugin_manager.PluginManagerWindow method) (scipion.scripts.kickoff.KickoffWindow method) (sphire.convert.CoordBoxReader method) (sphire.convert.CoordBoxWriter method) (spider.protocols.protocol_projmatch.DefocusGroupInfo method) (spider.utils.SpiderDocAliFile method) (spider.utils.SpiderDocFile method) (spider.utils.SpiderShell method) (tomo.objects.ClassSubTomogram method) (tomo.objects.TiltSeriesBase method) (topaz.convert.CsvImageList method) closeConnection() (pyworkflow.mapper.sqlite_db.SqliteDb class method) closeMapper() (pyworkflow.project.project.Project method) closeMappers() (pyworkflow.protocol.protocol.Protocol method) closeOutputSetsStep() (imod.protocols.protocol_applyTransformationMatrix.ProtImodApplyTransformationMatrix method) (imod.protocols.protocol_ctfCorrection.ProtImodCtfCorrection method) (imod.protocols.protocol_ctfEstimation_automatic.ProtImodAutomaticCtfEstimation method) (imod.protocols.protocol_doseFilter.ProtImodDoseFilter method) (imod.protocols.protocol_excludeViews.ProtImodExcludeViews method) (imod.protocols.protocol_importSetOfCTFTomoSeries.ProtImodImportSetOfCtfTomoSeries method) (imod.protocols.protocol_tomoNormalization.ProtImodTomoNormalization method) (imod.protocols.protocol_tomoProjection.ProtImodTomoProjection method) (imod.protocols.protocol_tomoReconstruction.ProtImodTomoReconstruction method) (imod.protocols.protocol_tsNormalization.ProtImodTSNormalization method) (imod.protocols.protocol_xCorrPrealignment.ProtImodXcorrPrealignment method) (novactf.protocols.protocol_tomoReconstruction.ProtNovaCtfTomoReconstruction method) (xmipptomo.protocols.protocol_rotate_astigmatism.XmippProtRotateAstigmatism method) closeOutputSetStep() (imod.protocols.protocol_goldBeadPicker3d.ProtImodGoldBeadPicker3d method) closeOutputStep() (imod.protocols.protocol_goldBeadEraser.ProtImodGoldBeadEraser method) (imod.protocols.protocol_xRaysEraser.ProtImodXraysEraser method) closeSetsStep() (dynamo.protocols.protocol_subtomo_MRA.DynamoSubTomoMRA method) closeStreamStep() (xmipptomo.protocols.protocol_resize_tomograms.XmippProtResizeTomograms method) (xmipptomo.protocols.protocol_resizeTS.XmippProtResizeTiltSeries method) ClusteringWindow (class in continuousflex.viewers.nma_gui.tk_clustering) ClusteringWindowVol (class in continuousflex.viewers.nma_vol_gui.tk_clustering_vol) ClusteringWindowVolHeteroFlow (class in continuousflex.viewers.nma_vol_gui.tk_clustering_vol) 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) codespeed (class in pwperformance.main) CODESPEED_ENV (pwperformance.main.codespeed attribute) CODESPEED_PROJECT (pwperformance.main.codespeed attribute) CODESPEED_REVISION (pwperformance.main.codespeed attribute) CODESPEED_URL (pwperformance.main.codespeed attribute) CodespeedHandler (class in pwperformance.main) COL_ALIGNED (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider attribute) COL_COOR3D (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider attribute) COL_CTF_EST_AST (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider attribute) COL_CTF_EST_DEFOCUS_U (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider attribute) COL_CTF_EST_DEFOCUS_V (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider attribute) COL_CTF_EST_FIT (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider attribute) COL_CTF_EST_PHASE (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider attribute) COL_CTF_EST_RES (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider attribute) COL_CTF_SERIE (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider attribute) COL_INFO (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider attribute) (xmipptomo.viewers.monotomo_tree_provider.MonoTomoTreeProvider attribute) COL_LANDMODEL_NO_GAPS (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider attribute) COL_PREALIGNED (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider attribute) COL_PREPROCESS_RECONST_TOMOGRAM (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider attribute) COL_RECONST_TOMOGRAM (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider attribute) COL_STATUS (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider attribute) COL_TI (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider attribute) COL_TI_ACQ_ORDER (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider attribute) COL_TI_ANGLE (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider attribute) COL_TI_DEFOCUS_U (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider attribute) COL_TI_DOSE (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider attribute) COL_TILT_ANG (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider attribute) COL_TS (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider attribute) (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider attribute) (xmipptomo.viewers.monotomo_tree_provider.MonoTomoTreeProvider attribute) Color (class in pyworkflow.utils.properties) color (emfacilities.protocols.pynvml.c_nvmlLedState_t attribute) COLOR_MODE_AGE (pyworkflow.project.config.ProjectSettings attribute) COLOR_MODE_LABELS (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) colorMapToColorList() (xmipp3.viewers.viewer_resolution_directional.XmippMonoDirViewer static method) ColorScaleDialog (class in pwem.wizards.wizard) ColorScaleWizard (class in xmipp3.wizards) (class in xmipptomo.wizards) ColorScaleWizardBase (class in pwem.wizards.wizard) colorText (class in pyworkflow.utils.properties) Column (class in pyworkflow.utils.dataset) 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) commandDropView (chimera.protocols.protocol_contacts.ChimeraProtContacts attribute) 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.mapper.xmlmapper.XmlMapper 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) compareFirstStep() (tomo.protocols.protocol_consensus_classes_subtomo.ProtConsensusClassesSubtomo method) (xmipp3.protocols.protocol_consensus_classes3D.XmippProtConsensusClasses3D method) compareOthersStep() (tomo.protocols.protocol_consensus_classes_subtomo.ProtConsensusClassesSubtomo method) (xmipp3.protocols.protocol_consensus_classes3D.XmippProtConsensusClasses3D method) compareSets() (pyworkflow.tests.tests.BaseTest class method) compareVolumeStep() (xmipp3.protocols.protocol_multiple_fscs.XmippProtMultipleFSCs method) completeInfoFromList() (tomo.objects.CTFTomo method) completeLandmarkModel() (tomo.objects.SetOfLandmarkModels method) composePSD() (pwem.protocols.protocol_align_movies.ProtAlignMovies method) composePSDImages() (pwem.protocols.protocol_align_movies.ProtAlignMovies method) composeTransform() (pwem.objects.data.Transform method) compute_length() (localrec.utils.Vector3 method) compute_matrix() (localrec.utils.Vector3 method) compute_unit_vector() (localrec.utils.Vector3 method) computeAlignmentStep() (imod.protocols.protocol_applyTransformationMatrix.ProtImodApplyTransformationMatrix method) computeAtomShiftsStep() (continuousflex.protocols.protocol_nma.FlexProtNMA method) computeAverage() (pwem.emlib.image.image_handler.ImageHandler method) computeAveragedSubUnit() (atomstructutils.protocols.protocol_average_subunits.ProtAverageSubunits method) computeBfactorStep() (xmipp3.protocols.protocol_resolution3d.XmippProtResolution3D method) computeConnectedComponentsStep() (xmipptomo.protocols.protocol_connected_components.XmippProtConnectedComponents method) computeDefocusStep() (novactf.protocols.protocol_tomoDefocus.ProtNovaCtfTomoDefocus method) computeDistances() (xmipptomo.protocols.protocol_coords_roi.XmippProtCCroi method) computeFiducialAlignmentStep() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) computeInterpolatedStackStep() (imod.protocols.protocol_xCorrPrealignment.ProtImodXcorrPrealignment method) (jjsoft.protocols.protocol_align_ts.ProtJjsoftAlignTs method) (tomoj.protocols.protocol_xCorrPrealignment.ProtTomojXcorrPrealignment method) computeModesStep() (continuousflex.protocols.protocol_nma_base.FlexProtNMABase method) computeNMAStep() (continuousflex.protocols.protocol_nma_choose.FlexrotNMAChoose method) computeNormals() (in module tomo3D.utils) computeNormalStep() (tomo3D.protocols.protocol_mesh_normal.XmippProtFilterbyNormal method) computeOutputInterpolatedStackStep() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) computeOutputModelsStep() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) (imod.protocols.protocol_fiducialModel.ProtImodFiducialModel method) computeOutputStackStep() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) computeParams() (xmipptomo.protocols.protocol_score_coordinates.XmippProtScoreCoordinates method) computePdbModesStep() (continuousflex.protocols.protocol_nma.FlexProtNMA 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) computeReconstructionStep() (imod.protocols.protocol_tomoReconstruction.ProtImodTomoReconstruction method) (novactf.protocols.protocol_tomoReconstruction.ProtNovaCtfTomoReconstruction method) computeSampling() (pwem.convert.headers.Ccp4Header method) computeStats() (relion.objects.CtfRefineMicInfo method) computeThumbnail() (pwem.emlib.image.image_handler.ImageHandler method) (pwem.protocols.protocol_align_movies.ProtAlignMovies method) computeTrainingSet() (xmipp3.protocols.protocol_deep_align.XmippProtDeepAlign method) computeTransformationMatrices() (atomstructutils.protocols.protocol_average_subunits.ProtAverageSubunits method) computeXcorrStep() (imod.protocols.protocol_xCorrPrealignment.ProtImodXcorrPrealignment method) (tomoj.protocols.protocol_xCorrPrealignment.ProtTomojXcorrPrealignment method) Conditional (class in pyworkflow.protocol.params) Config (class in pwem) (class in pyworkflow.config) (class in pyworkflow.gui.gui) 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) configureTags() (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider method) (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) (tomo.viewers.views_tkinter_tree.TomogramsTreeProvider method) (tomo3D.viewers.views_tkinter_tree.Tomo3DTreeProvider method) configureWeights() (pyworkflow.gui.gui.Window method) configureWeigths() (in module pyworkflow.gui.gui) Connect (class in emfacilities.protocols.transport) connect() (pwem.wizards.wizards_3d.callbacks.DraggablePoint method) connectDB() (in module chimera.protocols.protocol_contacts) 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) consensusWorker() (in module tomo3D.protocols.protocol_particle_pick_consensus) (in module xmipp3.protocols.protocol_particle_pick_consensus) constructGroupsStep() (xmipp3.protocols.protocol_solid_angles.XmippProtSolidAngles method) (xmipp3.protocols.protocol_split_volume_hierarchical_cluster.XmippProtSplitVolumeHierarchical method) 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) continueStep() (cistem.protocols.protocol_refine2d.CistemProtRefine2D method) continuousflex (module) continuousflex.bibtex (module) continuousflex.constants (module) continuousflex.protocols (module) continuousflex.protocols.convert (module) continuousflex.protocols.data (module) continuousflex.protocols.pdb (module) continuousflex.protocols.pdb.protocol_convert_pdb (module) continuousflex.protocols.pdb.protocol_pseudoatoms (module) continuousflex.protocols.pdb.protocol_pseudoatoms_base (module) continuousflex.protocols.protocol_apply_volumeset_alignment (module) continuousflex.protocols.protocol_batch_cluster (module) continuousflex.protocols.protocol_batch_cluster_vol (module) continuousflex.protocols.protocol_denoise_volumes (module) continuousflex.protocols.protocol_image_synthesize (module) continuousflex.protocols.protocol_missing_wedge_filling (module) continuousflex.protocols.protocol_nma (module) continuousflex.protocols.protocol_nma_alignment (module) continuousflex.protocols.protocol_nma_alignment_vol (module) continuousflex.protocols.protocol_nma_base (module) continuousflex.protocols.protocol_nma_choose (module) continuousflex.protocols.protocol_nma_dimred (module) continuousflex.protocols.protocol_nma_dimred_vol (module) continuousflex.protocols.protocol_pdb_dimred (module) continuousflex.protocols.protocol_structure_mapping (module) continuousflex.protocols.protocol_subtomogram_averaging (module) continuousflex.protocols.protocol_subtomograms_classify (module) continuousflex.protocols.protocol_subtomogrmas_synthesize (module) continuousflex.protocols.utilities (module) continuousflex.protocols.utilities.bm4d (module) continuousflex.protocols.utilities.dynamo (module) continuousflex.protocols.utilities.mwr (module) continuousflex.protocols.utilities.mwr.utils (module) continuousflex.protocols.utilities.mwr.utils.BM4D_v3p2 (module) continuousflex.protocols.utilities.mwr.utils.freezeColors (module) continuousflex.protocols.utilities.mwr.utils.freezeColors.demo (module) continuousflex.protocols.utilities.mwr.utils.freezeColors.demo.html (module) continuousflex.protocols.utilities.mwr.utils.freezeColors.test (module) continuousflex.protocols.utilities.mwr_wrapper (module) continuousflex.protocols.utilities.spider_files3 (module) continuousflex.protocols.utilities.spider_matlab (module) continuousflex.viewers (module) continuousflex.viewers.nma_gui (module) continuousflex.viewers.nma_gui.matplotlib_point_path (module) continuousflex.viewers.nma_gui.matplotlib_point_selector (module) continuousflex.viewers.nma_gui.tk_clustering (module) continuousflex.viewers.nma_gui.tk_trajectories (module) continuousflex.viewers.nma_plotter (module) continuousflex.viewers.nma_vol_gui (module) continuousflex.viewers.nma_vol_gui.PointPathVol (module) continuousflex.viewers.nma_vol_gui.PointSelectorVol (module) continuousflex.viewers.nma_vol_gui.tk_clustering_vol (module) continuousflex.viewers.nma_vol_gui.tk_trajectories_vol (module) continuousflex.viewers.plotter (module) continuousflex.viewers.plotter_vol (module) continuousflex.viewers.viewer_image_synthesize (module) continuousflex.viewers.viewer_nma (module) continuousflex.viewers.viewer_nma_alignment (module) continuousflex.viewers.viewer_nma_alignment_vol (module) continuousflex.viewers.viewer_nma_dimred (module) continuousflex.viewers.viewer_nma_dimred_vol (module) continuousflex.viewers.viewer_pdb_dimred (module) continuousflex.viewers.viewer_structure_mapping (module) continuousflex.viewers.viewer_subtomograms_classify (module) continuousflex.viewers.viewer_subtomograms_synthesize (module) contours() (tomo3D.viewers.viewer_mrc.MrcPlot method) convert() (pwem.emlib.image.image_handler.ImageHandler method) (pyworkflow.utils.dataset.Column method) (xmipp3.base.XmippSet method) CONVERT_TO_MRC (cistem.protocols.protocol_unblur.CistemProtUnblur attribute) (pwem.protocols.protocol_movies.ProtProcessMovies attribute) (xmipp3.protocols.protocol_movie_average.XmippProtMovieAverage attribute) (xmipp3.protocols.protocol_movie_opticalflow.XmippProtOFAlignment attribute) convertAtomicModel2UnitCellMatrix() (atomstructutils.protocols.protocol_average_subunits.ProtAverageSubunits method) convertAveragesStep() (xmipp3.protocols.protocol_classification_gpuCorr_semi.XmippProtStrGpuCrrSimple method) convertBinaryFiles() (in module cryosparc2.convert.convert) (in module relion.convert.convert_utils) convertBinaryVol() (in module cryosparc2.convert.convert) (in module locscale.convert) (in module relion.convert.convert_utils) convertCs2Star() (in module cryosparc2.convert.convert) convertCTFXmippStep() (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippProtFilterParticles method) convertEndian() (in module spider.convert) convertFiducialTextStep() (jjsoft.protocols.protocol_motion_compensation.ProtJjsoftAlignReconstructTomogram method) convertImage() (in module eman2.convert.convert) (in module emantomo.convert.convert) convertImagesStep() (eman2.protocols.protocol_ctf.EmanProtCTFAuto method) (eman2.protocols.protocol_reconstruct.EmanProtReconstruct method) (eman2.protocols.protocol_refine2d.EmanProtRefine2D method) (eman2.protocols.protocol_refineasy.EmanProtRefine method) (eman2.protocols.protocol_tiltvalidate.EmanProtTiltValidate method) (emantomo.protocols.protocol_tomo_initialmodel.EmanProtTomoInitialModel method) convertInput() (spider.protocols.protocol_base.SpiderProtocol method) (xmipptomo.protocols.protocol_subtomo_map_back.XmippProtSubtomoMapBack method) convertInputAndSaveToDBStep() (ccp4.protocols.protocol_coot.CootRefine method) convertInputs() (xmipp3.protocols.protocol_mltomo.XmippProtMLTomo method) convertInputStep() (bsoft.protocols.protocol_bfilter.BsoftProtBfilter method) (bsoft.protocols.protocol_blocres.BsoftProtBlocres method) (ccp4.protocols.protocol_refmac.CCP4ProtRunRefmac method) (cistem.protocols.protocol_picking.CistemProtFindParticles method) (cistem.protocols.protocol_refine2d.CistemProtRefine2D method) (continuousflex.protocols.protocol_apply_volumeset_alignment.FlexProtApplyVolSetAlignment method) (continuousflex.protocols.protocol_batch_cluster.FlexBatchProtNMACluster method) (continuousflex.protocols.protocol_batch_cluster_vol.FlexBatchProtNMAClusterVol method) (continuousflex.protocols.protocol_denoise_volumes.FlexProtVolumeDenoise method) (continuousflex.protocols.protocol_missing_wedge_filling.FlexProtMissingWedgeRestoration method) (continuousflex.protocols.protocol_nma_alignment.FlexProtAlignmentNMA method) (continuousflex.protocols.protocol_nma_alignment_vol.FlexProtAlignmentNMAVol method) (continuousflex.protocols.protocol_nma_dimred.FlexProtDimredNMA method) (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) (continuousflex.protocols.protocol_subtomogram_averaging.FlexProtSubtomogramAveraging method) (cryoef.protocols.protocol_cryoef.ProtCryoEF method) (cryosparc2.protocols.protocol_base.ProtCryosparcBase method) (dynamo.protocols.protocol_subtomo_MRA.DynamoSubTomoMRA method) (eman2.protocols.protocol_autopick_boxer.EmanProtAutopick method) (emantomo.protocols.protocol_tomo_boxing_convnet.EmanProtTomoConvNet method) (emantomo.protocols.protocol_tomo_subtomogram_refinement.EmanProtTomoRefinement method) (fsc3d.protocols.protocol_3dfsc.Prot3DFSC method) (gautomatch.protocols.protocol_gautomatch.ProtGautomatch method) (gctf.protocols.protocol_gctf_refine.ProtGctfRefine method) (imod.protocols.protocol_base.ProtImodBase method) (imod.protocols.protocol_etomo.ProtImodEtomo method) (imod.protocols.protocol_goldBeadEraser.ProtImodGoldBeadEraser method) (jjsoft.protocols.protocol_align_ts.ProtJjsoftAlignTs method) (jjsoft.protocols.protocol_motion_compensation.ProtJjsoftAlignReconstructTomogram method) (jjsoft.protocols.protocol_reconstruct_tomogram.ProtJjsoftReconstructTomogram method) (localrec.protocols.protocol_localized_stitch.ProtLocalizedStich method) (novactf.protocols.protocol_tomoDefocus.ProtNovaCtfTomoDefocus method) (novactf.protocols.protocol_tomoReconstruction.ProtNovaCtfTomoReconstruction method) (phenix.protocols.protocol_dock_in_map.PhenixProtRunDockInMap method) (phenix.protocols.protocol_emringer.PhenixProtRunEMRinger method) (phenix.protocols.protocol_refinement_base.PhenixProtRunRefinementBase method) (pwem.protocols.protocol_movies.ProtProcessMovies method) (pyseg.protocols.protocol_2d_classification.ProtPySegPlaneAlignClassification method) (pyseg.protocols.protocol_post_rec_particles.ProtPySegPostRecParticles method) (relion.protocols.protocol_autopick_ref.ProtRelion2Autopick method) (relion.protocols.protocol_base.ProtRelionBase method) (relion.protocols.protocol_bayesian_polishing.ProtRelionBayesianPolishing method) (relion.protocols.protocol_compress_estimate_gain.ProtRelionCompressEstimateGain method) (relion.protocols.protocol_create_mask3d.ProtRelionCreateMask3D method) (relion.protocols.protocol_crop_resize.ProtRelionResizeVolume method) (relion.protocols.protocol_ctf_refinement.ProtRelionCtfRefinement method) (relion.protocols.protocol_expand_symmetry.ProtRelionExpandSymmetry method) (relion.protocols.protocol_extract_particles.ProtRelionExtractParticles method) (relion.protocols.protocol_localres.ProtRelionLocalRes method) (relion.protocols.protocol_multibody.ProtRelionMultiBody method) (relion.protocols.protocol_postprocess.ProtRelionPostprocess method) (relion.protocols.protocol_reconstruct.ProtRelionReconstruct method) (relion.protocols.protocol_remove_views.ProtRelionRemovePrefViews method) (relion.protocols.protocol_subtract.ProtRelionSubtract method) (reliontomo.protocols.protocol_base_tomo.ProtRelionBaseTomo method) (reliontomo.protocols.protocol_reconstruct_subtomo.ProtRelionSubTomoReconstruct method) (resmap.protocols.protocol_resmap.ProtResMap method) (sidesplitter.protocols.protocol_sidesplitter.ProtSideSplitter method) (sphire.protocols.protocol_cryolo_training.SphireProtCRYOLOTraining method) (spider.protocols.protocol_custommask.SpiderProtCustomMask method) (spider.protocols.protocol_projmatch.SpiderProtRefinement method) (spider.protocols.protocol_reconstruct.SpiderProtReconstruct method) (tomo.protocols.protocol_ts_base.ProtTsProcess method) (tomo.protocols.protocol_ts_correct_motion.ProtTsCorrectMotion method) (tomoj.protocols.protocol_xCorrPrealignment.ProtTomojXcorrPrealignment method) (topaz.protocols.protocol_topaz_training.TopazProtTraining method) (xmipp2.protocols.protocol_mltomo.Xmipp2ProtMLTomo 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_compare_angles.XmippProtCompareAngles method) (xmipp3.protocols.protocol_ctf_correct_wiener2d.XmippProtCTFCorrectWiener2D method) (xmipp3.protocols.protocol_ctf_defocus_group.XmippProtCTFDefocusGroup method) (xmipp3.protocols.protocol_kerdensom.KendersomBaseClassify method) (xmipp3.protocols.protocol_metaprotocol_discrete_heterogeneity_scheduler.XmippMetaProtDiscreteHeterogeneityScheduler method) (xmipp3.protocols.protocol_metaprotocol_golden_highres.XmippMetaProtGoldenHighRes method) (xmipp3.protocols.protocol_ml2d.XmippProtML2D method) (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) (xmipp3.protocols.protocol_particle_boxsize.XmippProtParticleBoxsize 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_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_heterogeneous.XmippProtReconstructHeterogeneous 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_solid_angles.XmippProtSolidAngles method) (xmipp3.protocols.protocol_split_volume.XmippProtSplitvolume method) (xmipp3.protocols.protocol_split_volume_hierarchical_cluster.XmippProtSplitVolumeHierarchical method) (xmipp3.protocols.protocol_validate_fscq.XmippProtValFit method) (xmipp3.protocols.protocol_validate_nontilt.XmippProtValidateNonTilt method) (xmipp3.protocols.protocol_volume_local_sharpening.XmippProtLocSharp method) (xmipptomo.protocols.protocol_apply_alignment_subtomo.XmippProtApplyTransformSubtomo method) (xmipptomo.protocols.protocol_resolution_local_monotomo.XmippProtMonoTomo method) convertInputToXmipp() (xmipp3.base.XmippProtocol method) convertInputVolume() (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) convertMask() (in module relion.convert.convert_utils) (in module sidesplitter.convert) convertMaskStep() (spider.protocols.protocol_ca_pca.SpiderProtCAPCA method) convertMicrographs() (in module sphire.convert) (in module topaz.convert) convertModelToCoordinatesStep() (imod.protocols.protocol_goldBeadPicker3d.ProtImodGoldBeadPicker3d method) convertPdbStep() (continuousflex.protocols.pdb.protocol_convert_pdb.FlexProtConvertPdb method) (xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb method) (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolSubtraction method) convertPixToLength() (in module pwem.utils) convertReferences() (gautomatch.protocols.protocol_gautomatch.ProtGautomatch method) (in module eman2.convert.convert) (in module emantomo.convert.convert) convertSetStep() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) convertStack() (pwem.emlib.image.image_handler.ImageHandler method) convertStep() (locscale.protocols.protocol_locscale.ProtLocScale method) (xmipp3.protocols.protocol_align_volume_and_particles.XmippProtAlignVolumeParticles method) (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) (xmipp3.protocols.protocol_deep_align.XmippProtDeepAlign method) (xmipp3.protocols.protocol_generate_reprojections.XmippProtGenerateReprojections method) (xmipp3.protocols.protocol_local_ctf.XmippProtLocalCTF method) (xmipp3.protocols.protocol_shift_particles.XmippProtShiftParticles method)

convertToMrc() (in module xmipp3.convert.convert) convertToPseudoAtomsStep() (continuousflex.protocols.pdb.protocol_pseudoatoms_base.FlexProtConvertToPseudoAtomsBase method) (continuousflex.protocols.protocol_nma_choose.FlexrotNMAChoose method) convertUnitCell2AtomicModelMatrix() (atomstructutils.protocols.protocol_average_subunits.ProtAverageSubunits method) convertXmdToStackStep() (xmipp3.protocols.protocol_movie_split_frames.XmippProtSplitFrames method) (xmipptomo.protocols.protocol_splitTS.XmippProtSplitTiltSeries method) COORD_LABELS (relion.convert.convert31.Reader attribute) CoordBoxReader (class in sphire.convert) CoordBoxWriter (class in sphire.convert) Coordinate (class in pwem.objects.data) Coordinate3D (class in tomo.objects) Coordinate3DWithScore (class in deepfinder.objects) COORDINATEFILENAME (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases attribute) CoordinatesObjectView (class in pwem.viewers.views) CoordinatesTiltPair (class in pwem.objects.data_tiltpairs) CoordinatesWriter (class in gctf.convert.convert) coordinateSystemTransform() (pwem.convert.symmetry.Icosahedron method) coordinateToRow() (in module cryosparc2.convert.convert) (in module relion.convert.convert_deprecated) (in module xmipp3.convert.convert) coords() (pyworkflow.gui.tooltip.ToolTip method) CoordStarWriter (class in gautomatch.convert) COOT (ccp4.protocols.protocol_coot.CootRefine attribute) (phenix.viewers.viewer_refinement_base.PhenixProtRefinementBaseViewer attribute) COOTINI (ccp4.protocols.protocol_coot.CootRefine attribute) CootRefine (class in ccp4.protocols.protocol_coot) CootRefineViewer (class in ccp4.viewers.viewer_coot) copy() (pyworkflow.object.Object method) (pyworkflow.protocol.protocol.Protocol method) copy_deformations() (continuousflex.protocols.protocol_image_synthesize.FlexProtSynthesizeImages method) (continuousflex.protocols.protocol_subtomogrmas_synthesize.FlexProtSynthesizeSubtomo 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) copyDeformationsStep() (continuousflex.protocols.protocol_nma_alignment.FlexProtAlignmentNMA method) (continuousflex.protocols.protocol_nma_alignment_vol.FlexProtAlignmentNMAVol method) copyFile() (in module pyworkflow.utils.path) copyFiles() (in module cryosparc2.utils) copyFromRow() (pwem.emlib.metadata.utils.Row method) copyInfo() (pwem.objects.data.Acquisition method) (pwem.objects.data.CTFModel method) (pwem.objects.data.Class2D method) (pwem.objects.data.Class3D method) (pwem.objects.data.Coordinate 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) (tomo.objects.CTFTomo method) (tomo.objects.ClassSubTomogram method) (tomo.objects.Coordinate3D method) (tomo.objects.SetOfCTFTomoSeries method) (tomo.objects.SetOfCoordinates3D method) (tomo.objects.SetOfSubTomograms method) (tomo.objects.SetOfTiltSeriesBase method) (tomo.objects.SetOfTiltSeriesM method) (tomo.objects.TiltImage method) (tomo.objects.TiltImageBase method) (tomo.objects.TiltImageM method) (tomo.objects.TiltSeriesBase method) (tomo.objects.Tomogram method) copyInput() (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery method) (xmipp3.protocols.protocol_helical_parameters.XmippProtHelicalParameters method) (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry method) copyInputCoords() (emantomo.protocols.protocol_tomo_boxing.EmanProtTomoBoxing method) copyInputFilesStep() (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) copyInputMeshes() (dynamo.protocols.protocol_boxing.DynamoBoxing method) copyinputPdb() (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) copyItems() (pwem.objects.data.EMSet method) (tomo.objects.SetOfTiltSeriesBase method) copyLocation() (pwem.objects.data.Image method) copyMaskFileStep() (xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMask method) copyObjId() (pyworkflow.object.Object method) copyOrLink() (tomo.protocols.protocol_ts_import.ProtImportTsBase method) copyOrLinkFileName() (in module relion.convert.convert_deprecated) copyPattern() (in module pyworkflow.utils.path) copyPdbStep() (continuousflex.protocols.protocol_nma.FlexProtNMA method) copyProtocol() (pyworkflow.project.project.Project method) copyStackAndResize() (xmipp3.protocols.protocol_deep_denoising.XmippProtDeepDenoising 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) correlationCudaStep() (xmipp3.protocols.protocol_deep_align.XmippProtDeepAlign method) correlationSignificantStep() (xmipp3.protocols.protocol_deep_align.XmippProtDeepAlign method) count (emfacilities.protocols.pynvml.c_nvmlUnitFanSpeeds_t attribute) count() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) countChilds() (pyworkflow.utils.graph.Node method) countSockets() (pyworkflow.gui.canvas.Item method) cpuTime (pyworkflow.protocol.protocol.Protocol attribute) create() (pwem.objects.data.EMSet class method) (pwem.objects.data.Transform class method) (pyworkflow.project.project.Project method) (relion.convert.convert31.OpticsGroups static method) (xmipp3.programs.ProgramDb method) create_contents() (pyworkflow.gui.tooltip.ToolTip method) create_phantom() (continuousflex.protocols.protocol_subtomogrmas_synthesize.FlexProtSynthesizeSubtomo method) create_subparticles() (in module localrec.utils) 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) createBgImage() (in module pyworkflow.gui.matplotlib_image) createBoolWidget() (pyworkflow.gui.form.ParamWidget static method) createBsoftInputParticles() (in module bsoft.convert) createCable() (pyworkflow.gui.canvas.Canvas method) createCanvas() (pyworkflow.gui.plotter.Plotter method) createChimeraOutput() (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes method) createChimeraScript() (continuousflex.protocols.pdb.protocol_pseudoatoms_base.FlexProtConvertToPseudoAtomsBase method) (pwem.viewers.viewer_localres.LocalResolutionViewer method) (xmipp3.protocols.protocol_volume_consensus.XmippProtVolConsensus method) (xmipp3.protocols.protocol_volume_strain.XmippProtVolumeStrain method) createChimeraScriptDoA() (xmipp3.viewers.viewer_resolution_directional.XmippMonoDirViewer 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) createCommandStep() (emantomo.protocols.protocol_align_ts.EmanProtAlignTs method) (emantomo.protocols.protocol_tomo_fill_mw.EmanProtTomoFillMW method) (emantomo.protocols.protocol_tomo_reconstruction.EmanProtTomoReconstruction method) createConf() (in module scipion.scripts.config) createConfigStep() (sphire.protocols.protocol_cryolo_picking.SphireProtCRYOLOPicking method) (sphire.protocols.protocol_cryolo_training.SphireProtCRYOLOTraining method) 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) createCtfMonitor() (emfacilities.protocols.protocol_monitor_summary.ProtMonitorSummary method) createCtfPlot() (in module cistem.viewers) (in module gctf.viewers) createDataDictStep() (ccp4.protocols.protocol_refmac.CCP4ProtRunRefmac method) createDataView() (relion.viewers.viewer_base.RelionViewer method) (xmipp3.viewers.viewer_mltomo.XmippMLTomoViewer method) (xmipp3.viewers.viewer_projmatch.XmippProjMatchViewer method) createDebugOutput() (gautomatch.protocols.protocol_gautomatch.ProtGautomatch method) createDefocusGroups() (relion.protocols.protocol_base.ProtRelionBase method) createDirectoryStep() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) createDiscardedStep() (xmipp3.protocols.protocol_particle_pick.XmippProtParticlePicking method) createDistanceProfilePlot() (in module continuousflex.viewers.viewer_nma) createEdge() (pyworkflow.gui.canvas.Canvas method) createEllipsoid() (xmipp3.protocols.protocol_resolution_directional.XmippProtMonoDir method) createEmailNotifier() (emfacilities.protocols.protocol_monitor.ProtMonitor method) createEmanProcess() (eman2.Plugin class method) (emantomo.Plugin class method) createEmptyImage() (pwem.emlib.image.image_handler.ImageHandler class method) createEmptyPoint() (continuousflex.protocols.data.PathData method) (xmipp3.utils.PathData method) createEmptyProject() (in module cryosparc2.utils) createEmptyWorkSpace() (in module cryosparc2.utils) createExtraLabels() (relion.convert.convert_base.ReaderBase method) createFailedMoviesSqlite() (cistem.viewers.ProtUnblurViewer method) (motioncorr.viewers.ProtMotioncorrViewer method) (relion.viewers.viewer_motioncor.RelionMotioncorrViewer 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) createFSC() (cryosparc2.protocols.protocol_base.ProtCryosparcBase method) createFSCObject() (pwem.viewers.viewer_fsc.FscViewer method) createGallery() (xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery method) createGlobalAlignmentPlot() (in module cistem.protocols.protocol_unblur) (in module motioncorr.protocols.protocol_motioncorr) (in module relion.protocols.protocol_motioncor) createGlobalInfo() (relion.protocols.protocol_ctf_refinement.ProtRelionCtfRefinement method) createGlobalInfoStep() (relion.protocols.protocol_ctf_refinement.ProtRelionCtfRefinement 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) (xmipptomo.protocols.protocol_resolution_local_monotomo.XmippProtMonoTomo method) createHistrogramStep() (xmipp3.protocols.protocol_resolution_directional.XmippProtMonoDir method) createHtmlReport() (emfacilities.protocols.protocol_monitor_summary.ProtMonitorSummary method) createImage() (pwem.emlib.image.image_handler.ImageHandler method) createInitialModelStep() (eman2.protocols.protocol_initialmodel.EmanProtInitModel method) (eman2.protocols.protocol_initialmodel_sgd.EmanProtInitModelSGD method) (emantomo.protocols.protocol_tomo_initialmodel.EmanProtTomoInitialModel method) createInputMd() (xmipp3.protocols.protocol_mltomo.XmippProtMLTomo method) createItemMatrix() (in module cryosparc2.convert.convert) (in module spider.convert) (in module xmipp3.convert.convert) createIterDirsStep() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) createLink() (in module pyworkflow.utils.path) createLinksStep() (eman2.protocols.protocol_refine2d_bispec.EmanProtRefine2DBispec method) createLinkSteps() (eman2.protocols.protocol_refine2d.EmanProtRefine2D method) (eman2.protocols.protocol_refineasy.EmanProtRefine method) createMainMenu() (pyworkflow.gui.gui.Window method) createMANIFEST() (in module pyworkflow.apps.pw_sync_data) createMapMtzRefmacStep() (ccp4.protocols.protocol_refmac.CCP4ProtRunRefmac method) 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) createMaskLogFileName (ccp4.protocols.protocol_refmac.CCP4ProtRunRefmac attribute) createMaskStep() (pwem.protocols.protocol_batch.ProtCreateMask method) (relion.protocols.protocol_create_mask3d.ProtRelionCreateMask3D method) (spider.protocols.protocol_custommask.SpiderProtCustomMask method) (xmipp3.protocols.protocol_volume_local_sharpening.XmippProtLocSharp method) createMessageBody() (in module pyworkflow.gui.dialog) createMetadataImageStep() (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) createMonitor() (emfacilities.protocols.protocol_monitor_ctf.ProtMonitorCTF method) (emfacilities.protocols.protocol_monitor_movie_gain.ProtMonitorMovieGain method) (emfacilities.protocols.protocol_monitor_system.ProtMonitorSystem method) createMovieGainMonitor() (emfacilities.protocols.protocol_monitor_summary.ProtMonitorSummary method) createNewProject() (pyworkflow.gui.project.viewprojects.ProjectsView method) createNode() (pyworkflow.utils.graph.Graph method) createObject() (emxlib.utils.EmxXmlMapper method) createOutput() (atomstructutils.protocols.protocol_average_subunits.ProtAverageSubunits method) (ccp4.protocols.protocol_coot.CootRefine method) (chimera.protocols.protocol_base.ChimeraProtBase method) (chimera.protocols.protocol_subtraction_maps.ChimeraSubtractionMaps method) (continuousflex.protocols.pdb.protocol_convert_pdb.FlexProtConvertPdb method) (imod.protocols.protocol_ctfEstimation_manual.ProtImodManualCtfEstimation method) (imod.protocols.protocol_etomo.ProtImodEtomo method) (pwem.protocols.protocol_set_editor.ProtSetEditor method) (pwem.protocols.protocol_set_filter.ProtSetFilter method) (tomo.protocols.protocol_import_subtomograms.ProtImportSubTomograms method) (xmipp2.protocols.protocol_mltomo.Xmipp2ProtMLTomo 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_mltomo.XmippProtMLTomo method) (xmipp3.protocols.protocol_reconstruct_heterogeneous.XmippProtReconstructHeterogeneous method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) (xmipp3.protocols.protocol_reconstruct_swarm.XmippProtReconstructSwarm method) (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry method) (xmipp3.protocols.protocol_split_volume.XmippProtSplitvolume method) (xmipptomo.protocols.protocol_cltomo.XmippProtCLTomo method) (xmipptomo.protocols.protocol_subtomo_map_back.XmippProtSubtomoMapBack method) createOutputClasses() (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyClasses method) createOutputFailedSet() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) (imod.protocols.protocol_fiducialModel.ProtImodFiducialModel method) createOutputMetadataStep() (xmipp3.protocols.protocol_deep_align.XmippProtDeepAlign method) createOutputPath() (xmipptomo.protocols.protocol_resolution_local_monotomo.XmippProtMonoTomo 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) createOutputStep() (appion.protocols.protocol_dogpicker.DogPickerProtPicking method) (atomstructutils.protocols.protocol_convertsymmetry.ProtAtomStrucConvertSymmetry method) (atomstructutils.protocols.protocol_operate.ProtAtomStrucOperate method) (bamfordlab.protocols.protocol_ethan_picking.ProtEthanPicker method) (bsoft.protocols.protocol_bfilter.BsoftProtBfilter method) (bsoft.protocols.protocol_blocres.BsoftProtBlocres method) (cistem.protocols.protocol_picking.CistemProtFindParticles method) (cistem.protocols.protocol_refine2d.CistemProtRefine2D method) (continuousflex.protocols.pdb.protocol_pseudoatoms.FlexProtConvertToPseudoAtoms method) (continuousflex.protocols.protocol_apply_volumeset_alignment.FlexProtApplyVolSetAlignment method) (continuousflex.protocols.protocol_batch_cluster.FlexBatchProtNMACluster method) (continuousflex.protocols.protocol_batch_cluster_vol.FlexBatchProtNMAClusterVol method) (continuousflex.protocols.protocol_denoise_volumes.FlexProtVolumeDenoise method) (continuousflex.protocols.protocol_image_synthesize.FlexProtSynthesizeImages method) (continuousflex.protocols.protocol_nma.FlexProtNMA method) (continuousflex.protocols.protocol_nma_alignment.FlexProtAlignmentNMA method) (continuousflex.protocols.protocol_nma_alignment_vol.FlexProtAlignmentNMAVol method) (continuousflex.protocols.protocol_nma_dimred.FlexProtDimredNMA method) (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) (continuousflex.protocols.protocol_pdb_dimred.FlexProtDimredPdb method) (continuousflex.protocols.protocol_subtomogram_averaging.FlexProtSubtomogramAveraging method) (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify method) (continuousflex.protocols.protocol_subtomogrmas_synthesize.FlexProtSynthesizeSubtomo method) (cryocare.protocols.protocol_load_model.ProtCryoCARELoadModel method) (cryocare.protocols.protocol_predict.ProtCryoCAREPrediction method) (cryocare.protocols.protocol_prepare_training_data.ProtCryoCAREPrepareTrainingData method) (cryocare.protocols.protocol_training.ProtCryoCARETraining method) (cryoef.protocols.protocol_cryoef.ProtCryoEF method) (cryosparc2.protocols.protocol_cryorefine.ProtCryoSparcRefine3D method) (cryosparc2.protocols.protocol_cryosparc2d.ProtCryo2D method) (cryosparc2.protocols.protocol_cryosparc_3D_classification.ProtCryoSparc3DClassification method) (cryosparc2.protocols.protocol_cryosparc_ab.ProtCryoSparcInitialModel method) (cryosparc2.protocols.protocol_cryosparc_global_ctf_refinement.ProtCryoSparcGlobalCtfRefinement method) (cryosparc2.protocols.protocol_cryosparc_homogeneous_refine.ProtCryoSparc3DHomogeneousRefine method) (cryosparc2.protocols.protocol_cryosparc_local_ctf_refinement.ProtCryoSparcLocalCtfRefinement method) (cryosparc2.protocols.protocol_cryosparc_naive_local_refine.ProtCryoSparcNaiveLocalRefine method) (cryosparc2.protocols.protocol_cryosparc_new_local_refine.ProtCryoSparcLocalRefine method) (cryosparc2.protocols.protocol_cryosparc_part_subtract.ProtCryoSparcSubtract method) (cryosparc2.protocols.protocol_cryosparc_sharppening.ProtCryoSparcSharppening method) (cryosparc2.protocols.protocol_cryosparc_symmetry_expansion.ProtCryoSparcSymmetryExpansion method) (deepfinder.protocols.protocol_cluster.DeepFinderCluster method) (deepfinder.protocols.protocol_load_training_model.ProtDeepFinderLoadTrainingModel method) (deepfinder.protocols.protocol_segment.DeepFinderSegment method) (deepfinder.protocols.protocol_target_generation.DeepFinderGenerateTrainingTargetsSpheres method) (deepfinder.protocols.protocol_train.DeepFinderTrain method) (dynamo.protocols.protocol_bin_tomograms.DynamoBinTomograms method) (dynamo.protocols.protocol_extraction.DynamoExtraction method) (dynamo.protocols.protocol_import_subtomos.DynamoImportSubtomos method) (dynamo.protocols.protocol_model_workflow.DynamoModelWorkflow method) (dynamo.protocols.protocol_subBoxing.DynamoSubBoxing method) (dynamo.protocols.protocol_subtomo_MRA.DynamoSubTomoMRA method) (eman2.protocols.protocol_autopick_boxer.EmanProtAutopick method) (eman2.protocols.protocol_ctf.EmanProtCTFAuto method) (eman2.protocols.protocol_initialmodel.EmanProtInitModel method) (eman2.protocols.protocol_initialmodel_sgd.EmanProtInitModelSGD method) (eman2.protocols.protocol_reconstruct.EmanProtReconstruct method) (eman2.protocols.protocol_refine2d.EmanProtRefine2D method) (eman2.protocols.protocol_refine2d_bispec.EmanProtRefine2DBispec method) (eman2.protocols.protocol_refineasy.EmanProtRefine method) (eman2.protocols.protocol_tiltvalidate.EmanProtTiltValidate method) (emantomo.protocols.protocol_align_ts.EmanProtAlignTs method) (emantomo.protocols.protocol_tomo_fill_mw.EmanProtTomoFillMW method) (emantomo.protocols.protocol_tomo_initialmodel.EmanProtTomoInitialModel method) (emantomo.protocols.protocol_tomo_reconstruction.EmanProtTomoReconstruction method) (emantomo.protocols.protocol_tomo_subtomogram_refinement.EmanProtTomoRefinement method) (emantomo.protocols.protocol_tomo_template_match.EmanProtTomoTempMatch method) (fsc3d.protocols.protocol_3dfsc.Prot3DFSC method) (gautomatch.protocols.protocol_gautomatch.ProtGautomatch method) (gctf.protocols.protocol_gctf_refine.ProtGctfRefine method) (imod.protocols.protocol_ctfCorrection.ProtImodCtfCorrection method) (imod.protocols.protocol_ctfEstimation_automatic.ProtImodAutomaticCtfEstimation method) (imod.protocols.protocol_doseFilter.ProtImodDoseFilter method) (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) (imod.protocols.protocol_fiducialModel.ProtImodFiducialModel method) (imod.protocols.protocol_goldBeadEraser.ProtImodGoldBeadEraser method) (imod.protocols.protocol_goldBeadPicker3d.ProtImodGoldBeadPicker3d method) (imod.protocols.protocol_tomoReconstruction.ProtImodTomoReconstruction method) (imod.protocols.protocol_xRaysEraser.ProtImodXraysEraser method) (jjsoft.protocols.protocol_align_ts.ProtJjsoftAlignTs method) (jjsoft.protocols.protocol_denoise_tomogram.ProtJjsoftProtDenoiseTomogram method) (jjsoft.protocols.protocol_motion_compensation.ProtJjsoftAlignReconstructTomogram method) (jjsoft.protocols.protocol_reconstruct_tomogram.ProtJjsoftReconstructTomogram method) (localrec.protocols.protocol_filter_subparticles.ProtFilterSubParts method) (localrec.protocols.protocol_localized.ProtLocalizedRecons method) (localrec.protocols.protocol_localized_extraction.ProtLocalizedExtraction method) (localrec.protocols.protocol_localized_stitch.ProtLocalizedStich method) (localrec.protocols.protocol_localized_subset.ProtParticleSubset method) (locscale.protocols.protocol_locscale.ProtLocScale method) (novactf.protocols.protocol_tomoReconstruction.ProtNovaCtfTomoReconstruction method) (phenix.protocols.protocol_dock_in_map.PhenixProtRunDockInMap method) (phenix.protocols.protocol_emringer.PhenixProtRunEMRinger method) (phenix.protocols.protocol_molprobity.PhenixProtRunMolprobity method) (phenix.protocols.protocol_real_space_refine.PhenixProtRunRSRefine method) (phenix.protocols.protocol_search_fit.PhenixProtSearchFit method) (phenix.protocols.protocol_superpose_pdbs.PhenixProtRunSuperposePDBs method) (phenix.protocols.protocol_validation_cryoem.PhenixProtRunValidationCryoEM method) (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_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.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) (pyseg.protocols.protocol_2d_classification.ProtPySegPlaneAlignClassification method) (pyseg.protocols.protocol_picking.ProtPySegPicking method) (pyseg.protocols.protocol_post_rec_particles.ProtPySegPostRecParticles method) (pyseg.protocols.protocol_pre_seg.ProtPySegPreSegParticles method) (relion.protocols.protocol_assign_optic_groups.ProtRelionAssignOpticsGroup method) (relion.protocols.protocol_autopick_ref.ProtRelion2Autopick method) (relion.protocols.protocol_base.ProtRelionBase method) (relion.protocols.protocol_bayesian_polishing.ProtRelionBayesianPolishing method) (relion.protocols.protocol_center_averages.ProtRelionCenterAverages method) (relion.protocols.protocol_classify2d.ProtRelionClassify2D method) (relion.protocols.protocol_classify3d.ProtRelionClassify3D method) (relion.protocols.protocol_compress_estimate_gain.ProtRelionCompressEstimateGain method) (relion.protocols.protocol_create_mask3d.ProtRelionCreateMask3D method) (relion.protocols.protocol_crop_resize.ProtRelionResizeVolume method) (relion.protocols.protocol_ctf_refinement.ProtRelionCtfRefinement method) (relion.protocols.protocol_expand_symmetry.ProtRelionExpandSymmetry method) (relion.protocols.protocol_extract_particles.ProtRelionExtractParticles method) (relion.protocols.protocol_gentle_clean.ProtRelionCleanJobs method) (relion.protocols.protocol_initialmodel.ProtRelionInitialModel method) (relion.protocols.protocol_motioncor.ProtRelionMotioncor method) (relion.protocols.protocol_multibody.ProtRelionMultiBody method) (relion.protocols.protocol_postprocess.ProtRelionPostprocess method) (relion.protocols.protocol_preprocess.ProtRelionPreprocessParticles method) (relion.protocols.protocol_reconstruct.ProtRelionReconstruct method) (relion.protocols.protocol_refine3d.ProtRelionRefine3D method) (relion.protocols.protocol_remove_views.ProtRelionRemovePrefViews method) (relion.protocols.protocol_subtract.ProtRelionSubtract method) (relion.protocols.protocol_symmetrize_volume.ProtRelionSymmetrizeVolume method) (reliontomo.protocols.protocol_base_tomo.ProtRelionBaseTomo method) (reliontomo.protocols.protocol_classify_3d_tomo.ProtRelionSubtomoClassif3D method) (reliontomo.protocols.protocol_ctf_3d_estimation.ProtRelionEstimateCTF3D method) (reliontomo.protocols.protocol_reconstruct_subtomo.ProtRelionSubTomoReconstruct method) (reliontomo.protocols.protocol_refine_3d_tomo.ProtRelionSubtomoRefine3D method) (resmap.protocols.protocol_resmap.ProtResMap method) (sidesplitter.protocols.protocol_sidesplitter.ProtSideSplitter method) (sphire.protocols.protocol_cryolo_picking.SphireProtCRYOLOPicking method) (sphire.protocols.protocol_cryolo_training.SphireProtCRYOLOTraining method) (sphire.protocols.protocol_janni_denoise.SphireProtJanniDenoising method) (spider.protocols.protocol_align_base.SpiderProtAlign method) (spider.protocols.protocol_ca_pca.SpiderProtCAPCA method) (spider.protocols.protocol_classify_base.SpiderProtClassifyCluster method) (spider.protocols.protocol_classify_kmeans.SpiderProtClassifyKmeans method) (spider.protocols.protocol_custommask.SpiderProtCustomMask method) (spider.protocols.protocol_filters.SpiderProtFilter method) (spider.protocols.protocol_projmatch.SpiderProtRefinement method) (spider.protocols.protocol_reconstruct.SpiderProtReconstruct method) (tomo.protocols.protocol_alignment_assign.ProtAlignmentAssignSubtomo method) (tomo.protocols.protocol_assign_tomo2subtomo.ProtAssignTomo2Subtomo method) (tomo.protocols.protocol_consensus_classes_subtomo.ProtConsensusClassesSubtomo method) (tomo.protocols.protocol_ctf_validate.ProtCTFTomoSeriesValidate method) (tomo.protocols.protocol_extract_coordinates.ProtTomoExtractCoords method) (tomo.protocols.protocol_split_evenodd_subtomos.ProtSplitEvenOddTomoSet method) (tomo.protocols.protocol_ts_base.ProtTsProcess method) (tomo.protocols.protocol_ts_correct_motion.ProtTsCorrectMotion method) (tomo.protocols.protocol_ts_estimate_ctf.ProtTsEstimateCTF method) (tomo3D.protocols.protocol_mesh_normal.XmippProtFilterbyNormal method) (tomo3D.protocols.protocol_particle_pick_consensus.ProtTomoConsensusPicking method) (topaz.protocols.protocol_topaz_training.TopazProtTraining 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_transformation_matrix.XmippProtApplyTransformationMatrix 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_classification_gpuCorr.XmippProtGpuCrrCL2D method) (xmipp3.protocols.protocol_classification_gpuCorr_full.XmippProtStrGpuCrrCL2D method) (xmipp3.protocols.protocol_classification_gpuCorr_semi.XmippProtStrGpuCrrSimple method) (xmipp3.protocols.protocol_classify_kmeans2d.XmippProtKmeansClassif2D method) (xmipp3.protocols.protocol_compare_angles.XmippProtCompareAngles method) (xmipp3.protocols.protocol_compare_reprojections.XmippProtCompareReprojections method) (xmipp3.protocols.protocol_consensus_classes3D.XmippProtConsensusClasses3D method) (xmipp3.protocols.protocol_consensus_local_ctf.XmippProtConsensusLocalCTF 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_align.XmippProtDeepAlign method) (xmipp3.protocols.protocol_deep_denoising.XmippProtDeepDenoising 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_metaprotocol_create_output.XmippMetaProtCreateOutput method) (xmipp3.protocols.protocol_metaprotocol_create_subset.XmippMetaProtCreateSubset method) (xmipp3.protocols.protocol_metaprotocol_discrete_heterogeneity_scheduler.XmippMetaProtDiscreteHeterogeneityScheduler method) (xmipp3.protocols.protocol_metaprotocol_golden_highres.XmippMetaProtGoldenHighRes method) (xmipp3.protocols.protocol_ml2d.XmippProtML2D 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_boxsize.XmippProtParticleBoxsize method) (xmipp3.protocols.protocol_particle_pick.XmippProtParticlePicking method) (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking 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_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_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_rotational_spectra.XmippProtRotSpectra 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_solid_angles.XmippProtSolidAngles method) (xmipp3.protocols.protocol_split_volume_hierarchical_cluster.XmippProtSplitVolumeHierarchical 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_local_sharpening.XmippProtLocSharp method) (xmipptomo.protocols.protocol_align_transform.XmippProtAlignTransform method) (xmipptomo.protocols.protocol_apply_alignment_subtomo.XmippProtApplyTransformSubtomo method) (xmipptomo.protocols.protocol_connected_components.XmippProtConnectedComponents method) (xmipptomo.protocols.protocol_coords_roi.XmippProtCCroi method) (xmipptomo.protocols.protocol_fit_ellipsoid.XmippProtFitEllipsoid method) (xmipptomo.protocols.protocol_phantom_subtomo.XmippProtPhantomSubtomo method) (xmipptomo.protocols.protocol_project_top.XmippProtSubtomoProject method) (xmipptomo.protocols.protocol_resizeTS.XmippProtResizeTiltSeries method) (xmipptomo.protocols.protocol_resolution_local_monotomo.XmippProtMonoTomo method) (xmipptomo.protocols.protocol_score_coordinates.XmippProtScoreCoordinates method) (xmipptomo.protocols.protocol_score_transform.XmippProtScoreTransform method) (xmipptomo.protocols.protocol_splitTS.XmippProtSplitTiltSeries method) (xmipptomo.protocols.protocol_subtraction_subtomo.XmippProtSubtractionSubtomo method) createOutputStep_MCSFILL() (continuousflex.protocols.protocol_missing_wedge_filling.FlexProtMissingWedgeRestoration method) createPackageLink() (scipion.install.funcs.Link method) createParamPhantomFile() (in module xmipp3.convert.convert) createParticles() (relion.protocols.protocol_extract_particles.ProtRelionExtractParticles method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) createParticlesStep() (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData method) createPath() (xmipptomo.viewers.viewer_resolution_local_monotomo.XmippMonoTomoViewer method) createPhantomsStep() (xmipptomo.protocols.protocol_phantom_subtomo.XmippProtPhantomSubtomo method) createPlot2D() (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability method) createPlots() (continuousflex.viewers.nma_gui.matplotlib_point_selector.PointSelector method) (continuousflex.viewers.nma_vol_gui.PointSelectorVol.PointSelectorVol method) (in module xmipp3.viewers.viewer_ml2d) createPreliminarOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) createProgramsAutocomplete() (in module xmipp3.programs) createProgramsDb() (in module xmipp3.programs) createProject() (pyworkflow.project.manager.Manager method) createProjectDir() (in module cryosparc2.utils) 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) createReader() (in module relion.convert) (in module reliontomo.convert) createReferenceStep() (xmipp3.protocols.protocol_write_testP.XmippProtWriteTestP method) createRefineScriptFileStep() (ccp4.protocols.protocol_refmac.CCP4ProtRunRefmac method) createRefmacOutputStep() (ccp4.protocols.protocol_refmac.CCP4ProtRunRefmac method) createRefMd() (xmipp3.protocols.protocol_mltomo.XmippProtMLTomo method) createReport() (pwem.protocols.protocol_pdf_report.ProtPDFReport method) createReportDir() (emfacilities.protocols.protocol_monitor_summary.ProtMonitorSummary 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) createScipionPartView() (cryosparc2.viewers.viewer_partsubtract.CryosPARCViewerPartSubtract method) (cryosparc2.viewers.viewer_refinement.CryosPARCViewer3DRefinement method) (eman2.viewers.viewers.RefineEasyViewer method) (relion.viewers.viewer_base.RelionViewer method) (relion.viewers.viewer_ctfrefine.ProtCtfRefineViewer method) (relion.viewers.viewer_polishing.RelionPolishViewer method) (xmipp3.viewers.viewer_projmatch.XmippProjMatchViewer method) createScipionView() (cryosparc2.viewers.viewer_2Dclassify.CryosPARCViewer2D method) (eman2.viewers.viewers.Refine2DViewer method) (relion.viewers.viewer_base.RelionViewer method) (xmipp3.viewers.viewer_mltomo.XmippMLTomoViewer method) createScriptFile() (in module ccp4.protocols.protocol_coot) createSelectionPlot() (continuousflex.viewers.nma_gui.matplotlib_point_selector.PointSelector method) (continuousflex.viewers.nma_vol_gui.PointSelectorVol.PointSelectorVol method) createSetFromImages() (in module pwem.protocols.protocol_classes_selector) createSetFromRepresentative() (in module pwem.protocols.protocol_classes_selector) createSetObject() (pwem.protocols.protocol_batch.ProtUserSubSet method) createSetStep() (pwem.protocols.protocol_batch.ProtUserSubSet method) createSettings() (pyworkflow.project.project.Project method) createShiftPlot() (in module continuousflex.viewers.viewer_nma) createStackImgsStep() (eman2.protocols.protocol_initialmodel.EmanProtInitModel method) (eman2.protocols.protocol_initialmodel_sgd.EmanProtInitModelSGD method) createStep() (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData method) createSubPlot() (continuousflex.viewers.nma_plotter.FlexNmaPlotter method) (continuousflex.viewers.plotter_vol.FlexNmaVolPlotter method) (pyworkflow.gui.plotter.Plotter method) createSummaryStep() (xmipp3.protocols.protocol_resolution3d.XmippProtResolution3D method) createSystemMonitor() (emfacilities.protocols.protocol_monitor_summary.ProtMonitorSummary method) createTable() (phenix.protocols.protocol_search_fit.PhenixProtSearchFit method) createTables() (pyworkflow.mapper.sqlite.SqliteFlatDb method) (xmipp3.programs.ProgramDb method) createTemplateFile() (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) createVector() (localrec.protocols.protocol_localized_stitch.ProtLocalizedStich method) createViewer() (tomo3D.viewers.views_tkinter_tree.Tomo3DDialog method) createVmdView() (in module continuousflex.viewers.viewer_nma) createVolumesSqlite() (pwem.viewers.viewer_base.EmProtocolViewer method) (xmipp3.viewers.viewer_projmatch.XmippProjMatchViewer method) createWidgets() (pyworkflow.gui.text.TextFileViewer method) createWriter() (in module relion.convert) (in module reliontomo.convert) createWriterTomo() (in module reliontomo.convert) CREATION_COLUMN (pyworkflow.gui.form.ScalarTreeProvider attribute) (pyworkflow.gui.form.SubclassesTreeProvider attribute) CRITERIA_1 (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider attribute) cryocare (module) cryocare.bibtex (module) cryocare.constants (module) cryocare.objects (module) cryocare.protocols (module) cryocare.protocols.protocol_load_model (module) cryocare.protocols.protocol_predict (module) cryocare.protocols.protocol_prepare_training_data (module) cryocare.protocols.protocol_training (module) cryocare.utils (module) cryocare.wizards (module) CryocareModel (class in cryocare.objects) cryoCAREPatchSizeWizard (class in cryocare.wizards) CryocareTrainData (class in cryocare.objects) CryocareUtils (class in cryocare.utils) cryoef (module) cryoef.bibtex (module) cryoef.constants (module) cryoef.convert (module) cryoef.protocols (module) cryoef.protocols.protocol_cryoef (module) cryoef.viewers (module) cryoef.wizards (module) cryoEFMaskDiameterWizard (class in cryoef.wizards) CryoEFViewer (class in cryoef.viewers) CryoloModel (class in sphire.objects) cryoloModelingStep() (sphire.protocols.protocol_cryolo_training.SphireProtCRYOLOTraining method) cryosparc2 (module) cryosparc2.bibtex (module) cryosparc2.constants (module) cryosparc2.convert (module) cryosparc2.convert.convert (module) cryosparc2.protocols (module) cryosparc2.protocols.protocol_base (module) cryosparc2.protocols.protocol_cryorefine (module) cryosparc2.protocols.protocol_cryosparc2d (module) cryosparc2.protocols.protocol_cryosparc_3D_classification (module) cryosparc2.protocols.protocol_cryosparc_ab (module) cryosparc2.protocols.protocol_cryosparc_global_ctf_refinement (module) cryosparc2.protocols.protocol_cryosparc_helical_refinement (module) cryosparc2.protocols.protocol_cryosparc_homogeneous_refine (module) cryosparc2.protocols.protocol_cryosparc_local_ctf_refinement (module) cryosparc2.protocols.protocol_cryosparc_naive_local_refine (module) cryosparc2.protocols.protocol_cryosparc_new_local_refine (module) cryosparc2.protocols.protocol_cryosparc_new_nonuniform_refine (module) cryosparc2.protocols.protocol_cryosparc_nonuniform_refine (module) cryosparc2.protocols.protocol_cryosparc_part_subtract (module) cryosparc2.protocols.protocol_cryosparc_sharppening (module) cryosparc2.protocols.protocol_cryosparc_symmetry_expansion (module) cryosparc2.utils (module) cryosparc2.viewers (module) cryosparc2.viewers.viewer_2Dclassify (module) cryosparc2.viewers.viewer_initialmodel (module) cryosparc2.viewers.viewer_partsubtract (module) cryosparc2.viewers.viewer_refinement (module) cryosparc2.wizards (module) cryosparcExists() (in module cryosparc2.utils) cryosparcToLocation() (in module cryosparc2.convert.convert) cryosparcValidate() (in module cryosparc2.utils) CryosPARCViewer2D (class in cryosparc2.viewers.viewer_2Dclassify) CryosPARCViewer3DRefinement (class in cryosparc2.viewers.viewer_refinement) CryosPARCViewerInitialModel (class in cryosparc2.viewers.viewer_initialmodel) CryosPARCViewerPartSubtract (class in cryosparc2.viewers.viewer_partsubtract) cryosPARCwriteSetOfParticles() (in module cryosparc2.convert.convert) crysolWrapper() (atsas.protocols.protocol_pdb_to_saxs.AtsasProtConvertPdbToSAXS method) CsvCoordinateList (class in topaz.convert) CsvImageList (class in topaz.convert) CsvList (class in pyworkflow.object) CsvMicrographList (class in topaz.convert) ctf2Json() (in module emantomo.convert.convert) CTF_LABELS (relion.convert.convert31.Reader attribute) CTF_STAR_FILE (relion.protocols.protocol_export_ctf.ProtRelionExportCtf attribute) ctfCorrection() (imod.protocols.protocol_ctfCorrection.ProtImodCtfCorrection method) CtfDialog (class in pwem.wizards.wizard) CtfDownsampleDialog (class in pwem.wizards.wizard) ctfEstimation() (imod.protocols.protocol_ctfEstimation_automatic.ProtImodAutomaticCtfEstimation method) CtfEstimationListDialog (class in tomo.viewers.views_tkinter_tree) CtfEstimationTomoViewer (class in tomo.viewers.viewers_data) CtfEstimationTomoViewerCistem (class in cistem.viewers) CtfEstimationTomoViewerGctf (class in gctf.viewers) CTFEstimationTree (class in tomo.viewers.views_tkinter_tree) CtfEstimationTreeProvider (class in tomo.viewers.views_tkinter_tree) CtffindViewer (class in cistem.viewers) CTFModel (class in pwem.objects.data) ctfModelToCtfTomo() (tomo.objects.CTFTomo static method) ctfModelToRow() (in module cryosparc2.convert.convert) (in module relion.convert.convert_deprecated) (in module xmipp3.convert.convert) CtfMonitorPlotter (class in emfacilities.viewers.viewer_monitors) CtfRefineGlobalInfo (class in relion.objects) CtfRefineMicInfo (class in relion.objects) CTFSerieStates (class in tomo.viewers.views_tkinter_tree) CTFTomo (class in tomo.objects) CTFTomoSeries (class in tomo.objects) ctfValidateStep() (tomo.protocols.protocol_ctf_validate.ProtCTFTomoSeriesValidate method) CtfView (class in pwem.viewers.views) CtfViewer (class in eman2.viewers.viewers) CtfWizard (class in pwem.wizards.wizard) CUDA_BIN (pwem.Config attribute) CUDA_LIB (pwem.Config attribute) current (emfacilities.protocols.pynvml.c_nvmlPSUInfo_t attribute) currentTable() (pyworkflow.utils.dataset.DataSet method) customLoggingActive (pyworkflow.utils.log.LoggingConfigurator attribute) CustomMaskDialog (class in spider.wizards) CYAN (pyworkflow.utils.properties.colorText attribute) cyan (pyworkflow.utils.utils.StrColors 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)

D

DARK_GREY_COLOR (pyworkflow.utils.properties.Color attribute) DARKCYAN (pyworkflow.utils.properties.colorText attribute) Data (class in continuousflex.protocols.data) (class in xmipp3.utils) DataSet (class in pyworkflow.tests.tests) (class in pyworkflow.utils.dataset) dataTable (reliontomo.protocols.protocol_base_tomo.ProtRelionBaseTomo attribute) 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_TIMEOUT (xmipp3.programs.ProgramDb attribute) DbTreeProvider (class in pyworkflow.gui.tree) DEBUG (atomstructutils.protocols.protocol_average_subunits.ProtAverageSubunits attribute) debug() (pyworkflow.protocol.protocol.Protocol method) debugOn() (pyworkflow.config.Config static method) debugSQLOn() (pyworkflow.config.Config static method) DEBUGX (atomstructutils.protocols.protocol_average_subunits.ProtAverageSubunits attribute) deCrypt() (in module emfacilities.protocols.report_influx) deepfinder (module) deepfinder.bibtex (module) deepfinder.constants (module) deepfinder.convert (module) deepfinder.objects (module) deepfinder.protocols (module) deepfinder.protocols.protocol_annotation (module) deepfinder.protocols.protocol_base (module) deepfinder.protocols.protocol_cluster (module) deepfinder.protocols.protocol_import_coordinates (module) deepfinder.protocols.protocol_load_training_model (module) deepfinder.protocols.protocol_segment (module) deepfinder.protocols.protocol_target_generation (module) deepfinder.protocols.protocol_train (module) deepfinder.protocols.protocol_utilities (module) deepfinder.viewers (module) deepfinder.viewers.particle_annotator_tomo_viewer (module) deepfinder.viewers.particle_annotator_tree (module) deepfinder.viewers.viewer_deepfinder (module) DeepFinderAnnotations (class in deepfinder.protocols.protocol_annotation) DeepFinderCluster (class in deepfinder.protocols.protocol_cluster) DeepFinderDisplay (class in deepfinder.protocols.protocol_utilities) DeepFinderGenerateTrainingTargetsSpheres (class in deepfinder.protocols.protocol_target_generation) DeepFinderNet (class in deepfinder.objects) DeepFinderSegment (class in deepfinder.protocols.protocol_segment) DeepFinderSetOfTomogramsView (class in deepfinder.viewers.viewer_deepfinder) DeepFinderSetOfTomoMasksView (class in deepfinder.viewers.viewer_deepfinder) DeepFinderTrain (class in deepfinder.protocols.protocol_train) DeepFinderViewer (class in deepfinder.viewers.viewer_deepfinder) deepVolPostProStep() (xmipp3.protocols.protocol_postProcessing_deepPostProcessing.XmippProtDeepVolPostProc method) DEFAULT (localrec.progressbar.ProgressBar attribute) (pyworkflow.utils.progressbar.ProgressBar attribute) defineArgs() (in module cryosparc2.convert.convert) defineBinaries() (appion.Plugin class method) (atomstructutils.Plugin class method) (atsas.Plugin class method) (bamfordlab.Plugin class method) (bsoft.Plugin class method) (ccp4.Plugin class method) (chimera.Plugin class method) (cistem.Plugin class method) (continuousflex.Plugin class method) (cryocare.Plugin class method) (cryoef.Plugin class method) (cryosparc2.Plugin class method) (deepfinder.Plugin class method) (dynamo.Plugin class method) (eman2.Plugin class method) (emantomo.Plugin class method) (emfacilities.Plugin class method) (emxlib.Plugin class method) (fsc3d.Plugin class method) (gautomatch.Plugin class method) (gctf.Plugin class method) (imod.Plugin class method) (localrec.Plugin class method) (locscale.Plugin class method) (motioncorr.Plugin class method) (novactf.Plugin class method) (phenix.Plugin class method) (pwem.Plugin class method) (pyseg.Plugin class method) (pyworkflow.plugin.Plugin class method) (relion.Plugin class method) (reliontomo.Plugin class method) (resmap.Plugin class method) (sidesplitter.Plugin class method) (sphire.Plugin class method) (spider.Plugin class method) (topaz.Plugin class method) (xmipp2.Plugin class method) (xmipp3.Plugin class method) (xmipptomo.Plugin class method) defineBinariesMaxit() (pwem.Plugin class method) defineChimeraXInstallation() (chimera.Plugin class method) defineColorScaleParams() (pwem.wizards.wizard.ColorScaleWizardBase static method) defineExecutionPararell() (imod.protocols.protocol_base.ProtImodBase method) defineFilterParameters() (novactf.protocols.protocol_tomoDefocus.ProtNovaCtfTomoDefocus static method) defineInputParams() (cistem.protocols.program_ctffind.ProgramCtffind class method) (gctf.protocols.program_gctf.ProgramGctf class method) defineOutputsSetNames() (imod.viewers.viewers.ImodEtomoViewer method) defineParams() (xmipp3.protocols.protocol_preprocess.geometrical_mask.XmippGeometricalMask2D method) (xmipp3.protocols.protocol_preprocess.geometrical_mask.XmippGeometricalMask3D method) defineProcessParams() (cistem.protocols.program_ctffind.ProgramCtffind class method) (gctf.protocols.program_gctf.ProgramGctf class method) defineRelations() (tomo3D.protocols.protocol_particle_pick_consensus.ProtTomoConsensusPicking method) (tomo3D.protocols.protocol_particle_pick_remove_duplicates.ProtTomoPickingRemoveDuplicates method) (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking method) (xmipp3.protocols.protocol_particle_pick_remove_duplicates.XmippProtPickingRemoveDuplicates method) 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) DefocusGroupInfo (class in spider.protocols.protocol_projmatch) DefocusGroups (class in relion.convert) DefocusGroups.Group (class in relion.convert) defocusGroupSetToRow() (in module xmipp3.convert.convert) defocusUTolerance (imod.protocols.protocol_ctfEstimation_automatic.ProtImodAutomaticCtfEstimation attribute) (imod.protocols.protocol_importSetOfCTFTomoSeries.ProtImodImportSetOfCtfTomoSeries attribute) defocusVTolerance (imod.protocols.protocol_ctfEstimation_automatic.ProtImodAutomaticCtfEstimation attribute) (imod.protocols.protocol_importSetOfCTFTomoSeries.ProtImodImportSetOfCtfTomoSeries attribute) delaunayTriangulation() (in module tomo3D.utils) 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) 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) DendroNode (class in spider.protocols.protocol_classify_base) denoise_b4md() (continuousflex.protocols.protocol_denoise_volumes.FlexProtVolumeDenoise method) denoiseImages() (xmipp3.protocols.protocol_denoise_particles.XmippProtDenoiseParticles method) denoiseStep() (topaz.protocols.protocol_topaz_training.TopazProtTraining method) denoiseTomogramStep() (jjsoft.protocols.protocol_denoise_tomogram.ProtJjsoftProtDenoiseTomogram method) denoisingStep() (sphire.protocols.protocol_janni_denoise.SphireProtJanniDenoising method) DeprecatedParam (class in pyworkflow.protocol.params) (class in xmipp3.utils) desiredDimensions() (pyworkflow.gui.gui.Window method) destroy() (pyworkflow.gui.dialog.Dialog method) detectCarbonCloseness() (xmipptomo.protocols.protocol_score_coordinates.XmippProtScoreCoordinates method) detectOutliers() (xmipptomo.protocols.protocol_score_coordinates.XmippProtScoreCoordinates method) device (emfacilities.protocols.pynvml.c_nvmlEventData_t attribute) (emfacilities.protocols.pynvml.nvmlPciInfo_t attribute) deviceMemory (emfacilities.protocols.pynvml.c_nvmlEccErrorCounts_t attribute) Dialog (class in pyworkflow.gui.dialog) Dict (class in pyworkflow.object) DigFreqParam (class in pyworkflow.protocol.params) directionalResolutionStep() (xmipp3.protocols.protocol_resolution_directional.XmippProtMonoDir method) disable() (scipion.install.plugin_manager.PluginTree method) DISCARDED (continuousflex.protocols.data.Point attribute) (xmipp3.utils.Point attribute) disconnect() (pwem.wizards.wizards_3d.callbacks.DraggablePoint method) display() (pyworkflow.gui.form.ParamWidget method) DISPLAY_COMBO (pyworkflow.protocol.params.EnumParam attribute) DISPLAY_HLIST (pyworkflow.protocol.params.EnumParam attribute) DISPLAY_LIST (pyworkflow.protocol.params.EnumParam attribute) displayStep() (deepfinder.protocols.protocol_utilities.DeepFinderDisplay method) distanceBetweenCoorStep() (pwem.protocols.protocol_set_filter.ProtSetFilter method) distanceCenterStep() (pwem.protocols.protocol_set_filter.ProtSetFilter method) do3DClasification() (cryosparc2.protocols.protocol_cryosparc_3D_classification.ProtCryoSparc3DClassification method) doAlignmentStep() (continuousflex.protocols.protocol_subtomogram_averaging.FlexProtSubtomogramAveraging method) doAlignmentStep_MCSFILL() (continuousflex.protocols.protocol_missing_wedge_filling.FlexProtMissingWedgeRestoration method) DOCKINMAPFILE (phenix.protocols.protocol_dock_in_map.PhenixProtRunDockInMap 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) doGlobalCtfRefinement() (cryosparc2.protocols.protocol_cryosparc_global_ctf_refinement.ProtCryoSparcGlobalCtfRefinement method) DogpickerImport (class in appion.convert.dataimport) DogPickerProtPicking (class in appion.protocols.protocol_dogpicker) DogPickerWizard (class in appion.wizards) doImportParticlesStar() (in module cryosparc2.utils) doImportVolumes() (in module cryosparc2.utils) doIteration000() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) doJob() (in module cryosparc2.utils) doLocalCtfRefinement() (cryosparc2.protocols.protocol_cryosparc_local_ctf_refinement.ProtCryoSparcLocalCtfRefinement method) doLocalRefine() (cryosparc2.protocols.protocol_cryosparc_naive_local_refine.ProtCryoSparcNaiveLocalRefine method) (cryosparc2.protocols.protocol_cryosparc_new_local_refine.ProtCryoSparcLocalRefine method) Domain (class in pwem) (class in pyworkflow.plugin) domain (emfacilities.protocols.pynvml.nvmlPciInfo_t attribute) doPartStract() (cryosparc2.protocols.protocol_cryosparc_part_subtract.ProtCryoSparcSubtract method) doRefresh() (pyworkflow.gui.text.OutputText method) doReport() (pyworkflow.tests.tests.GTestResult method) doRunAbinit() (cryosparc2.protocols.protocol_cryosparc_ab.ProtCryoSparcInitialModel method) doRunClass2D() (cryosparc2.protocols.protocol_cryosparc2d.ProtCryo2D method) doRunRefine() (cryosparc2.protocols.protocol_cryorefine.ProtCryoSparcRefine3D method) (cryosparc2.protocols.protocol_cryosparc_helical_refinement.ProtCryoSparcHelicalRefine3D method) (cryosparc2.protocols.protocol_cryosparc_homogeneous_refine.ProtCryoSparc3DHomogeneousRefine method) (cryosparc2.protocols.protocol_cryosparc_nonuniform_refine.ProtCryoSparcNonUniformRefine3D method) doSaveAveMic (xmipp3.protocols.protocol_movie_average.XmippProtMovieAverage attribute) DoseFile (class in reliontomo.protocols.protocol_ctf_3d_estimation) doseFilterStep() (imod.protocols.protocol_doseFilter.ProtImodDoseFilter method) doSharppening() (cryosparc2.protocols.protocol_cryosparc_sharppening.ProtCryoSparcSharppening method) doSymmetryExpansion() (cryosparc2.protocols.protocol_cryosparc_symmetry_expansion.ProtCryoSparcSymmetryExpansion method) DOT (localrec.progressbar.ProgressBar attribute) (pyworkflow.utils.progressbar.ProgressBar attribute) doTraining() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) doubleClickOnItem() (imod.viewers.views_tkinter_tree.ImodListDialog method) (xmipptomo.viewers.monotomo_tree_provider.MonoTomoListDialog method) doubleClickOnTomogram() (deepfinder.viewers.particle_annotator_tomo_viewer.ParticleAnnotatorDialog method) (dynamo.viewers.views_tkinter_tree.DynamoTomoDialog method) (emantomo.viewers.views_tkinter_tree.EmanDialog method) (tomo.viewers.views_tkinter_tree.TomogramsDialog method) (tomo3D.viewers.views_tkinter_tree.Tomo3DDialog method) (tomo3D.viewers.views_tkinter_tree.ViewerMRCDialog method) doubleClickViewer() (tomo.viewers.views_tkinter_tree.TomogramsDialog method) doWeightSSNR() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) downKeyPress() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.MaskRadiiPreviewDialog method) download() (in module pyworkflow.apps.pw_sync_data) downloadPdb() (in module pwem.convert.utils) downloadSeqFromDatabase() (pwem.convert.sequence.SequenceHandler method) downloadSeqFromFile() (pwem.convert.sequence.SequenceHandler method) DownsampleDialog (class in pwem.wizards.wizard) 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) (tomo3D.viewers.viewer_mrc.MrcPlot method) DraggablePoint (class in pwem.wizards.wizards_3d.callbacks) draw() (pyworkflow.gui.graph_layout.BasicLayout method) (pyworkflow.gui.graph_layout.GraphLayout method) (pyworkflow.gui.graph_layout.LevelTreeLayout method) (pyworkflow.gui.plotter.Plotter method) drawGraph() (pyworkflow.gui.canvas.Canvas method) drawRunsGraph() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) dropColumns() (in module pwem.emlib.metadata.utils) dstMoved() (pyworkflow.gui.canvas.Cable method) duplicatedIds() (pwem.protocols.protocol_sets.ProtUnionSet method) dVal (emfacilities.protocols.pynvml.c_nvmlValue_t attribute) dynamo (module) dynamo.bibtex (module) dynamo.constants (module) dynamo.convert (module) dynamo.convert.convert (module) dynamo.protocols (module) dynamo.protocols.protocol_bin_tomograms (module) dynamo.protocols.protocol_boxing (module) dynamo.protocols.protocol_extraction (module) dynamo.protocols.protocol_import_subtomos (module) dynamo.protocols.protocol_import_tomograms (module) dynamo.protocols.protocol_model_workflow (module) dynamo.protocols.protocol_subBoxing (module) dynamo.protocols.protocol_subtomo_MRA (module) dynamo.viewers (module) dynamo.viewers.viewers_data (module) dynamo.viewers.views_tkinter_tree (module) dynamo.wizards (module) dynamo_mat() (in module continuousflex.protocols.utilities.dynamo) DynamoBinTomograms (class in dynamo.protocols.protocol_bin_tomograms) DynamoBoxing (class in dynamo.protocols.protocol_boxing) DynamoDataViewer (class in dynamo.viewers.viewers_data) DynamoExtraction (class in dynamo.protocols.protocol_extraction) DynamoExtractionWizard (class in dynamo.wizards) DynamoImportSubtomos (class in dynamo.protocols.protocol_import_subtomos) DynamoImportTomograms (class in dynamo.protocols.protocol_import_tomograms) DynamoModelWorkflow (class in dynamo.protocols.protocol_model_workflow) DynamoModelWorkflowWizard (class in dynamo.wizards) DynamoSubBoxing (class in dynamo.protocols.protocol_subBoxing) DynamoSubTomoMRA (class in dynamo.protocols.protocol_subtomo_MRA) DynamoTomoDialog (class in dynamo.viewers.views_tkinter_tree)

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) editionListOfResidues() (chimera.wizards.GetChainResiduesWizardChimera method) EditLabelDialog (class in pyworkflow.gui.project.labels) editObject() (in module pyworkflow.gui.form) EditObjectDialog (class in pyworkflow.gui.dialog) elasticAlignmentStep() (continuousflex.protocols.protocol_structure_mapping.FlexProtStructureMapping method) ElementGroup (class in pyworkflow.protocol.params) eliminationStep() (xmipp3.protocols.protocol_eliminate_empty_images.XmippProtEliminateEmptyBase method) Ellipsoid (class in tomo.objects) EM_ROOT (pwem.Config attribute) EmailNotifier (class in emfacilities.protocols.protocol_monitor) eman2 (module) eman2.bibtex (module) eman2.constants (module) eman2.convert (module) eman2.convert.convert (module) eman2.convert.dataimport (module) eman2.protocols (module) eman2.protocols.protocol_autopick_boxer (module) eman2.protocols.protocol_boxing (module) eman2.protocols.protocol_ctf (module) eman2.protocols.protocol_initialmodel (module) eman2.protocols.protocol_initialmodel_sgd (module) eman2.protocols.protocol_reconstruct (module) eman2.protocols.protocol_refine2d (module) eman2.protocols.protocol_refine2d_bispec (module) eman2.protocols.protocol_refineasy (module) eman2.protocols.protocol_tiltvalidate (module) eman2.viewers (module) eman2.viewers.viewers (module) EmanDataViewer (class in emantomo.viewers.viewers_data) EmanDialog (class in emantomo.viewers.views_tkinter_tree) EmanImport (class in eman2.convert.dataimport) EmanProtAlignTs (class in emantomo.protocols.protocol_align_ts) EmanProtAutopick (class in eman2.protocols.protocol_autopick_boxer) EmanProtBoxing (class in eman2.protocols.protocol_boxing) EmanProtCTFAuto (class in eman2.protocols.protocol_ctf) EmanProtInitModel (class in eman2.protocols.protocol_initialmodel) EmanProtInitModelSGD (class in eman2.protocols.protocol_initialmodel_sgd) EmanProtReconstruct (class in eman2.protocols.protocol_reconstruct) EmanProtRefine (class in eman2.protocols.protocol_refineasy) EmanProtRefine2D (class in eman2.protocols.protocol_refine2d) EmanProtRefine2DBispec (class in eman2.protocols.protocol_refine2d_bispec) EmanProtTiltValidate (class in eman2.protocols.protocol_tiltvalidate) EmanProtTomoBoxing (class in emantomo.protocols.protocol_tomo_boxing) EmanProtTomoConvNet (class in emantomo.protocols.protocol_tomo_boxing_convnet) EmanProtTomoFillMW (class in emantomo.protocols.protocol_tomo_fill_mw) EmanProtTomoInitialModel (class in emantomo.protocols.protocol_tomo_initialmodel) EmanProtTomoReconstruction (class in emantomo.protocols.protocol_tomo_reconstruction) EmanProtTomoRefinement (class in emantomo.protocols.protocol_tomo_subtomogram_refinement) EmanProtTomoTempMatch (class in emantomo.protocols.protocol_tomo_template_match) emantomo (module) emantomo.bibtex (module) emantomo.constants (module) emantomo.convert (module) emantomo.convert.convert (module) emantomo.convert.dataimport (module) emantomo.protocols (module) emantomo.protocols.protocol_align_ts (module) emantomo.protocols.protocol_tomo_boxing (module) emantomo.protocols.protocol_tomo_boxing_convnet (module) emantomo.protocols.protocol_tomo_fill_mw (module) emantomo.protocols.protocol_tomo_initialmodel (module) emantomo.protocols.protocol_tomo_reconstruction (module) emantomo.protocols.protocol_tomo_subtomogram_refinement (module) emantomo.protocols.protocol_tomo_template_match (module) emantomo.viewers (module) emantomo.viewers.viewers (module) emantomo.viewers.viewers_data (module) emantomo.viewers.views_tkinter_tree (module) emantomo.wizards (module) EmanTomoExtractionWizard (class in emantomo.wizards) EmanTomoImport (class in emantomo.convert.dataimport) EmanTomoResizeWizard (class in emantomo.wizards) EmanTomoTempMatchWizard (class in emantomo.wizards) EmanViewer (class in eman2.viewers.viewers) emfacilities (module) emfacilities.bibtex (module) emfacilities.constants (module) emfacilities.protocols (module) emfacilities.protocols.getnifs (module) emfacilities.protocols.protocol_monitor (module) emfacilities.protocols.protocol_monitor_2d_streamer (module) emfacilities.protocols.protocol_monitor_ctf (module) emfacilities.protocols.protocol_monitor_movie_gain (module) emfacilities.protocols.protocol_monitor_summary (module) emfacilities.protocols.protocol_monitor_system (module) emfacilities.protocols.pynvml (module) emfacilities.protocols.report_html (module) emfacilities.protocols.report_influx (module) emfacilities.protocols.summary_provider (module) emfacilities.protocols.transport (module) emfacilities.viewers (module) emfacilities.viewers.viewer_monitors (module) EMFile (class in pwem.objects.data) emit() (pwperformance.loggers.influxdb.BufferingInfluxHandler method) (pwperformance.loggers.influxdb.InfluxHandler method) (pwperformance.main.CodespeedHandler method) 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() (emfacilities.viewers.viewer_monitors.MovieGainMonitorPlotter method) (pyworkflow.object.String method) EMRINGERFILE (phenix.protocols.protocol_emringer.PhenixProtRunEMRinger attribute) EMRINGERMAXZSCOREFILENAME (phenix.protocols.protocol_emringer.PhenixProtRunEMRinger attribute) EMRINGEROPTIMALTHRESHOLDFILENAME (phenix.protocols.protocol_emringer.PhenixProtRunEMRinger attribute) EMRINGERROTAMERRATIOSFILENAME (phenix.protocols.protocol_emringer.PhenixProtRunEMRinger attribute) EMRINGERSCORESFILENAME (phenix.protocols.protocol_emringer.PhenixProtRunEMRinger attribute) EMRINGERSUBPLOTSFILENAME (phenix.viewers.viewer_emringer.PhenixProtRunEMRingerViewer attribute) EMRINGERTOTALTHRESH (phenix.viewers.viewer_emringer.PhenixProtRunEMRingerViewer attribute) EMRINGERTRANSFERFILENAME (phenix.protocols.protocol_emringer.PhenixProtRunEMRinger attribute) EMSet (class in pwem.objects.data) EmWizard (class in pwem.wizards.wizard) EmxData (class in emxlib.utils) EmxImage (class in emxlib.utils) EmxImport (class in emxlib.convert.dataimport) EmxLabel (class in emxlib.utils) emxlib (module) emxlib.bibtex (module) emxlib.constants (module) emxlib.convert (module) emxlib.convert.convert (module) emxlib.convert.dataimport (module) emxlib.protocols (module) emxlib.protocols.protocol_export (module) emxlib.utils (module) emxlib.viewers (module) emxlib.viewers.emxlib_viewers (module) EmxMicrograph (class in emxlib.utils) EmxObject (class in emxlib.utils) EmxParticle (class in emxlib.utils) EMXViewer (class in emxlib.viewers.emxlib_viewers) EmxXmlMapper (class in emxlib.utils) enable() (scipion.install.plugin_manager.PluginTree method) enableAppend() (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.object.Set method) encodePresegArea() (in module pyseg.utils)

enCrypt() (in module emfacilities.protocols.report_influx) END (pyworkflow.utils.properties.colorText attribute) (pyworkflow.utils.utils.Environ attribute) endChimeraScript() (chimera.protocols.protocol_contacts.ChimeraProtContacts method) 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) enqueueJob() (in module cryosparc2.utils) ENTER (pyworkflow.constants.TK attribute) enter() (pyworkflow.gui.tooltip.ToolTip method) EntryDialog (class in pyworkflow.gui.dialog) EntryGrid (class in chimera.editList) EntryWidget (class in chimera.editList) EnumParam (class in pyworkflow.protocol.params) 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.Float method) (pyworkflow.object.Object method) (pyworkflow.object.Scalar method) equalItemAttributes() (pyworkflow.object.Set method) eraseGoldBeadsStep() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) eraseXraysStep() (imod.protocols.protocol_goldBeadEraser.ProtImodGoldBeadEraser method) (imod.protocols.protocol_xRaysEraser.ProtImodXraysEraser method) 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 ccp4.viewers.viewer_refmac) (in module phenix.viewers.viewer_emringer) (in module phenix.viewers.viewer_refinement_base) (in module phenix.viewers.viewer_search_fit) (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) estimateGainStep() (relion.protocols.protocol_compress_estimate_gain.ProtRelionCompressEstimateGain method) estimateOrientationStep() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) estimateResolutionStep() (resmap.protocols.protocol_resmap.ProtResMap method) euler2Matrix() (tomo.objects.Coordinate3D method) eulerAngles() (tomo.objects.Coordinate3D method) eulerAngles2matrix() (in module dynamo.convert.convert) (in module xmipp2.convert.convert) eval() (continuousflex.protocols.data.Point method) (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) evaluateConvergence() (xmipp3.protocols.protocol_reconstruct_heterogeneous.XmippProtReconstructHeterogeneous method) evaluateDeformationsStep() (continuousflex.protocols.protocol_nma_choose.FlexrotNMAChoose 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) EVEN (tomo.viewers.views_tkinter_tree.CTFSerieStates attribute) evenAvgFrameList (tomo.protocols.protocol_ts_correct_motion.ProtTsCorrectMotion attribute) evenOddCapable (tomo.protocols.protocol_ts_correct_motion.ProtTsCorrectMotion attribute) (xmipptomo.protocols.protocol_flexalign.XmippProtTsFlexAlign attribute) EVENT (pyworkflow.utils.log.STATUS attribute) eventData (emfacilities.protocols.pynvml.c_nvmlEventData_t attribute) eventType (emfacilities.protocols.pynvml.c_nvmlEventData_t attribute) ExceptionDialog (class in pyworkflow.gui.dialog) excludeViewsInfoMatrix (imod.protocols.protocol_excludeViews.ProtImodExcludeViews attribute) excludeViewsStep() (imod.protocols.protocol_excludeViews.ProtImodExcludeViews method) 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) executeLongRemote() (in module pyworkflow.utils.utils) executeMapMtzRefmacStep() (ccp4.protocols.protocol_refmac.CCP4ProtRunRefmac method) executeProtocol() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) executeRefineRefmacStep() (ccp4.protocols.protocol_refmac.CCP4ProtRunRefmac method) executeRemote() (in module pyworkflow.utils.utils) executeRemoteX() (in module pyworkflow.utils.utils) 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) existsPlugin() (in module tomo.utils) existsVariablePaths() (in module pyworkflow.utils.utils) expandPattern() (in module pyworkflow.utils.path) expandSymmetryStep() (relion.protocols.protocol_expand_symmetry.ProtRelionExpandSymmetry method) 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) exportCoordsStep() (relion.protocols.protocol_export_coords.ProtRelionExportCoordinates method) exportData() (in module emxlib.convert.convert) exportDataStep() (emxlib.protocols.protocol_export.ProtEmxExport 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) exportParticlesStep() (relion.protocols.protocol_export_particles.ProtRelionExportParticles method) exportProtocols() (pyworkflow.project.project.Project method) exportVolumeStep() (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) EXPOSE_ITEMS (pwem.objects.data.SetOfAtomStructs attribute) (pwem.objects.data.SetOfVolumes attribute) (tomo.objects.SetOfTiltSeriesBase attribute) (tomo.objects.SetOfTomoMasks attribute) (tomo.objects.SetOfTomograms attribute) EXTENDED_ATTR (pyworkflow.object.Pointer attribute) EXTENDED_ITEMID (pyworkflow.object.Pointer attribute) ExtendedTS (class in reliontomo.protocols.protocol_ctf_3d_estimation) extendImageList() (spider.protocols.protocol_classify_base.DendroNode method) EXTRA_LABELS (pwem.viewers.views.CtfView attribute) (pwem.viewers.views.MicrographsView attribute) extractAllChainsStep() (atomstructutils.protocols.protocol_operate.ProtAtomStrucOperate method) extractChain() (pwem.convert.atom_struct.AtomicStructHandler method) extractChainStep() (atomstructutils.protocols.protocol_operate.ProtAtomStrucOperate method) extractCoordinates() (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) extractCoordinatesStep() (tomo.protocols.protocol_extract_coordinates.ProtTomoExtractCoords method) extractCoordsStep() (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) extractElements() (pwem.protocols.protocol_classes_selector.ProtClassesSelector 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) extractNumber() (phenix.protocols.protocol_search_fit.PhenixProtSearchFit method) extractParticles() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) extractParticlesStep() (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) extractUnit() (xmipp3.protocols.protocol_extract_asymmetric_unit.XmippProtExtractUnit method) extractVesicles() (in module tomo.utils)

F

factory() (pyworkflow.gui.browser.ShortCut static method) FAILED (tomo.viewers.views_tkinter_tree.CTFSerieStates attribute) FAILURE (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) failure_item() (scipion.install.plugin_manager.PluginTree method) fans (emfacilities.protocols.pynvml.c_nvmlUnitFanSpeeds_t attribute) fastCheckingAtt() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) fetch_emdb_map() (in module pwem.protocols.protocol_import.volumes) fetch_file() (in module pwem.protocols.protocol_import.volumes) FIELD_TYPE_BOOLEAN (pyworkflow.template.Validations attribute) FIELD_TYPE_DECIMAL (pyworkflow.template.Validations attribute) FIELD_TYPE_INTEGER (pyworkflow.template.Validations attribute) FIELD_TYPE_PATH (pyworkflow.template.Validations attribute) FIELD_TYPE_STR (pyworkflow.template.Validations attribute) FigureFrame (class in pyworkflow.gui.matplotlib_image) FILE_COLUMN (pyworkflow.gui.browser.FileTreeProvider attribute) FILE_KEYS (relion.protocols.protocol_base.ProtRelionBase attribute) (reliontomo.protocols.protocol_base_tomo.ProtRelionBaseTomo attribute) FileBrowseDialog (class in pyworkflow.gui.dialog) 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) (tomo.protocols.protocol_ts_import.ProtImportTsBase method) FILENAMENUMBERLENGTH (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch attribute) FileParam (class in pyworkflow.protocol.params) filesToCopy (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic attribute) FileTransform (class in relion.convert.dataimport) FileTreeProvider (class in pyworkflow.gui.browser) fill_statistics() (xmipp3.viewers.viewer_validate_fscq.Statistics method) fillAcquisition() (pwem.protocols.protocol_import.images.ProtImportImages method) fillClasses() (in module xmipp3.convert.convert) fillClassesFromIter() (relion.convert.ClassesLoader method) (reliontomo.convert.ClassesLoader method) fillMessageText() (in module pyworkflow.gui.dialog) fillObjDict() (pyworkflow.object.Object static method) fillObject() (pyworkflow.mapper.sqlite.SqliteMapper method) (pyworkflow.mapper.xmlmapper.XmlMapper method) fillObjectWithRow() (pyworkflow.mapper.sqlite.SqliteMapper method) fillOutput() (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method) fillToolBar() (pyworkflow.gui.project.viewprotocols.StepsWindow method) filter_distorigin() (in module localrec.utils) filter_lowpass() (continuousflex.protocols.protocol_denoise_volumes.FlexProtVolumeDenoise method) filter_mindist() (in module localrec.utils) filter_side() (in module localrec.utils) filter_spider() (in module spider.wizards) filter_subparticles() (in module localrec.utils) filter_top() (in module localrec.utils) filter_unique() (in module localrec.utils) FilterParticlesWizard (class in pwem.wizards.wizard) filterStep() (bsoft.protocols.protocol_bfilter.BsoftProtBfilter method) (spider.protocols.protocol_filters.SpiderProtFilter method) (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) FINALRESULTS (ccp4.viewers.viewer_refmac.ParseFile attribute) find_covariance_matrix() (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify method) find_prog() (in module pyworkflow.gui.text) findAlignment() (xmipptomo.protocols.protocol_align_transform.XmippProtAlignTransform method) findAttributeName() (pyworkflow.protocol.protocol.Protocol method) findClass() (pyworkflow.plugin.Domain class method) findClosestConnectors() (in module pyworkflow.gui.canvas) findClosestPoints() (in module pyworkflow.gui.canvas) findFile() (in module pyworkflow.utils.path) findFileRecursive() (in module pyworkflow.utils.path) findLastIteration() (cryosparc2.protocols.protocol_base.ProtCryosparcBase method) (cryosparc2.protocols.protocol_cryosparc_3D_classification.ProtCryoSparc3DClassification method) findPrevText() (pyworkflow.gui.text.TextFileViewer method) findRelionProtsStep() (relion.protocols.protocol_gentle_clean.ProtRelionCleanJobs method) findResource() (in module pyworkflow.config) findRootFrom() (in module pyworkflow.utils.path) findRow() (in module xmipp3.base) findRowById() (in module xmipp3.base) findSphericity() (fsc3d.protocols.protocol_3dfsc.Prot3DFSC method) findStrictClosestConnectors() (in module pyworkflow.gui.canvas) findSubClasses() (pyworkflow.plugin.Domain class method) findText() (pyworkflow.gui.text.TextFileViewer method) findTotalAverage() (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify 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() (localrec.progressbar.ProgressBar method) (pyworkflow.utils.progressbar.ProgressBar method) finished (tomo3D.viewers.viewer_mrc.Worker attribute) firmwareVersion (emfacilities.protocols.pynvml.c_nvmlHwbcEntry_t attribute) (emfacilities.protocols.pynvml.c_nvmlUnitInfo_t attribute) first() (relion.convert.convert31.OpticsGroups method) firstObject() (emxlib.utils.EmxXmlMapper method) fit_ellipsoid() (in module tomo.utils) fitEllipsoidStep() (xmipptomo.protocols.protocol_fit_ellipsoid.XmippProtFitEllipsoid method) FITTEDFILE (phenix.protocols.protocol_search_fit.PhenixProtSearchFit attribute) fixFile() (pwem.convert.headers.Ccp4Header class method) fixHeaders() (spider.utils.SpiderDocFile method) fixLinks() (pyworkflow.project.project.Project method) fixVolume() (in module cryosparc2.utils) (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) FlexAlignmentNMAViewer (class in continuousflex.viewers.viewer_nma_alignment) FlexAlignmentNMAVolViewer (class in continuousflex.viewers.viewer_nma_alignment_vol) flexAnalysisStep() (relion.protocols.protocol_multibody.ProtRelionMultiBody method) FlexBatchProtNMACluster (class in continuousflex.protocols.protocol_batch_cluster) FlexBatchProtNMAClusterVol (class in continuousflex.protocols.protocol_batch_cluster_vol) FlexDimredNMAViewer (class in continuousflex.viewers.viewer_nma_dimred) FlexDimredNMAVolViewer (class in continuousflex.viewers.viewer_nma_dimred_vol) FlexNmaPlotter (class in continuousflex.viewers.nma_plotter) FlexNMAViewer (class in continuousflex.viewers.viewer_nma) FlexNmaVolPlotter (class in continuousflex.viewers.plotter_vol) FlexPlotter (class in continuousflex.viewers.plotter) FlexProtAlignmentNMA (class in continuousflex.protocols.protocol_nma_alignment) FlexProtAlignmentNMAVol (class in continuousflex.protocols.protocol_nma_alignment_vol) FlexProtApplyVolSetAlignment (class in continuousflex.protocols.protocol_apply_volumeset_alignment) FlexProtConvertPdb (class in continuousflex.protocols.pdb.protocol_convert_pdb) FlexProtConvertToPseudoAtoms (class in continuousflex.protocols.pdb.protocol_pseudoatoms) FlexProtConvertToPseudoAtomsBase (class in continuousflex.protocols.pdb.protocol_pseudoatoms_base) FlexProtDimredNMA (class in continuousflex.protocols.protocol_nma_dimred) FlexProtDimredNMAVol (class in continuousflex.protocols.protocol_nma_dimred_vol) FlexProtDimredPdb (class in continuousflex.protocols.protocol_pdb_dimred) FlexProtMissingWedgeRestoration (class in continuousflex.protocols.protocol_missing_wedge_filling) FlexProtNMA (class in continuousflex.protocols.protocol_nma) FlexProtNMABase (class in continuousflex.protocols.protocol_nma_base) FlexProtPdbDimredViewer (class in continuousflex.viewers.viewer_pdb_dimred) FlexProtStructureMapping (class in continuousflex.protocols.protocol_structure_mapping) FlexProtStructureMappingViewer (class in continuousflex.viewers.viewer_structure_mapping) FlexProtSubtomoClassify (class in continuousflex.protocols.protocol_subtomograms_classify) FlexProtSubtomoClassifyViewer (class in continuousflex.viewers.viewer_subtomograms_classify) FlexProtSubtomogramAveraging (class in continuousflex.protocols.protocol_subtomogram_averaging) FlexProtSynthesizeImages (class in continuousflex.protocols.protocol_image_synthesize) FlexProtSynthesizeImageViewer (class in continuousflex.viewers.viewer_image_synthesize) FlexProtSynthesizeSubtomo (class in continuousflex.protocols.protocol_subtomogrmas_synthesize) FlexProtSynthesizeSubtomoViewer (class in continuousflex.viewers.viewer_subtomograms_synthesize) FlexProtVolumeDenoise (class in continuousflex.protocols.protocol_denoise_volumes) FlexrotNMAChoose (class in continuousflex.protocols.protocol_nma_choose) flipYImage() (in module xmipp3.utils) Float (class in pyworkflow.object) FloatingMessage (class in pyworkflow.gui.dialog) FloatParam (class in pyworkflow.protocol.params) flush() (pwperformance.loggers.influxdb.BufferingInfluxHandler method) 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 (tomo3D.protocols.protocol_particle_pick_consensus.ProtTomoConsensusPicking attribute) (tomo3D.protocols.protocol_particle_pick_remove_duplicates.ProtTomoPickingRemoveDuplicates attribute) (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking attribute) (xmipp3.protocols.protocol_particle_pick_remove_duplicates.XmippProtPickingRemoveDuplicates attribute) FolderParam (class in pyworkflow.protocol.params) FOMPLOT (ccp4.viewers.viewer_refmac.ParseFile attribute) Font_wm (class in scipion.scripts.fontbrowser) Form (class in pyworkflow.protocol.params) Format (class in pyworkflow.protocol.params) format3DCoordinatesList() (in module imod.utils) format_args() (in module pyworkflow.utils.echo) formatAngleFile() (in module imod.utils) formatAngleList() (in module imod.utils) formatExceptionInfo() (in module pyworkflow.utils.utils) formatFiducialList() (in module imod.utils) formatFiducialResidList() (in module imod.utils) formatGoldBead3DCoordinatesList() (in module imod.utils) formatTransformationMatrix() (in module imod.utils) formatTransformFile() (in module imod.utils) formatTransformFileFromTransformList() (in module imod.utils) FormElement (class in pyworkflow.protocol.params) FormulaDialog (class in pwem.wizards.wizard) 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) FrealignParFile (class in cistem.convert.convert) free (emfacilities.protocols.pynvml.c_nvmlMemory_t attribute) FROM_FILE_IMPORT (tomo.protocols.protocol_base.ProtTomoImportAcquisition attribute) fromCIFTommCIF() (in module pwem.convert.atom_struct) fromCIFToPDB() (in module pwem.convert.atom_struct) fromImages() (relion.convert.convert31.OpticsGroups static method) fromPDBToCIF() (in module pwem.convert.atom_struct) fromStar() (relion.convert.convert31.OpticsGroups static method) fromString() (relion.convert.convert31.OpticsGroups static method) FS (pyworkflow.object.String attribute) FSC (class in pwem.objects.data) fsc3d (module) fsc3d.bibtex (module) fsc3d.constants (module) fsc3d.protocols (module) fsc3d.protocols.protocol_3dfsc (module) fsc3d.viewers (module) FSCHALFMAPFILE (phenix.viewers.viewer_validation_cryoem.PhenixProtRunValidationCryoEMViewer attribute) FSCMODELMAPFILE (phenix.viewers.viewer_validation_cryoem.PhenixProtRunValidationCryoEMViewer attribute) FscViewer (class in pwem.viewers.viewer_fsc) FSOestimationStep() (xmipp3.protocols.protocol_resolution_fso.XmippProtFSO method) FULL (localrec.progressbar.ProgressBar attribute) (pyworkflow.utils.progressbar.ProgressBar attribute) FunctionStep (class in pyworkflow.protocol.protocol) fusionStep() (xmipp3.protocols.protocol_volume_consensus.XmippProtVolConsensus method) fwVersion (emfacilities.protocols.pynvml.c_nvmlBridgeChipInfo_t attribute)

G

gatherResultsStep() (continuousflex.protocols.protocol_structure_mapping.FlexProtStructureMapping method) (xmipp3.protocols.protocol_validate_overfitting.XmippProtValidateOverfitting method) gatherSingleVolumeStep() (continuousflex.protocols.protocol_structure_mapping.FlexProtStructureMapping method) GAUSSIAN_NOISE (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoise attribute) GaussianFilterDialog (class in pwem.wizards.wizard) GaussianParticlesWizard (class in pwem.wizards.wizard) GaussianVolumesWizard (class in pwem.wizards.wizard) GaussianWizard (class in pwem.wizards.wizard) gautomatch (module) gautomatch.bibtex (module) gautomatch.constants (module) gautomatch.convert (module) gautomatch.protocols (module) gautomatch.protocols.protocol_gautomatch (module) gautomatch.run_gautomatch (module) gautomatch.viewers (module) gautomatch.wizards (module) GautomatchBandpassWizard (class in gautomatch.wizards) GautomatchParticleWizard (class in gautomatch.wizards) GautomatchPickerWizard (class in gautomatch.wizards) GautomatchViewer (class in gautomatch.viewers) gctf (module) gctf.bibtex (module) gctf.constants (module) gctf.convert (module) gctf.convert.convert (module) gctf.convert.dataimport (module) gctf.protocols (module) gctf.protocols.program_gctf (module) gctf.protocols.protocol_gctf (module) gctf.protocols.protocol_gctf_refine (module) gctf.protocols.protocol_ts_gctf (module) gctf.viewers (module) gctf.wizards (module) GctfCTFWizard (class in gctf.wizards) GctfImportCTF (class in gctf.convert.dataimport) GctfViewer (class in gctf.viewers) GE (class in pyworkflow.protocol.params) genAsymUnit() (localrec.protocols.protocol_localized_stitch.ProtLocalizedStich method) GENERAL_MODELS (topaz.protocols.protocol_topaz_picking.TopazProtPicking attribute) generate() (emfacilities.protocols.report_html.ReportHtml method) (emfacilities.protocols.report_influx.ReportInflux method) generate_copies_of_volume() (continuousflex.protocols.protocol_subtomogrmas_synthesize.FlexProtSynthesizeSubtomo method) generate_deformations() (continuousflex.protocols.protocol_image_synthesize.FlexProtSynthesizeImages method) (continuousflex.protocols.protocol_subtomogrmas_synthesize.FlexProtSynthesizeSubtomo method) generate_links_to_volume() (continuousflex.protocols.protocol_image_synthesize.FlexProtSynthesizeImages method) generate_rotation_and_shift() (continuousflex.protocols.protocol_image_synthesize.FlexProtSynthesizeImages method) (continuousflex.protocols.protocol_subtomogrmas_synthesize.FlexProtSynthesizeSubtomo method) generate_volume_from_pdb() (continuousflex.protocols.protocol_image_synthesize.FlexProtSynthesizeImages method) (continuousflex.protocols.protocol_subtomogrmas_synthesize.FlexProtSynthesizeSubtomo method) generate_zero_rotation_and_shift() (continuousflex.protocols.protocol_image_synthesize.FlexProtSynthesizeImages method) generateConeCenters() (xmipp3.protocols.protocol_deep_align.XmippProtDeepAlign method) generateCoordList() (xmipptomo.protocols.protocol_score_coordinates.XmippProtScoreCoordinates method) generateCutOnFreqDictionary() (in module imod.utils) generateDefocusAngleDictionary() (in module imod.utils) generateDefocusFile() (imod.protocols.protocol_ctfCorrection.ProtImodCtfCorrection method) generateDefocusIMODFileFromObject() (in module imod.utils) generateDefocusUDictionary() (in module imod.utils) generateDefocusVDictionary() (in module imod.utils) generateDoseFileFromAccDoseTS() (in module imod.utils) generateDoseFileFromDoseTS() (in module imod.utils) generateExpImagesStep() (xmipp3.protocols.protocol_deep_align.XmippProtDeepAlign method) generateFiducialModelStep() (imod.protocols.protocol_fiducialModel.ProtImodFiducialModel method) (imod.protocols.protocol_goldBeadEraser.ProtImodGoldBeadEraser method) generateFiducialSeedStep() (imod.protocols.protocol_fiducialModel.ProtImodFiducialModel method) generateIMODFiducialTextFile() (in module imod.utils) generateInput() (xmipp3.protocols.protocol_classification_gpuCorr_full.XmippProtStrGpuCrrCL2D method) generateMask2Step() (xmipp3.protocols.protocol_volume_adjust_sub.XmippProtVolSubtraction method) generateMdForClassification() (xmipp3.protocols.protocol_classification_gpuCorr_full.XmippProtStrGpuCrrCL2D method) generateMetadata() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) generateOutputClasses() (xmipp3.protocols.protocol_classification_gpuCorr_full.XmippProtStrGpuCrrCL2D method) generateOutputStackStep() (imod.protocols.protocol_applyTransformationMatrix.ProtImodApplyTransformationMatrix method) (imod.protocols.protocol_excludeViews.ProtImodExcludeViews method) (imod.protocols.protocol_tomoNormalization.ProtImodTomoNormalization method) (imod.protocols.protocol_tomoProjection.ProtImodTomoProjection method) (imod.protocols.protocol_tsNormalization.ProtImodTSNormalization method) (imod.protocols.protocol_xCorrPrealignment.ProtImodXcorrPrealignment method) generatePhaseShiftDictionary() (in module imod.utils) generatePointCloud() (in module tomo.utils) generateReportImages() (emfacilities.protocols.report_html.ReportHtml method) generateSplittedVolumes() (xmipp3.protocols.protocol_split_volume.XmippProtSplitvolume method) generateTaSolutionText() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) (imod.protocols.protocol_fiducialModel.ProtImodFiducialModel method) generateTltFile() (tomo.objects.TiltSeriesBase method) generateTrackComStep() (imod.protocols.protocol_fiducialModel.ProtImodFiducialModel method) generateTransformFileStep() (imod.protocols.protocol_applyTransformationMatrix.ProtImodApplyTransformationMatrix method) (imod.protocols.protocol_importSetOfTM.ProtImodImportTransformationMatrix 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 cistem.convert.convert) (in module cryoef.convert) (in module cryosparc2.convert.convert) (in module eman2.convert.convert) (in module emantomo.convert.convert) (in module gctf.convert.convert) (in module localrec.utils) (in module relion.convert.convert_deprecated) (in module spider.convert) (in module xmipp3.convert.convert) (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) GEOMETRYPLOT (ccp4.viewers.viewer_refmac.ParseFile attribute) get() (chimera.editList.EntryGrid method) (emxlib.utils.EmxObject method) (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_full_message() (in module pwperformance.loggers.influxdb) get_IMOD_files() (jjsoft.protocols.protocol_align_ts.ProtJjsoftAlignTs method) get_job_streamlog() (in module cryosparc2.utils) get_length() (localrec.utils.Vector3 method) get_matrix() (localrec.utils.Vector3 method) get_network_interfaces() (in module emfacilities.protocols.getnifs) get_number_of_volumes() (continuousflex.protocols.protocol_image_synthesize.FlexProtSynthesizeImages method) (continuousflex.protocols.protocol_subtomogrmas_synthesize.FlexProtSynthesizeSubtomo method) get_parser() (in module pyworkflow.apps.pw_sync_data) get_point() (pwperformance.loggers.influxdb.InfluxHandler method) get_sphere_params() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) get_Ts_files() (jjsoft.protocols.protocol_motion_compensation.ProtJjsoftAlignReconstructTomogram method) (jjsoft.protocols.protocol_reconstruct_tomogram.ProtJjsoftReconstructTomogram method) getAccumDose() (tomo.objects.TomoAcquisition method) (tomo.protocols.protocol_ts_import.TiltMetadata method) getAcqOrder() (tomo.protocols.protocol_ts_import.TiltMetadata method) getAcquisition() (pwem.objects.data.Image method) (pwem.objects.data.SetOfImages method) (pwem.protocols.protocol_import.images.ProtImportImages method) (tomo.objects.SubTomogram method) (tomo.objects.Tomogram method) getAcquisitionOrder() (tomo.objects.TiltImageBase method) getAction() (scipion.scripts.kickoff.KickoffWindow method) getActions() (pwem.protocols.protocol_import.images.ProtImportImages method) (tomo.protocols.protocol_ts_import.ProtImportTsBase method) getActionsFromSelection() (pyworkflow.gui.project.viewprotocols.RunsTreeProvider method) getActiveVersion() (eman2.Plugin class method) (emantomo.Plugin class method) (pyworkflow.plugin.Plugin class method) getAddress() (pyworkflow.protocol.hosts.HostConfig method) getAddresses() (emfacilities.protocols.getnifs.NetworkInterface method) getAlgebraicDesc() (tomo.objects.Ellipsoid method) getAlias() (pyworkflow.template.TemplateParam method) getAlignDir() (spider.protocols.protocol_align_base.SpiderProtAlign method) getAlignment() (pwem.objects.data.Movie method) (pwem.objects.data.SetOfImages method) getAlignProgramsPath() (jjsoft.Plugin class method) getAllCoordsInputMicrographs() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getAllowMPI() (pyworkflow.protocol.hosts.QueueConfig method) getAllowThreads() (pyworkflow.protocol.hosts.QueueConfig method) getAllSetsAttributes() (pwem.protocols.protocol_sets.ProtUnionSet method) getAlphabet() (pwem.objects.data.Sequence method) getAmplitudeContrast() (pwem.objects.data.Acquisition method) getAngleAxis1() (tomo.objects.TomoAcquisition method) getAngleAxis2() (tomo.objects.TomoAcquisition method) getAngleMax() (tomo.objects.TomoAcquisition method) getAngleMin() (tomo.objects.TomoAcquisition method) getAngleMovieFile() (tomo.protocols.protocol_ts_import.TiltMetadata method) getAngles() (pwem.objects.data_tiltpairs.Angles method) (pwem.objects.data_tiltpairs.CoordinatesTiltPair method) (xmipp3.protocols.protocol_rotational_symmetry.XmippProtRotationalSymmetry method) getAnglesCount() (tomo.objects.SetOfTiltSeriesBase method) (tomo.objects.TiltSeriesBase method) getAnglesFromHeader() (in module tomo.convert) getAnglesFromMdoc() (in module tomo.convert) getAnglesFromTlt() (in module tomo.convert) getAngleStepFromSeries() (imod.protocols.protocol_tomoReconstruction.ProtImodTomoReconstruction static method) (novactf.protocols.protocol_tomoReconstruction.ProtNovaCtfTomoReconstruction static method) getAngleY() (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify method) getAnimationName() (continuousflex.viewers.nma_gui.tk_trajectories.TrajectoriesWindow method) (continuousflex.viewers.nma_vol_gui.tk_trajectories_vol.TrajectoriesWindowVol method) getAppsPath() (in module pyworkflow.config) getArchitecture() (in module pwem.viewers.showj) getArgs() (gautomatch.protocols.protocol_gautomatch.ProtGautomatch method) (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain 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() (pyworkflow.plugin.PluginInfo method) (scipion.install.plugin_funcs.PluginInfo method) getAuthorEmail() (pyworkflow.plugin.PluginInfo method) getAutodownsampling() (xmipp3.wizards.XmippCTFWizard method) getAutopickParams() (relion.protocols.protocol_autopick_log.ProtRelionAutopickLoG method) (relion.protocols.protocol_autopick_ref.ProtRelion2Autopick method) getAutoSuffix() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) getAvailablePalettes() (pwem.wizards.wizard.ColorScaleDialog method) getAverage() (spider.protocols.protocol_align_apsr.SpiderProtAlignAPSR method) (spider.protocols.protocol_align_base.SpiderProtAlign method) (spider.protocols.protocol_align_pairwise.SpiderProtAlignPairwise method) getAvgSet() (pwem.objects.data.SetOfDefocusGroup method) getBackGroundValue() (resmap.viewers.resmap_viewers.ResMapViewer class 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) getBinning() (tomo3D.viewers.viewer_mrc.MrcPlot 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() (relion.protocols.protocol_extract_particles.ProtRelionExtractParticles 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) getBoxSize() (eman2.convert.dataimport.EmanImport method) (emantomo.convert.dataimport.EmanTomoImport method) (pwem.objects.data.SetOfCoordinates method) (pwem.objects.data_tiltpairs.CoordinatesTiltPair method) (relion.protocols.protocol_autopick.ProtRelionAutopickBase method) (relion.protocols.protocol_autopick_log.ProtRelionAutopickLoG method) (relion.protocols.protocol_autopick_ref.ProtRelion2Autopick method) (tomo.objects.Coordinate3D method) (tomo.objects.SetOfCoordinates3D 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) (tomo.objects.Ellipsoid method) GetChainResidues2WizardChimera (class in chimera.wizards) GetChainResidues2WizardPhenix (class in phenix.wizards) GetChainResiduesWizardChimera (class in chimera.wizards) GetChainResiduesWizardPhenix (class in phenix.wizards) getCheckCommand() (pyworkflow.protocol.hosts.HostConfig method) (pyworkflow.protocol.hosts.QueueSystemConfig method) getChilds() (pyworkflow.utils.graph.Node method) (spider.protocols.protocol_classify_base.DendroNode method) getChimeraScriptFileName1() (chimera.protocols.protocol_contacts.ChimeraProtContacts method) getChimeraScriptFileName2() (chimera.protocols.protocol_contacts.ChimeraProtContacts method) getChimeraX() (in module chimera.getchimera) getCitations() (pyworkflow.protocol.protocol.Protocol method) getClass() (pyworkflow.object.Object method) (pyworkflow.protocol.params.Form method) getClassDir() (spider.protocols.protocol_classify_base.SpiderProtClassify 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 method) getClassPackage() (pyworkflow.protocol.protocol.Protocol class method) getClassPackageName() (chimera.protocols.protocol_base.ChimeraProtBase class method) (chimera.protocols.protocol_contacts.ChimeraProtContacts class method) (chimera.protocols.protocol_subtraction_maps.ChimeraSubtractionMaps class method) (pyworkflow.protocol.protocol.Protocol class method) getClassPlugin() (pyworkflow.protocol.protocol.Protocol class method) getClassRows() (pyworkflow.mapper.sqlite.SqliteFlatDb method) getCLTomoEnviron() (xmipptomo.protocols.protocol_cltomo.XmippProtCLTomo method) getClusterName() (continuousflex.viewers.nma_gui.tk_clustering.ClusteringWindow method) (continuousflex.viewers.nma_vol_gui.tk_clustering_vol.ClusteringWindowVol method) getCmdPath() (in module pwem.utils) getCode() (emxlib.utils.ValidateError method) getCodeSpeedClient() (pwperformance.main.codespeed class method) getCollectivity() (pwem.objects.data.NormalMode method) getColor() (pyworkflow.project.config.Label method) getColorBar() (pyworkflow.gui.plotter.Plotter method) getColorMap() (bsoft.viewers.bsoft_viewers.BsoftViewerBlocres method) (resmap.viewers.resmap_viewers.ResMapViewer method) (xmipp3.viewers.viewer_resolution_directional.XmippMonoDirViewer method) (xmipp3.viewers.viewer_resolution_fso.XmippProtFSOViewer method) (xmipp3.viewers.viewer_resolution_monogenic_signal.XmippMonoResViewer method) (xmipptomo.viewers.viewer_resolution_local_monotomo.XmippMonoTomoViewer method) getColorMapChoices() (resmap.viewers.resmap_viewers.ResMapViewer static method) (xmipp3.viewers.viewer_resolution_directional.XmippMonoDirViewer static method) (xmipp3.viewers.viewer_resolution_fso.XmippProtFSOViewer static method) (xmipp3.viewers.viewer_resolution_monogenic_signal.XmippMonoResViewer static method) (xmipptomo.viewers.viewer_resolution_local_monotomo.XmippMonoTomoViewer static method) getColorMode() (pyworkflow.project.config.ProjectSettings method) getColorPalette() (pwem.wizards.wizard.ColorScaleDialog method) getColorStr() (in module pyworkflow.utils.utils) getColumn() (pyworkflow.utils.dataset.Table method) getColumnKeyByColumnName() (pyworkflow.gui.tree.BoundTree method) getColumnProperty() (pwem.viewers.showj.ColumnsConfig method) getColumns() (deepfinder.viewers.particle_annotator_tree.ParticleAnnotatorProvider method) (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider method) (pyseg.viewers.vesicle_visualization_tree.VesicleViewerProvider 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.viewprotocols.RunIOTreeProvider static method) (pyworkflow.gui.tree.ProjectRunsTreeProvider method) (pyworkflow.gui.tree.TreeProvider method) (pyworkflow.utils.dataset.Table method) (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider method) (tomo.viewers.views_tkinter_tree.MeshesTreeProvider method) (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider method) (tomo.viewers.views_tkinter_tree.TomogramsTreeProvider method) (tomo3D.viewers.views_tkinter_tree.Tomo3DTreeProvider method) (xmipptomo.viewers.monotomo_tree_provider.MonoTomoTreeProvider method) getColumnType() (pwem.viewers.showj.ColumnProperties method) getColumnValues() (pyworkflow.utils.dataset.Table method) getCommand() (cistem.protocols.program_ctffind.ProgramCtffind method) (gctf.protocols.program_gctf.ProgramGctf method) getCommands() (scipion.install.funcs.Target method) getComment() (pyworkflow.gui.dialog.EditObjectDialog method) getCompatiblePipReleases() (scipion.install.plugin_funcs.PluginInfo method) getCondaActivationCmd() (pyworkflow.plugin.Plugin class method) getCondaEnv() (xmipp3.base.XmippProtocol class method) getConfig() (pyworkflow.project.config.ProjectSettings 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) getConvertedInput() (xmipp3.base.XmippProtocol method) getCoordinate() (pwem.objects.data.Particle method) getCoordinate3D() (tomo.objects.SubTomogram method) getCoordinates() (pwem.objects.data.SetOfParticles method) (pyworkflow.gui.canvas.Canvas method) (relion.objects.CtfRefineMicInfo method) getCoordinates3D() (tomo.objects.SetOfSubTomograms method) getCoordinatesOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getCoords() (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (relion.protocols.protocol_export_coords.ProtRelionExportCoordinates method) (relion.protocols.protocol_extract_particles.ProtRelionExtractParticles method) (reliontomo.protocols.protocol_ctf_3d_estimation.ExtendedTS 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() (relion.protocols.protocol_extract_particles.ProtRelionExtractParticles 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) getCoordsDir() (appion.protocols.protocol_dogpicker.DogPickerProtPicking method) (eman2.protocols.protocol_autopick_boxer.EmanProtAutopick method) (eman2.protocols.protocol_boxing.EmanProtBoxing method) (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (relion.protocols.protocol_autopick.ProtRelionAutopickBase 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() (localrec.protocols.protocol_localized_set_origin.ProtLocalOrigSampling method) (pwem.protocols.protocol_import.base.ProtImportFiles method) (pwem.protocols.protocol_import.micrographs.ProtImportMovies method) getCorners() (pyworkflow.gui.canvas.Item method) getCorrectionType() (novactf.protocols.protocol_tomoDefocus.ProtNovaCtfTomoDefocus method) (novactf.protocols.protocol_tomoReconstruction.ProtNovaCtfTomoReconstruction method) getCorrThreshStep() (xmipp3.protocols.protocol_ransac.XmippProtRansac method) getCounter() (ccp4.protocols.protocol_coot.CootRefine method) getCreationTime() (pyworkflow.project.config.ProjectSettings method) (pyworkflow.project.manager.ProjectInfo method) (pyworkflow.project.project.Project method) getCropCornerArg() (xmipp3.protocols.protocol_movie_correlation.XmippProtMovieCorr method) getCryocareEnvActivation() (cryocare.Plugin class method) getCryoloEnvActivation() (sphire.Plugin class method) getCryoloEnvName() (in module sphire.constants) getCryoloGeneralModel() (sphire.Plugin class method) getCryoloGeneralNNModel() (sphire.Plugin class method) getCryoloGeneralNSModel() (sphire.Plugin class method) getCryosparcDir() (in module cryosparc2.utils) getCryosparcEnvInformation() (in module cryosparc2.utils) getCryosparcProgram() (in module cryosparc2.utils) getCryosparcProjectsDir() (in module cryosparc2.utils) getCryosparcUser() (in module cryosparc2.utils) getCryosparcVersion() (in module cryosparc2.utils) getCtf() (cistem.protocols.protocol_ts_ctffind.CistemProtTsCtffind method) (gctf.protocols.protocol_ts_gctf.ProtTsGctf method) getCTF() (pwem.objects.data.Image method) getCtf() (tomo.protocols.protocol_ts_estimate_ctf.ProtTsEstimateCTF method) getCTFMRCList() (reliontomo.protocols.protocol_ctf_3d_estimation.ExtendedTS method) getCtfParamsDict() (pwem.protocols.protocol_micrographs.ProtCTFMicrographs method) (tomo.protocols.protocol_ts_estimate_ctf.ProtTsEstimateCTF method) getCTFSeries() (reliontomo.protocols.protocol_ctf_3d_estimation.ExtendedTS method) (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider method) getCTFStarList() (reliontomo.protocols.protocol_ctf_3d_estimation.ExtendedTS method) getCtfTomoSeriesFromTsId() (imod.protocols.protocol_ctfCorrection.ProtImodCtfCorrection method) (novactf.protocols.protocol_tomoDefocus.ProtNovaCtfTomoDefocus method) getCTFViews() (xmipp2.viewers.viewer.XmippViewer method) (xmipp3.viewers.viewer.XmippViewer method) getCurrentDir() (pyworkflow.gui.browser.FileBrowser method) (pyworkflow.gui.browser.FileBrowserWindow method) getCurrentProtocolView() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) getCutOnFreq() (tomo.objects.CTFTomo method) getCutOnFreqList() (tomo.objects.CTFTomo method) getDark() (pwem.objects.data.SetOfMovies method) (tomo.objects.SetOfTiltSeriesM method) getData() (continuousflex.protocols.data.Point method) (continuousflex.viewers.viewer_image_synthesize.FlexProtSynthesizeImageViewer method) (continuousflex.viewers.viewer_nma_alignment.FlexAlignmentNMAViewer method) (continuousflex.viewers.viewer_nma_alignment_vol.FlexAlignmentNMAVolViewer method) (continuousflex.viewers.viewer_nma_dimred.FlexDimredNMAViewer method) (continuousflex.viewers.viewer_nma_dimred_vol.FlexDimredNMAVolViewer method) (continuousflex.viewers.viewer_subtomograms_synthesize.FlexProtSynthesizeSubtomoViewer method) (emfacilities.protocols.protocol_monitor_ctf.MonitorCTF method) (emfacilities.protocols.protocol_monitor_movie_gain.MonitorMovieGain method) (emfacilities.protocols.protocol_monitor_system.MonitorSystem method) (pwem.objects.data.FSC method) (xmipp3.utils.Point method) (xmipp3.viewers.viewer_analyze_local_ctf.XmippAnalyzeLocalCTFViewer method) (xmipp3.viewers.viewer_angular_alignment_sph.XmippAngularAlignmentSphViewer method) getDataBaseName() (chimera.protocols.protocol_contacts.ChimeraProtContacts method) getDataChoice() (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) getDataHtml() (emfacilities.protocols.protocol_monitor_ctf.MonitorCTF method) (emfacilities.protocols.protocol_monitor_movie_gain.MonitorMovieGain method) (emfacilities.protocols.protocol_monitor_system.MonitorSystem method) getDataInflux() (emfacilities.protocols.protocol_monitor_ctf.MonitorCTF method) (emfacilities.protocols.protocol_monitor_movie_gain.MonitorMovieGain method) (emfacilities.protocols.protocol_monitor_system.MonitorSystem 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) getDeepFinderCmd() (deepfinder.Plugin class method) getDeepFinderEnvActivation() (deepfinder.Plugin class method) getDeepFinderProgram() (deepfinder.Plugin class 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) getDefocusAngleList() (tomo.objects.CTFTomo method) getDefocusAvg() (pwem.objects.data.DefocusGroup method) (pwem.objects.data.SetOfDefocusGroups method) getDefocusFileFlag() (in module imod.utils) 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) getDefocusUDeviation() (tomo.objects.CTFTomo method) getdefocusUDeviation() (tomo.objects.CTFTomo method) getDefocusUList() (tomo.objects.CTFTomo method) getDefocusV() (pwem.objects.data.CTFModel method) getDefocusVDeviation() (tomo.objects.CTFTomo method) getdefocusVDeviation() (tomo.objects.CTFTomo method) getDefocusVList() (tomo.objects.CTFTomo method) getDeformationFile() (continuousflex.protocols.protocol_nma_dimred.FlexProtDimredNMA method) (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) (continuousflex.protocols.protocol_pdb_dimred.FlexProtDimredPdb method) (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify method) getDenoiseArgs() (topaz.protocols.protocol_base.ProtTopazBase method) getDependencies() (cryocare.Plugin class method) (deepfinder.Plugin class method) (imod.Plugin class method) (novactf.Plugin class method) (sphire.Plugin class method) (topaz.Plugin class method) getDeps() (scipion.install.funcs.Target method) getDescription() (pwem.objects.data.Sequence method) (pyworkflow.template.Template static method) (tomo.objects.MeshPoint method) getDFEnvName() (in module deepfinder.constants) getDim() (pwem.objects.data.Image method) (pwem.objects.data.Movie method) (pwem.objects.data.SetOfImages method) (pwem.objects.data.Volume method) (tomo.objects.Tomogram method) getDimensions() (pwem.emlib.image.image_handler.ImageHandler 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() (continuousflex.protocols.data.Data method) (xmipp3.utils.Data method) getDistro() (pyworkflow.gui.project.utils.OS class method) getDoc() (pyworkflow.object.Object class method) getDocsLink() (in module spider.utils) getDomain() (pyworkflow.config.Config class method) (pyworkflow.project.project.Project method) getDoneMics() (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) getDoseFile() (reliontomo.protocols.protocol_ctf_3d_estimation.ExtendedTS method) getDoseFileNmae() (reliontomo.protocols.protocol_ctf_3d_estimation.DoseFile method) getDoseInitial() (pwem.objects.data.Acquisition method) getDosePerFrame() (pwem.objects.data.Acquisition method) getDoses() (reliontomo.protocols.protocol_ctf_3d_estimation.DoseFile method) (reliontomo.protocols.protocol_ctf_3d_estimation.ExtendedTS method) getDownsample() (pwem.wizards.wizard.CtfDialog method) (pwem.wizards.wizard.CtfDownsampleDialog method) (pwem.wizards.wizard.DownsampleDialog method) getDynamoProgram() (dynamo.Plugin class method) getEdges() (pwem.convert.symmetry.Icosahedron method) getElapsedTime() (pwperformance.main.Timer method) (pyworkflow.project.project.Project method) (pyworkflow.protocol.protocol.Step method) (pyworkflow.utils.utils.Timer method) getEm() (scipion.install.funcs.Environment static method) getEmanActivation() (emantomo.Plugin class method) getEmanCommand() (eman2.Plugin class method) (emantomo.Plugin class method) getEmanDependencies() (locscale.Plugin class method) getEmanPlugin() (locscale.Plugin class method) getEmanPythonProgram() (in module locscale.convert) getEmanVersion() (in module locscale.convert) 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) getEnv() (in module pwperformance.main) getEnvDictionary() (in module chimera.utils) getEnviron() (appion.Plugin class method) (atsas.Plugin class method) (bamfordlab.Plugin class method) (bsoft.Plugin class method) (ccp4.Plugin class method) (chimera.Plugin class method) (cistem.Plugin class method) (continuousflex.Plugin class method) (cryocare.Plugin class method) (cryoef.Plugin class method) (cryosparc2.Plugin class method) (deepfinder.Plugin class method) (dynamo.Plugin class method) (eman2.Plugin class method) (emantomo.Plugin class method) (emfacilities.Plugin class method) (emxlib.Plugin class method) (fsc3d.Plugin class method) (gautomatch.Plugin class method) (gctf.Plugin class method) (imod.Plugin class method) (in module pwem.convert.atom_struct) (localrec.Plugin class method) (locscale.Plugin class method) (motioncorr.Plugin class method) (novactf.Plugin class method) (phenix.Plugin class method) (pwem.viewers.viewer_chimera.Chimera class method) (pwem.viewers.viewer_vmd.Vmd class method) (pyseg.Plugin class method) (pyworkflow.plugin.Plugin class method) (relion.Plugin class method) (reliontomo.Plugin class method) (resmap.Plugin class method) (sidesplitter.Plugin class method) (sphire.Plugin class method) (spider.Plugin class method) (tomo.Plugin class method) (tomoj.Plugin class method) (topaz.Plugin class method) (xmipp2.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) getEven() (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) getEvenSet() (tomo.viewers.viewers_data.TSMotionCorrectionViewer method) getExpectedDefocus() (imod.protocols.protocol_ctfEstimation_automatic.ProtImodAutomaticCtfEstimation method) getExt() (gctf.protocols.program_gctf.ProgramGctf method) (in module pyworkflow.utils.path) (spider.protocols.protocol_base.SpiderProtocol method) 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) getExtraLogInfo() (in module pyworkflow.utils.log) getfamaddr() (in module emfacilities.protocols.getnifs) getFigure() (pyworkflow.gui.matplotlib_image.FigureFrame method) (pyworkflow.gui.plotter.Plotter method) getFile() (in module chimera.getchimera) (pyworkflow.tests.tests.DataSet method) getFileActions() (imod.file_handlers.ImodHandler method) (pwem.viewers.filehandlers.ChimeraHandler method) (pwem.viewers.filehandlers.ImageFileHandler method) (pyworkflow.gui.browser.FileHandler method) getFileFormat() (in module pwem.convert.headers) getFileHandlers() (pyworkflow.gui.browser.FileTreeProvider method) getFileIcon() (imod.file_handlers.ImodHandler method) (pwem.viewers.filehandlers.ChimeraHandler 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) (spider.objects.PcaFile method) (tomo.objects.LandmarkModel method) (tomo.protocols.protocol_ts_import.MDoc method) getFileNameNoisyStk() (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoiseParticles method) getFilePath() (imod.protocols.protocol_ctfEstimation_manual.ProtImodManualCtfEstimation method) (imod.protocols.protocol_etomo.ProtImodEtomo method) getFilePreview() (pwem.viewers.filehandlers.ImageFileHandler method) (pwem.viewers.filehandlers.MdFileHandler method) (pyworkflow.gui.browser.FileHandler method) getFiles() (eman2.protocols.protocol_autopick_boxer.EmanProtAutopick method) (eman2.protocols.protocol_boxing.EmanProtBoxing method) (in module pyworkflow.utils.path) (pwem.objects.data.EMObject method) (pwem.objects.data.EMSet method) (pwem.objects.data.Image 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) (tomo.objects.SetOfCoordinates3D method) getFileSize() (in module pyworkflow.utils.path) getFileTag() (pyworkflow.protocol.protocol.Protocol method) getFilterArgs() (bsoft.protocols.protocol_bfilter.BsoftProtBfilter method) getFinalCorrectionImagePath() (pwem.protocols.protocol_movies.ProtProcessMovies method) getFinalGainPath() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getFinalMaskFileName() (in module pyseg.utils) 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) (pyworkflow.object.Set method) (tomo.objects.SetOfCTFTomoSeries method) (tomo.objects.SetOfCoordinates3D method) (tomo.objects.SetOfTiltSeriesBase method) getFirstLine() (in module pyworkflow.apps.pw_protocol_list) getFirstObject() (emxlib.utils.EmxData method) getFirstRow() (in module pwem.emlib.metadata.utils) getFitQuality() (pwem.objects.data.CTFModel method) getFlagArg() (in module scipion.scripts.kickoff) getFlippedOrientedGainPath() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getFlipYHeight() (in module sphire.convert) getFloatListFromValues() (in module pyworkflow.utils.utils) getFnPath() (localrec.protocols.protocol_localized_set_origin.ProtLocalOrigSampling method) (pwem.protocols.protocol_export.protocol_export_DB.ProtExportDataBases method) (pwem.protocols.protocol_origin_sampling_volume.ProtOrigSampling method) getFormat() (pwem.objects.data.Image method) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) (pwem.protocols.protocol_import.ctfs.ProtImportCTF method) (tomo.protocols.protocol_import_coordinates.ProtImportCoordinates3D method) getFormula() (pwem.wizards.wizard.FormulaDialog method) getFrameId() (pwem.objects.data.MovieParticle method) getFramesRange() (pwem.objects.data.Movie method) (pwem.objects.data.SetOfMovies method) (tomo.objects.SetOfTiltSeriesM 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) getFSCEnvActivation() (fsc3d.Plugin class method) getFullID() (pwem.convert.atom_struct.AtomicStructHandler method) getFullName() (pyworkflow.mapper.mapper.Mapper method) getGain() (pwem.objects.data.SetOfMovies method) (tomo.objects.SetOfTiltSeriesM method) getGainAndDark() (pwem.protocols.protocol_movies.ProtProcessMovies method) (tomo.protocols.protocol_ts_correct_motion.ProtTsCorrectMotion method) getGeometry() (in module pyworkflow.gui.gui) getGPUArgs() (xmipp3.protocols.protocol_movie_correlation.XmippProtMovieCorr method) getGpuLib() (resmap.Plugin class 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) getGroup() (relion.convert.DefocusGroups method) getGroupByCTF() (pwem.objects.data.SetOfDefocusGroups method) getGroupByName() (pwem.objects.data.SetOfDefocusGroups method) getGroupId() (tomo.objects.Coordinate3D 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) (spider.wizards.SpiderFilterDialog 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) getHomeFromVersion() (bsoft.Plugin class method) getHomePage() (pyworkflow.plugin.PluginInfo method) (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) getHTMLReportText() (emfacilities.protocols.report_html.ReportHtml method) getId() (continuousflex.protocols.data.Point method) (pwem.objects.data.Sequence method) (pyworkflow.project.config.Label 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) (pyworkflow.gui.canvas.Canvas method) (pyworkflow.gui.dialog.Dialog method) (pyworkflow.gui.gui.Window method) (pyworkflow.gui.tree.Tree method) (spider.protocols.protocol_classify_base.SpiderProtClassifyCluster method) getImageDimensions() (in module eman2.convert.convert) (in module emantomo.convert.convert) getImageFromPath() (in module pwem.viewers.filehandlers) getImageLocation() (in module sidesplitter.convert) (in module xmipp3.convert.convert) getImagePath() (pwem.viewers.views.ImageView method) getImages() (pwem.objects.data.SetOfClasses method) getImagesClass() (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) getImagesType() (xmipp3.protocols.protocol_trigger_data.XmippProtTriggerData method) getImgData() (bsoft.viewers.bsoft_viewers.BsoftViewerBlocres method) (pwem.viewers.viewer_localres.LocalResolutionViewer method) (resmap.viewers.resmap_viewers.ResMapViewer method) getImodCmd() (imod.Plugin class method) getImodCTFEstimationColumnValues() (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider method) getIMODDefocusFileFlag() (tomo.objects.CTFTomoSeries method) getImodEtomoColumnValues() (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider 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) (tomo.protocols.protocol_import_coordinates.ProtImportCoordinates3D method) getImportFrom() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) (tomo.protocols.protocol_import_coordinates.ProtImportCoordinates3D method) getIncludeFolder() (scipion.install.funcs.Environment static method) getIncomingDose() (tomo.protocols.protocol_ts_import.TiltMetadata method) getIndex() (emfacilities.protocols.getnifs.NetworkInterface method) (pwem.objects.data.Image method) (pyworkflow.gui.text.TextFileViewer method) (pyworkflow.gui.widgets.ComboBox method) (pyworkflow.protocol.protocol.Step method) (pyworkflow.template.TemplateParam method) (tomo.objects.CTFTomo method) getIndexFromValue() (pyworkflow.utils.dataset.Table method) getInfo() (emantomo.protocols.protocol_tomo_boxing_convnet.EmanProtTomoConvNet method) (emantomo.protocols.protocol_tomo_fill_mw.EmanProtTomoFillMW 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.PythonTopRankWizard method) getInputConnectorCoordinates() (pyworkflow.gui.canvas.Item method) getInputDimA() (relion.protocols.protocol_autopick_ref.ProtRelion2Autopick method) getInputGain() (relion.protocols.protocol_compress_movies.ProtRelionCompressMovies method) (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getInputMicrographs() (cistem.protocols.protocol_picking.CistemProtFindParticles method) (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) (relion.protocols.protocol_autopick.ProtRelionAutopickBase method) (relion.protocols.protocol_extract_particles.ProtRelionExtractParticles 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) getInputMicrographsPointer() (pwem.protocols.protocol_micrographs.ProtCTFMicrographs method) (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (relion.protocols.protocol_autopick.ProtRelionAutopickBase method) (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) (xmipp3.protocols.protocol_pick_noise.XmippProtPickNoise method) getInputMicsFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getInputModel() (sphire.protocols.protocol_cryolo_picking.SphireProtCRYOLOPicking method) (sphire.protocols.protocol_cryolo_training.SphireProtCRYOLOTraining method) (sphire.protocols.protocol_janni_denoise.SphireProtJanniDenoising method) getInputMovies() (cistem.protocols.protocol_unblur.CistemProtUnblur method) (motioncorr.protocols.protocol_motioncorr.ProtMotionCorr method) getInputParticles() (continuousflex.protocols.protocol_nma_dimred.FlexProtDimredNMA method) (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) getInputPdb() (continuousflex.protocols.protocol_image_synthesize.FlexProtSynthesizeImages method) (continuousflex.protocols.protocol_nma_alignment.FlexProtAlignmentNMA method) (continuousflex.protocols.protocol_nma_alignment_vol.FlexProtAlignmentNMAVol method) (continuousflex.protocols.protocol_nma_dimred.FlexProtDimredNMA method) (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) (continuousflex.protocols.protocol_subtomogrmas_synthesize.FlexProtSynthesizeSubtomo method) getInputPdbs() (continuousflex.protocols.protocol_pdb_dimred.FlexProtDimredPdb method) getInputProtocols() (emfacilities.protocols.protocol_monitor.ProtMonitor method) getInputReferences() (cistem.protocols.protocol_picking.CistemProtFindParticles method) (relion.protocols.protocol_autopick_ref.ProtRelion2Autopick 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() (emxlib.protocols.protocol_export.ProtEmxExport method) getInputStatus() (pyworkflow.protocol.protocol.Protocol method) getInputSubTomos() (tomo.protocols.protocol_extract_coordinates.ProtTomoExtractCoords method) getInputTomograms() (dynamo.protocols.protocol_extraction.DynamoExtraction method) getInputTomos() (tomo.protocols.protocol_extract_coordinates.ProtTomoExtractCoords method) getInstallenv() (scipion.install.plugin_funcs.PluginInfo method) getInstallPath() (in module scipion.utils) getInstancesCount() (in module pyworkflow.utils.profiler) getInteractionFileName() (chimera.viewers.viewer_contacts.ChimeraProtContactsViewer method) getIntervals() (pwem.wizards.wizard.ColorScaleDialog method) getIsAminoacids() (pwem.objects.data.Sequence method) getIsDefocusUDeviationInRange() (tomo.objects.CTFTomo method) (tomo.objects.CTFTomoSeries method) getIsDefocusVDeviationInRange() (tomo.objects.CTFTomo method) (tomo.objects.CTFTomoSeries method) getISPG() (pwem.convert.headers.Ccp4Header method) getItem() (pwem.wizards.wizard.FormulaDialog 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) getJanniGeneralModel() (sphire.Plugin class method) getJavaIJappArguments() (in module pwem.viewers.showj) getJobDoneRegex() (pyworkflow.protocol.hosts.HostConfig method) getJobId() (pyworkflow.protocol.protocol.Protocol method) getJobLog() (in module cryosparc2.utils) getJobStatus() (in module cryosparc2.utils) getJvmMaxMemory() (in module pwem.viewers.showj) getKeywords() (pyworkflow.plugin.PluginInfo 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() (emfacilities.protocols.protocol_monitor_system.MonitorSystem method) (pyworkflow.project.config.NodeConfig method) (pyworkflow.project.config.ProjectSettings method) getLandmarkModelFromTsId() (tomo.objects.SetOfLandmarkModels method) getLastEpochModel() (topaz.protocols.protocol_base.ProtTopazBase method) getLastFile() (in module pyworkflow.utils.path) getLastFinishedIter() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) getLastFrame() (pwem.objects.data.FramesRange method) getLastFromOutputPath() (emantomo.protocols.protocol_tomo_subtomogram_refinement.EmanProtTomoRefinement method) getLastIter() (xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch method) getLastIteration() (xmipp3.protocols.protocol_reconstruct_significant.XmippProtReconstructSignificant method) getLastName() (pyworkflow.object.Object method) getLastOutputFolder() (emantomo.protocols.protocol_tomo_subtomogram_refinement.EmanProtTomoRefinement method) getLastParticlesParams() (in module eman2.convert.convert) (in module emantomo.convert.convert)

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) getLicenseURLwithFile() (in module chimera.getchimera) getLifeTime() (pyworkflow.project.config.ProjectSettings method) getLineInFile() (in module pyworkflow.utils.utils) getListFromRangeString() (in module pyworkflow.utils.utils) getListFromValues() (in module pyworkflow.utils.utils) 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) (spider.wizards.SpiderFilterDialog 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) (tomo.protocols.protocol_ts_import.MDoc method) getMagnificationType() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) getMainInput() (tomo3D.protocols.protocol_particle_pick_consensus.ProtTomoConsensusPicking method) (tomo3D.protocols.protocol_particle_pick_remove_duplicates.ProtTomoPickingRemoveDuplicates method) (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking method) (xmipp3.protocols.protocol_particle_pick_remove_duplicates.XmippProtPickingRemoveDuplicates 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() (tomo.protocols.protocol_ts_import.ProtImportTsBase method) getMatchingMic() (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates method) getMatlabEnviron() (xmipp3.Plugin class method) getMatrix() (pwem.objects.data.Matrix method) (pwem.objects.data.Transform method) (tomo.objects.Coordinate3D method) getMatrixAsList() (pwem.objects.data.Transform method) getMaxCores() (pyworkflow.protocol.hosts.QueueConfig method) getMaxHours() (pyworkflow.protocol.hosts.QueueConfig method) getMaxitBin() (pwem.Plugin class method) getMaxitHome() (pwem.Plugin class method) getMaxSet() (pwem.objects.data.SetOfDefocusGroup method) getMaxXY() (relion.objects.CtfRefineGlobalInfo method) getMdFirstRow() (in module xmipp3.base) getMembraneCenterStep() (pyseg.protocols.protocol_pre_seg.ProtPySegPreSegParticles method) getMemoryAvailable() (in module pyworkflow.utils.utils) getMeshVolFileName() (in module tomo.convert.convert) getMessage() (emxlib.utils.ValidateError method) (pyworkflow.viewer.MessageView method) getMethodName() (continuousflex.protocols.protocol_nma_dimred.FlexProtDimredNMA method) (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) getMethods() (deepfinder.protocols.protocol_segment.DeepFinderSegment method) (dynamo.protocols.protocol_boxing.DynamoBoxing method) (emantomo.protocols.protocol_tomo_boxing.EmanProtTomoBoxing method) (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) getMicCTF() (pwem.protocols.protocol_import.dataimport.ScipionImport method) getMicFromMovie() (xmipp3.protocols.protocol_movie_max_shift.XmippProtMovieMaxShift method) getMicId() (pwem.objects.data.Coordinate method) (pwem.objects.data.Particle method) (xmipp3.protocols.protocol_particle_pick_consensus.XmippProtConsensusPicking class method) getMicIdName() (in module sphire.convert) (in module topaz.convert) getMicName() (pwem.objects.data.Coordinate method) (pwem.objects.data.Micrograph method) getMicNameOrId() (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) getMicrograph() (emxlib.utils.EmxParticle method) (pwem.objects.data.CTFModel method) (pwem.objects.data.Coordinate method) getMicrographFnsWithCoordinates() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getMicrographList() (relion.protocols.protocol_autopick.ProtRelionAutopickBase method) (relion.protocols.protocol_autopick_ref.ProtRelion2Autopick method) getMicrographs() (pwem.objects.data.SetOfCoordinates method) (pwem.objects.data.SetOfCTF method) getMicrographsDir() (gautomatch.protocols.protocol_gautomatch.ProtGautomatch 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) getMicsWorkingDir() (sphire.protocols.protocol_cryolo_picking.SphireProtCRYOLOPicking method) getMinMax() (bsoft.protocols.protocol_blocres.BsoftProtBlocres method) (xmipp3.protocols.protocol_resolution_deepres.XmippProtDeepRes method) (xmipp3.protocols.protocol_resolution_monogenic_signal.XmippProtMonoRes method) (xmipptomo.protocols.protocol_resolution_local_monotomo.XmippProtMonoTomo method) getMinSet() (pwem.objects.data.SetOfDefocusGroup method) getMLTomoEnviron() (xmipp3.protocols.protocol_mltomo.XmippProtMLTomo method) getModeFile() (pwem.objects.data.NormalMode method) getModel() (xmipp3.base.XmippProtocol class method) getModelName() (tomo.objects.LandmarkModel method) getModels() (in module ccp4.protocols.protocol_coot) getModelsChains() (pwem.convert.atom_struct.AtomicStructHandler method) getModelsChainsStep() (pwem.wizards.wizards.GetStructureChainsWizard class method) getModesCondition() (xmipp3.protocols.protocol_preprocess.protocol_filter.XmippFilterHelper class method) getModeToOutput() (imod.protocols.protocol_tomoNormalization.ProtImodTomoNormalization method) (imod.protocols.protocol_tsNormalization.ProtImodTSNormalization 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 motioncorr.convert) (in module xmipp3.convert.convert) getMpiCommand() (pyworkflow.protocol.hosts.HostConfig method) getName() (emfacilities.protocols.getnifs.NetworkInterface method) (pwem.viewers.showj.ColumnProperties method) (pyworkflow.object.Object method) (pyworkflow.plugin.Domain class method) (pyworkflow.plugin.Plugin class method) (pyworkflow.project.config.Label method) (pyworkflow.project.manager.ProjectInfo method) (pyworkflow.project.project.Project method) (pyworkflow.protocol.hosts.QueueConfig 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) (scipion.install.funcs.Target method) getNamedFont() (in module pyworkflow.gui.gui) getNameId() (pyworkflow.object.Object method) getNbOfClasses() (deepfinder.objects.DeepFinderNet method) getNestedValue() (pyworkflow.object.Object method) getNewImgSize() (relion.protocols.protocol_extract_particles.ProtRelionExtractParticles method) getNifsNameList() (emfacilities.protocols.protocol_monitor_system.MonitorSystem class method) getNMAEnviron() (in module continuousflex.protocols.convert) getNNModelFn() (topaz.protocols.protocol_topaz_training.TopazProtTraining method) getNode() (pyworkflow.project.config.NodeConfigList method) (pyworkflow.utils.graph.Graph method) getNodeById() (pyworkflow.project.config.ProjectSettings method) getNodes() (pyworkflow.project.config.ProjectSettings method) (pyworkflow.utils.graph.Graph method) getNumberOfClasses() (spider.protocols.protocol_classify_base.SpiderProtClassify method) (spider.protocols.protocol_classify_kmeans.SpiderProtClassifyKmeans method) getNumberOfColumns() (pyworkflow.utils.dataset.Table method) getNumberOfEstimationsInRange() (tomo.objects.CTFTomoSeries method) getNumberOfFrames() (pwem.objects.data.Movie method) getNumberOfIntermediateStacksStep() (novactf.protocols.protocol_tomoDefocus.ProtNovaCtfTomoDefocus method) getNumberOfMeshes() (tomo.objects.SetOfMeshes method) getNumberOfObjects() (pwem.convert.headers.Ccp4Header method) getNumberOfPreviousIterations() (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) getNumberOfReconstructedVolumes() (xmipp3.protocols.protocol_reconstruct_heterogeneous.XmippProtReconstructHeterogeneous 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() (pwem.protocols.protocol_sets.ProtUnionSet method) (pyworkflow.object.Object method) getObject() (emxlib.utils.EmxData method) (pyworkflow.project.project.Project method) getObjectActions() (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider method) (pyworkflow.gui.browser.FileTreeProvider method) (pyworkflow.gui.form.SubclassesTreeProvider method) (pyworkflow.gui.project.labels.LabelsTreeProvider method) (pyworkflow.gui.project.viewprotocols.RunIOTreeProvider method) (pyworkflow.gui.project.viewprotocols.RunsTreeProvider method) (pyworkflow.gui.tree.ObjectTreeProvider method) (pyworkflow.gui.tree.TreeProvider method) (tomo.viewers.views_tkinter_tree.MeshesTreeProvider method) (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider method) (tomo.viewers.views_tkinter_tree.TomogramsTreeProvider method) (tomo3D.viewers.views_tkinter_tree.Tomo3DTreeProvider method) (xmipptomo.viewers.monotomo_tree_provider.MonoTomoTreeProvider method) getObjectFromId() (pyworkflow.gui.tree.BoundTree method) (pyworkflow.gui.tree.ProjectRunsTreeProvider method) getObjectInfo() (deepfinder.viewers.particle_annotator_tree.ParticleAnnotatorProvider method) (emfacilities.protocols.summary_provider.SummaryProvider method) (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider method) (pyseg.viewers.vesicle_visualization_tree.VesicleViewerProvider method) (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.viewprotocols.RunIOTreeProvider method) (pyworkflow.gui.project.viewprotocols.StepsTreeProvider static 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) (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider method) (tomo.viewers.views_tkinter_tree.MeshesTreeProvider method) (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider method) (tomo.viewers.views_tkinter_tree.TomogramsTreeProvider method) (tomo3D.viewers.views_tkinter_tree.Tomo3DTreeProvider method) (xmipptomo.viewers.monotomo_tree_provider.MonoTomoTreeProvider method) getObjectLabel() (in module pyworkflow.gui.form) (pyworkflow.gui.project.viewprotocols.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.viewprotocols.RunIOTreeProvider static method) (pyworkflow.gui.project.viewprotocols.StepsTreeProvider static method) (pyworkflow.gui.tree.ObjectTreeProvider method) (pyworkflow.gui.tree.TreeProvider method) (tomo.viewers.views_tkinter_tree.TomogramsTreeProvider method) (tomo3D.viewers.views_tkinter_tree.Tomo3DTreeProvider method) getObjects() (emfacilities.protocols.summary_provider.SummaryProvider method) (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider method) (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.viewprotocols.RunIOTreeProvider method) (pyworkflow.gui.project.viewprotocols.StepsTreeProvider method) (pyworkflow.gui.tree.ObjectTreeProvider method) (pyworkflow.gui.tree.ProjectRunsTreeProvider method) (pyworkflow.gui.tree.TreeProvider method) (pyworkflow.plugin.Domain class method) (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider method) (tomo.viewers.views_tkinter_tree.MeshesTreeProvider method) (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider method) (tomo.viewers.views_tkinter_tree.TomogramsTreeProvider method) (tomo3D.viewers.views_tkinter_tree.Tomo3DTreeProvider method) (xmipptomo.viewers.monotomo_tree_provider.MonoTomoTreeProvider 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() (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider method) (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) (xmipp3.utils.DeprecatedParam method) getOddSet() (tomo.viewers.viewers_data.TSMotionCorrectionViewer 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) (tomo.objects.TiltSeriesBase method) getOutpuCBOXtDir() (sphire.protocols.protocol_cryolo_picking.SphireProtCRYOLOPicking method) getOutput() (relion.protocols.protocol_extract_particles.ProtRelionExtractParticles method) (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) (xmipp3.protocols.protocol_extract_particles.XmippProtExtractParticles method) (xmipp3.protocols.protocol_extract_particles_pairs.XmippProtExtractParticlesPairs method) getOutputAssignedTransformSetOfTiltSeries() (tomo.protocols.protocol_assignTransformationTS.ProtAssignTransformationMatrixTiltSeries method) getOutputConnectorCoordinates() (pyworkflow.gui.canvas.Item method) getOutputDISTRDir() (sphire.protocols.protocol_cryolo_picking.SphireProtCRYOLOPicking method) getOutputEvenSetOfTiltSeries() (xmipptomo.protocols.protocol_splitTS.XmippProtSplitTiltSeries method) getOutputFailedSetOfTiltSeries() (imod.protocols.protocol_base.ProtImodBase method) getOutputFiducialModelGaps() (imod.protocols.protocol_base.ProtImodBase method) getOutputFiducialModelNoGaps() (imod.protocols.protocol_base.ProtImodBase method) getOutputFile() (emantomo.protocols.protocol_tomo_subtomogram_refinement.EmanProtTomoRefinement method) getOutputFiles() (pyworkflow.protocol.protocol.Protocol method) getOutputFn() (locscale.protocols.protocol_locscale.ProtLocScale method) getOutputGain() (relion.protocols.protocol_compress_estimate_gain.ProtRelionCompressEstimateGain method) getOutputInterpolatedSetOfTiltSeries() (imod.protocols.protocol_base.ProtImodBase method) (jjsoft.protocols.protocol_align_ts.ProtJjsoftAlignTs method) (tomoj.protocols.protocol_xCorrPrealignment.ProtTomojXcorrPrealignment method) (xmipptomo.protocols.protocol_applyAlignmentTS.XmippProtApplyTransformationMatrixTS method) (xmipptomo.protocols.protocol_misalignTS.XmippProtMisalignTiltSeries method) getOutputLocalResolutionSetOfTomograms() (xmipptomo.protocols.protocol_resolution_local_monotomo.XmippProtMonoTomo method) getOutputMatrixFile() (continuousflex.protocols.protocol_nma_dimred.FlexProtDimredNMA method) (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) (continuousflex.protocols.protocol_pdb_dimred.FlexProtDimredPdb method) (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify method) getOutputMisalignedSetOfTiltSeries() (xmipptomo.protocols.protocol_misalignTS.XmippProtMisalignTiltSeries method) getOutputModelPath() (sphire.protocols.protocol_cryolo_training.SphireProtCRYOLOTraining method) (topaz.protocols.protocol_base.ProtTopazBase method) getOutputName() (gautomatch.protocols.protocol_gautomatch.ProtGautomatch method) (xmipp3.protocols.protocol_deep_micrograph_screen.XmippProtDeepMicrographScreen method) getOutputOddSetOfTiltSeries() (xmipptomo.protocols.protocol_splitTS.XmippProtSplitTiltSeries method) getOutputPath() (emantomo.protocols.protocol_tomo_initialmodel.EmanProtTomoInitialModel method) (emantomo.protocols.protocol_tomo_subtomogram_refinement.EmanProtTomoRefinement method) (pyworkflow.tests.tests.BaseTest class method) getOutputSetOfCoordinates3Ds() (imod.protocols.protocol_base.ProtImodBase method) getOutputSetOfCTFTomoSeries() (imod.protocols.protocol_base.ProtImodBase method) (xmipptomo.protocols.protocol_rotate_astigmatism.XmippProtRotateAstigmatism method) getOutputSetOfTiltSeries() (emantomo.protocols.protocol_align_ts.EmanProtAlignTs method) (imod.protocols.protocol_base.ProtImodBase method) (tomoj.protocols.protocol_xCorrPrealignment.ProtTomojXcorrPrealignment method) (xmipptomo.protocols.protocol_resizeTS.XmippProtResizeTiltSeries method) getOutputSetOfTomograms() (imod.protocols.protocol_base.ProtImodBase method) (novactf.protocols.protocol_tomoReconstruction.ProtNovaCtfTomoReconstruction method) (xmipptomo.protocols.protocol_resize_tomograms.XmippProtResizeTomograms method) getOutputSetOfXraysErasedTiltSeries() (imod.protocols.protocol_goldBeadEraser.ProtImodGoldBeadEraser method) getOutputsSize() (pyworkflow.protocol.protocol.Protocol method) getOutsideModeArg() (xmipp3.protocols.protocol_movie_correlation.XmippProtMovieCorr 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) getPairChainsFileName() (chimera.viewers.viewer_contacts.ChimeraProtContactsViewer method) getParam() (pyworkflow.protocol.params.Form method) (pyworkflow.protocol.protocol.Protocol 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) getParticlesMD() (continuousflex.protocols.protocol_nma_dimred.FlexProtDimredNMA method) (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) getParticlesOutput() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getPassword() (pyworkflow.protocol.hosts.HostConfig method) getPatchSize() (cryocare.objects.CryocareTrainData method) getPath() (cryocare.objects.CryocareModel method) (deepfinder.objects.DeepFinderNet method) (pwem.viewers.views.DataView method) (pyworkflow.gui.browser.FileInfo method) (pyworkflow.project.project.Project method) (pyworkflow.tests.tests.DataSet method) (sphire.objects.CryoloModel method) (topaz.objects.TopazModel method) getPattern() (pwem.protocols.protocol_import.base.ProtImportFiles method) getPdb() (pwem.objects.data.SetOfNormalModes method) getPhaseShift() (pwem.objects.data.CTFModel method) getPhaseShiftList() (tomo.objects.CTFTomo method) getPhenixVersion() (phenix.Plugin class method) getPickingFileName() (topaz.protocols.protocol_topaz_picking.TopazProtPicking method) (topaz.protocols.protocol_topaz_training.TopazProtTraining method) getPid() (pyworkflow.protocol.protocol.Protocol method) getPILImage() (in module pwem.viewers.filehandlers) getPipJsonData() (scipion.install.plugin_funcs.PluginInfo method) getPipName() (scipion.install.plugin_funcs.PluginInfo method) getPipVersion() (scipion.install.plugin_funcs.PluginInfo method) getPixelSizeLabel() (in module relion.convert.convert31) getPixSizeFromDimensions() (imod.protocols.protocol_etomo.ProtImodEtomo method) getPlatform() (pyworkflow.gui.project.utils.OS static method) getPlot1DCallback() (tomo.viewers.viewers_data.CtfEstimationTomoViewer method) getPlot2DCallback() (tomo.viewers.viewers_data.CtfEstimationTomoViewer method) getPlotSubtitle() (in module cistem.viewers) (in module gctf.viewers) getPlugin() (pyworkflow.plugin.Domain class method) getPluginClass() (scipion.install.plugin_funcs.PluginInfo method) getPluginLogoPath() (pyworkflow.protocol.protocol.Protocol 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 class method) getPngData() (in module pyworkflow.gui.matplotlib_image) getPoint() (continuousflex.protocols.data.Data method) (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) (tomo.objects.Coordinate3D method) getPossibleOutputs() (pyworkflow.protocol.protocol.Protocol method) getPrecedents() (tomo.objects.SetOfCoordinates3D 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) getPreprocessArgs() (topaz.protocols.protocol_base.ProtTopazBase method) getPreprocessedMicFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getPreProcParamsFromForm() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getPrerequisites() (pyworkflow.protocol.protocol.Step method) getPresegOutputFile() (pyseg.protocols.protocol_pre_seg.ProtPySegPreSegParticles 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) getProgram() (atsas.Plugin class method) (bamfordlab.Plugin class method) (bsoft.Plugin class method) (ccp4.Plugin class method) (chimera.Plugin class method) (cistem.Plugin class method) (cryoef.Plugin class method) (eman2.Plugin class method) (emantomo.Plugin class method) (gautomatch.Plugin class method) (gctf.Plugin class method) (motioncorr.Plugin class method) (phenix.Plugin class method) (pwem.viewers.viewer_chimera.Chimera class method) (resmap.Plugin class method) (sidesplitter.Plugin class method) (spider.Plugin class 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) getProjectionRange() (imod.protocols.protocol_tomoProjection.ProtImodTomoProjection method) getProjectName() (in module cryosparc2.utils) getProjectorFile() (continuousflex.protocols.protocol_nma_dimred.FlexProtDimredNMA method) (continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol method) getProjectPath() (in module cryosparc2.utils) (pyworkflow.project.manager.Manager method) getProperty() (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) getProtocolClass() (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider method) getProtocolFromDb() (in module pyworkflow.protocol.protocol) 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) getProtocolTag() (pyworkflow.gui.project.viewprotocols.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) getPsdName() (cistem.protocols.protocol_ts_ctffind.CistemProtTsCtffind method) getPseudoAtoms() (pwem.objects.data.AtomStruct method) getPWEMPath() (in module pwem.utils) getPwProtMpiRunScript() (in module pyworkflow.config) getPysegEnvActivation() (pyseg.Plugin class method) getPython() (scipion.install.funcs.Environment static method) getPythonLibFolder() (pyworkflow.config.Config static method) getPythonPackagesFolder() (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) getRadii() (tomo.objects.Ellipsoid method) getRadius() (pwem.wizards.wizard.MaskPreviewDialog static method) (spider.wizards.SpiderFilterDialog 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) getReadOnly() (pyworkflow.project.config.ProjectSettings method) getReadyMics() (in module xmipp3.protocols.protocol_particle_pick_consensus) getReadyTomos() (in module tomo3D.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) getReportPath() (emfacilities.protocols.protocol_monitor_summary.ProtMonitorSummary method) getRepresentative() (pyworkflow.object.Set method) getResidualGainPath() (xmipp3.protocols.protocol_movie_gain.XmippProtMovieGain method) getResidues() (chimera.wizards.GetChainResiduesWizardChimera method) getResizeFactorFromDimensions() (imod.protocols.protocol_etomo.ProtImodEtomo method) getResolution() (pwem.objects.data.CTFModel method) getResolutionHistogram() (emfacilities.protocols.report_html.ReportHtml method) getResolutionVolumeFileName() (relion.viewers.viewer_locres.RelionLocalResViewer method) getResult() (pyworkflow.gui.dialog.Dialog method) getRightConnectorCoordinates() (pyworkflow.gui.canvas.Item method) getRoi() (pwem.objects.data.MovieAlignment method) getRoot() (pyworkflow.gui.gui.Window method) (pyworkflow.utils.graph.Graph method) getRootNodes() (pyworkflow.utils.graph.Graph method) getRotatingFileLogger() (in module scipion.install.plugin_manager) getRotationAxis() (imod.protocols.protocol_tomoProjection.ProtImodTomoProjection method) getRotationMatrix() (pwem.objects.data.Transform method) getRotationType() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment 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() (locscale.protocols.protocol_locscale.ProtLocScale method) (pwem.convert.headers.Ccp4Header method) getSamplingRate() (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify method) (motioncorr.protocols.protocol_motioncorr.ProtMotionCorr method) (pwem.objects.data.Image method) (pwem.objects.data.SetOfClasses method) (pwem.objects.data.SetOfImages method) (tomo.objects.SetOfCoordinates3D method) (tomo.protocols.protocol_ts_import.MDoc method) getScaleFactor() (relion.protocols.protocol_extract_particles.ProtRelionExtractParticles method) getScannedPixelSize() (pwem.objects.data.SetOfMicrographsBase method) (tomo.objects.SetOfTiltSeriesBase method) (tomo.objects.TiltSeriesBase 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() (deepfinder.objects.Coordinate3DWithScore method) (pwem.objects.data.NormalMode method) getScript() (spider.Plugin class method) (spider.protocols.protocol_base.SpiderProtocol method) getScriptsPath() (in module scipion.utils) getSection() (pyworkflow.protocol.params.Form method) getSelected() (pyworkflow.gui.browser.ObjectBrowser method) (pyworkflow.gui.canvas.Item method) getSelectedData() (continuousflex.viewers.nma_gui.matplotlib_point_selector.PointSelector method) (continuousflex.viewers.nma_vol_gui.PointSelectorVol.PointSelectorVol method) getSelectedItem() (tomo.viewers.views_tkinter_tree.CTFEstimationTree method) getSelectedNodesCount() (spider.viewers.viewer_classify.SpiderViewerWard method) getSelectedObj() (tomo.viewers.views_tkinter_tree.CTFEstimationTree method) getSelectedObjects() (pyworkflow.gui.form.MultiPointerVar method) (pyworkflow.gui.tree.BoundTree method) getSelectedProtocol() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) getSelectedSize() (continuousflex.protocols.data.Data method) (xmipp3.utils.Data method) getSelfClassName() (pyworkflow.mapper.sqlite.SqliteFlatDb method) getSeqName() (pwem.objects.data.Sequence method) getSequence() (pwem.objects.data.Sequence method) getSequenceFromChain() (pwem.convert.atom_struct.AtomicStructHandler method) getSequenceOfChainStep() (pwem.protocols.protocol_import.sequence.ProtImportSequence method) getSequenceStep() (phenix.wizards.GetChainResiduesWizardPhenix method) getSetOfTiltSeries() (tomo.objects.SetOfCTFTomoSeries method) (tomo.objects.SetOfLandmarkModels method) getSettings() (pyworkflow.gui.project.project.ProjectWindow method) (pyworkflow.project.project.Project method) getSettingsCreationTime() (pyworkflow.project.project.Project method) getShifts() (in module gctf.convert.convert) (pwem.objects.data.MovieAlignment method) (pwem.objects.data.Transform method) (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) getShiftsFromOrigin() (pwem.objects.data.Image method) (tomo.objects.TiltSeriesBase 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() (continuousflex.protocols.data.Data method) (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.utils.dataset.Table method) (spider.protocols.protocol_classify_base.DendroNode method) (xmipp3.base.XmippSet method) (xmipp3.utils.Data method) getSizeStr() (pyworkflow.gui.browser.FileInfo method) getSkewType() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment 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) getStackOrResize() (xmipp3.protocols.protocol_deep_denoising.XmippProtDeepDenoising method) getStartAngstrom() (pwem.convert.headers.Ccp4Header method) getStartPixel() (pwem.convert.headers.Ccp4Header method) getState() (continuousflex.protocols.data.Point method) (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) getStep() (tomo.objects.TomoAcquisition 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) getStretchType() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) getStringIfActive() (in module xmipp3.viewers.viewer_ctf_consensus) getStringListFromValues() (in module pyworkflow.utils.utils) getStructure() (pwem.convert.atom_struct.AtomicStructHandler method) GetStructureChains2WizardChimera (class in chimera.wizards) GetStructureChainsWizard (class in pwem.wizards.wizards) GetStructureChainsWizardAtomStruct (class in atomstructutils.wizards) GetStructureChainsWizardChimera (class in chimera.wizards) 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) getSubset() (pyworkflow.object.Set method) getSubsetByDefocus() (in module pwem.convert.utils) getSubtomoMetaData() (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify method) getSuffix() (pwem.protocols.protocol_extract_coordinates.ProtExtractCoords method) (tomo.protocols.protocol_extract_coordinates.ProtTomoExtractCoords method) getSummary() (eman2.protocols.protocol_ctf.EmanProtCTFAuto method) (emantomo.protocols.protocol_tomo_template_match.EmanProtTomoTempMatch method) (pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs method) (pwem.protocols.protocol_particles_picking.ProtParticlePicking method) (scipion.install.plugin_funcs.PluginInfo method) (tomo.objects.SetOfCoordinates3D method) (xmipp3.protocols.protocol_particle_pick_automatic.XmippParticlePickingAutomatic method) (xmipp3.protocols.protocol_preprocess.protocol_add_noise.XmippProtAddNoise method) (xmipptomo.protocols.protocol_project_top.XmippProtSubtomoProject method) getSupportedDataType() (pwem.emlib.image.image_handler.ImageHandler class method) getSupportedEmanVersions() (in module locscale.convert) getSupportedVersions() (in module locscale.convert) (pyworkflow.plugin.Plugin class method) getSurfaceToAnalyze() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) getSymmetrizedModelName() (chimera.protocols.protocol_contacts.ChimeraProtContacts method) getSymmetry() (in module cryosparc2.utils) (pwem.viewers.viewer_chimera.Chimera class method) (xmipp3.base.HelicalFinder method) getSymmetryMatrices() (in module pwem.convert.symmetry) getSyncDataScript() (in module pyworkflow.config) getSystemInfo() (in module cryosparc2.utils) getTable() (pyworkflow.utils.dataset.DataSet method) getTableColumns() (pyworkflow.mapper.sqlite_db.SqliteDb method) getTableName() (chimera.protocols.protocol_contacts.ChimeraProtContacts method) (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) getTemperature() (spider.wizards.SpiderFilterDialog 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 class method) getTemplatesPath() (in module scipion.utils) getTensorFlowEnviron() (xmipptomo.Plugin class method) 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) getTgz() (in module chimera.getchimera) getThumbnailFn() (pwem.emlib.image.image_handler.ImageHandler static method) (pwem.protocols.protocol_align_movies.ProtAlignMovies method) getThumbPaths() (emfacilities.protocols.report_html.ReportHtml method) getTi() (tomo.objects.TiltSeriesDict method) getTiDict() (tomo.objects.TiltSeriesDict method) getTiList() (tomo.objects.TiltSeriesDict method) getTiltAngle() (tomo.objects.TiltImageBase method) (tomo.protocols.protocol_ts_import.TiltMetadata method) getTiltAngleList() (imod.protocols.protocol_tomoProjection.ProtImodTomoProjection method) getTiltAngles() (reliontomo.protocols.protocol_ctf_3d_estimation.DoseFile method) (reliontomo.protocols.protocol_ctf_3d_estimation.ExtendedTS method) getTiltAngleType() (imod.protocols.protocol_fiducialAlignment.ProtImodFiducialAlignment method) getTiltAxisAngle() (tomo.objects.TomoAcquisition method) (tomo.protocols.protocol_ts_import.MDoc method) getTilted() (pwem.objects.data_tiltpairs.TiltPair method) (pwem.objects.data_tiltpairs.TiltPairSet method) getTiltRange() (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify method) getTiltSeries() (tomo.objects.CTFTomoSeries method) (tomo.objects.LandmarkModel method) getTiltsMetadata() (tomo.protocols.protocol_ts_import.MDoc method) getTimeInterval() (pwem.protocols.protocol_create_stream_data.ProtCreateStreamData method) getTimeSeries() (emfacilities.protocols.report_html.ReportHtml method) getTiPrefix() (tomo.protocols.protocol_ts_estimate_ctf.ProtTsEstimateCTF method) getTiRoot() (tomo.protocols.protocol_ts_estimate_ctf.ProtTsEstimateCTF 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) (tomo.protocols.protocol_extract_coordinates.ProtTomoExtractCoords method) getTmpPath() (pyworkflow.project.project.Project method) getToc() (pyworkflow.utils.utils.Timer method) getTomoAlignProgram() (jjsoft.Plugin class method) getTomoBFlowProgram() (jjsoft.Plugin class method) getTomoEEDProgram() (jjsoft.Plugin class method) getTomogram() (tomo.objects.TomoMask method) getTomoId() (tomo.objects.Coordinate3D method) (tomo3D.protocols.protocol_particle_pick_consensus.ProtTomoConsensusPicking class method) getTomoRecProgram() (jjsoft.Plugin class method) getTomoSetFromStar() (in module pyseg.convert) getTomowarpalignProgram() (jjsoft.Plugin class method) getTopazEnvActivation() (topaz.Plugin class method) getTopazEnvName() (in module topaz.constants) getTopConnectorCoordinates() (pyworkflow.gui.canvas.Item method) getTopRankItems() (pwem.protocols.protocol_set_filter.ProtSetFilter method) getTrainDataDir() (cryocare.objects.CryocareModel method) (cryocare.objects.CryocareTrainData method) getTrainedMicFns() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) getTransform() (pwem.objects.data.Image method) getTransformationMatrix() (atomstructutils.protocols.protocol_convertsymmetry.ProtAtomStrucConvertSymmetry method) (pyworkflow.utils.dataset.Table method) getTransformGraph() (pyworkflow.project.project.Project method) getTransformMatrix() (pwem.convert.atom_struct.AtomicStructHandler method) getTriangles() (pwem.convert.symmetry.Icosahedron method) getTS() (reliontomo.protocols.protocol_ctf_3d_estimation.ExtendedTS method) getTs() (tomo.objects.TiltSeriesDict method) getTsId() (tomo.objects.CTFTomoSeries method) (tomo.objects.LandmarkModel method) (tomo.objects.TiltImageBase method) (tomo.objects.TiltSeriesBase method) (tomo.objects.Tomogram method) (tomo.protocols.protocol_ts_import.MDoc method) getTSPath() (reliontomo.protocols.protocol_ctf_3d_estimation.ProtRelionEstimateCTF3D method) getTSSetFromCTFSeries() (reliontomo.protocols.protocol_ctf_3d_estimation.ProtRelionEstimateCTF3D method) getTsSize() (xmipptomo.protocols.protocol_resizeTS.XmippProtResizeTiltSeries method) getType() (emxlib.utils.EmxLabel method) (pyworkflow.template.TemplateParam method) (pyworkflow.utils.dataset.Column method) getTypeOfColumn() (pyworkflow.utils.dataset.DataSet method) getUniqueId() (pyworkflow.object.Pointer method) getUniqueItems() (in module pyworkflow.utils.utils) getUniqueValues() (pyworkflow.object.Set method) getUnit() (emxlib.utils.EmxLabel method) getUntilted() (pwem.objects.data_tiltpairs.TiltPair method) (pwem.objects.data_tiltpairs.TiltPairSet method) getUpdatedProtocol() (in module pyworkflow.protocol.protocol) 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_movie_correlation.XmippProtMovieCorr method) getUserFlip() (xmipp3.protocols.protocol_movie_correlation.XmippProtMovieCorr 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) getVar() (pyworkflow.plugin.Plugin class method) getVars() (pyworkflow.config.Config class method) (pyworkflow.plugin.Plugin class method) getVarValue() (pyworkflow.gui.form.FormWindow method) (spider.wizards.CustomMaskDialog method) getVersion() (gctf.protocols.program_gctf.ProgramGctf class method) (in module locscale.convert) (pyworkflow.mapper.sqlite_db.SqliteDb method) getVertices() (pwem.convert.symmetry.Icosahedron method) getVesiclesCenteredStarFile() (pyseg.protocols.protocol_pre_seg.ProtPySegPreSegParticles method) getView() (gctf.wizards.GctfCTFWizard class method) (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) (xmipp3.wizards.XmippCTFWizard class method) getView1Name() (chimera.protocols.protocol_contacts.ChimeraProtContacts method) getView2Name() (chimera.protocols.protocol_contacts.ChimeraProtContacts method) getViewers() (pyworkflow.plugin.Domain class method) getViewerScript() (in module pyworkflow.config) getViewParams() (in module xmipp3.viewers.viewer_movie_alignment) (pwem.viewers.views.DataView method) getViewWidget() (pyworkflow.gui.project.base.ProjectBaseWindow method) getVolFileName() (pwem.emlib.image.image_handler.ImageHandler class method) getVolId() (tomo.objects.Coordinate3D method) (tomo.objects.SubTomogram method) getVolName() (tomo.objects.Coordinate3D method) (tomo.objects.SubTomogram method) (tomo.objects.TomoMask method) getVoltage() (pwem.objects.data.Acquisition method) (tomo.protocols.protocol_ts_import.MDoc method) getVolume() (pwem.objects.data.AtomStruct method) (tomo.objects.Coordinate3D method) getVolumeName() (pyworkflow.utils.dataset.DataSet method) (tomo.objects.MeshPoint method) getVolumeNames() (spider.viewers.viewer_refinement.SpiderViewerRefinement method) getVolumeOrigin() (tomo.objects.Coordinate3D method) (tomo.objects.SubTomogram method) getVolumesFromPostprocess() (in module relion.convert.convert_utils) getVolumeSize() (continuousflex.protocols.protocol_subtomograms_classify.FlexProtSubtomoClassify method) getVScroll() (pyworkflow.gui.widgets.Scrollable method) getWedgeExtraParams() (in module pyworkflow.gui.matplotlib_image) getWeight() (continuousflex.protocols.data.Point method) (xmipp3.utils.Point method) getWeights() (continuousflex.protocols.data.Data method) (xmipp3.utils.Data method) getWidgetValue() (pyworkflow.gui.form.FormWindow method) getWindow() (pyworkflow.viewer.ProtocolViewer method) getWizardMaskColor() (pyworkflow.config.Config class method) getWizards() (pyworkflow.plugin.Domain class method) getWorkflow() (in module scipion.scripts.tutorial) getWorkingDir() (pyworkflow.protocol.protocol.Protocol method) getX() (continuousflex.protocols.data.Point method) (pwem.objects.data.Coordinate method) (pwem.objects.data.ImageDim method) (pyworkflow.project.config.NodeConfig method) (tomo.objects.Coordinate3D method) (xmipp3.utils.Point method) getXData() (continuousflex.protocols.data.Data method) (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) getXYData() (continuousflex.viewers.nma_gui.matplotlib_point_path.PointPath method) (continuousflex.viewers.nma_vol_gui.PointPathVol.PointPathVol method) (xmipp3.viewers.viewer_resolution3d.PointPath method) getxyz() (pwem.wizards.wizards_3d.callbacks.DraggablePoint method) getXYZN() (pwem.convert.headers.Ccp4Header method) getY() (continuousflex.protocols.data.Point method) (pwem.objects.data.Coordinate method) (pwem.objects.data.ImageDim method) (pyworkflow.project.config.NodeConfig method) (tomo.objects.Coordinate3D method) (xmipp3.utils.Point method) getYData() (continuousflex.protocols.data.Data method) (xmipp3.utils.Data method) getYDim() (pwem.objects.data.Image method) getZ() (continuousflex.protocols.data.Point method) (pwem.objects.data.ImageDim method) (tomo.objects.Coordinate3D method) (xmipp3.utils.Point method) getZData() (continuousflex.protocols.data.Data method) (xmipp3.utils.Data 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_reconstruct_heterogeneous.XmippProtReconstructHeterogeneous method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) goBegin() (pyworkflow.gui.text.Text method) goEnd() (pyworkflow.gui.text.Text method) gpu (emfacilities.protocols.pynvml.c_nvmlUtilization_t attribute) gpusValidate() (in module cryosparc2.utils) gpuUtilization (emfacilities.protocols.pynvml.c_nvmlAccountingStats_t attribute) GradientFrame (class in pyworkflow.gui.widgets) Graph (class in pyworkflow.utils.graph) GraphLayout (class in pyworkflow.gui.graph_layout) gray (pyworkflow.utils.utils.StrColors attribute) grayStr() (in module pyworkflow.utils.utils) GREEN (pyworkflow.utils.properties.colorText attribute) green (pyworkflow.utils.utils.StrColors 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) gridFromMRC() (tomo3D.viewers.viewer_mrc.MrcPlot method) GrigorieffLabImportCTF (class in cistem.convert.dataimport) GrigorieffLabImportParticles (class in cistem.convert.dataimport) Group (class in pyworkflow.protocol.params) GroupWidget (class in pyworkflow.gui.form) GT (class in pyworkflow.protocol.params) GTestResult (class in pyworkflow.tests.tests) guessJava() (in module scipion.scripts.config) guessMPI() (in module scipion.scripts.config) guiThread() (in module tomo3D.viewers.viewer_triangulations) 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) has() (emxlib.utils.EmxObject method) has_been_closed() (emfacilities.viewers.viewer_monitors.CtfMonitorPlotter method) (emfacilities.viewers.viewer_monitors.MovieGainMonitorPlotter method) (emfacilities.viewers.viewer_monitors.SystemMonitorPlotter method) hasAcquisition() (pwem.objects.data.Image method) (pwem.objects.data.SetOfImages method) (tomo.objects.SubTomogram method) (tomo.objects.Tomogram method) hasAlgebraicDesc() (tomo.objects.Ellipsoid method) hasAlignment() (cistem.protocols.protocol_refine2d.CistemProtRefine2D method) (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) hasAstigmatismInfoAsList() (tomo.objects.CTFTomo method) hasAttribute() (pyworkflow.object.Object method) hasAttributeExt() (pyworkflow.object.Object method) hasChangedSince() (pyworkflow.object.Set method) hasClassId() (pwem.objects.data.Particle method) (pwem.objects.data.Volume method) hasColumn() (pyworkflow.utils.dataset.Table method) (relion.convert.convert31.OpticsGroups method) hasCondition() (pyworkflow.protocol.params.FormElement method) hasCoordinate() (pwem.objects.data.Particle method) hasCoordinate3D() (tomo.objects.SubTomogram method) hasCoordinates() (pwem.objects.data.SetOfParticles method) hasCoordinates3D() (tomo.objects.SetOfSubTomograms method) hasCTF() (pwem.objects.data.Image method) (pwem.objects.data.SetOfImages method) hasCutOnFrequncyInfoAsList() (tomo.objects.CTFTomo method) hasDefault() (pyworkflow.utils.dataset.Column method) hasDefinition() (pyworkflow.protocol.protocol.Protocol static method) hasDescription() (tomo.objects.MeshPoint method) hasDoubleInheritance() (in module pyworkflow.apps.pw_protocol_list) hasDWMics() (cistem.viewers.ProtUnblurViewer method) (motioncorr.viewers.ProtMotioncorrViewer method) (relion.viewers.viewer_motioncor.RelionMotioncorrViewer method) hasEnableColumn() (pwem.viewers.showj.ColumnsConfig method) hasEnabledColumn() (pyworkflow.utils.dataset.Table method) hasEstimationInfoAsList() (tomo.objects.CTFTomo method) hasEvenSet() (tomo.viewers.viewers_data.TSMotionCorrectionViewer method) hasExpert() (pyworkflow.protocol.protocol.Protocol method) hasExtended() (pyworkflow.object.Pointer method) hasFont() (in module pyworkflow.gui.gui) hasGroupId() (tomo.objects.Coordinate3D method) hasHalfMaps() (pwem.objects.data.Volume method) HashTableDict (class in xmipp3.protocols.protocol_classification_gpuCorr_full) (class in xmipp3.protocols.protocol_classification_gpuCorr_semi) hasLabel() (in module pyworkflow.tests.tests) (pwem.emlib.metadata.utils.Row method) hasMicId() (pwem.objects.data.Particle method) hasMics() (cistem.viewers.ProtUnblurViewer method) (motioncorr.viewers.ProtMotioncorrViewer method) (relion.viewers.viewer_motioncor.RelionMotioncorrViewer method) hasName() (pyworkflow.protocol.hosts.QueueSystemConfig method) hasObjId() (pyworkflow.object.Object method) hasObjParentId() (pyworkflow.object.Object method)

hasOddSet() (tomo.viewers.viewers_data.TSMotionCorrectionViewer method) hasOrigin() (pwem.objects.data.AtomStruct method) (pwem.objects.data.Image method) (tomo.objects.TiltSeriesBase 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) hasPhaseShiftInfoAsList() (tomo.objects.CTFTomo 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) (tomo.objects.Coordinate3D method) hasTs() (tomo.objects.TiltSeriesDict method) hasUnit() (emxlib.utils.EmxLabel 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 (gautomatch.convert.CoordStarWriter attribute) (gctf.convert.convert.CoordinatesWriter attribute) HelicalFinder (class in xmipp3.base) HELP_MPI_THREADS (pyworkflow.utils.properties.Message attribute) HELP_RUNMODE (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) histogram() (tomo3D.viewers.viewer_mrc.MrcPlot method) histThresholding() (in module xmipp3.protocols.protocol_screen_particles) HOME (pyworkflow.constants.DOCSITEURLS attribute) (pyworkflow.utils.properties.Icon attribute) homogeneizeStep() (xmipp3.protocols.protocol_solid_angles.XmippProtSolidAngles method) (xmipp3.protocols.protocol_split_volume_hierarchical_cluster.XmippProtSplitVolumeHierarchical method) HOST_CONFIG (pyworkflow.constants.DOCSITEURLS attribute) HostConfig (class in pyworkflow.protocol.hosts) HotButton (class in pyworkflow.gui.widgets) hwbcId (emfacilities.protocols.pynvml.c_nvmlHwbcEntry_t attribute) HyperlinkManager (class in pyworkflow.gui.text)

I

ico() (chimera.editList.EntryGrid method) Icon (class in pyworkflow.utils.properties) IconButton (class in pyworkflow.gui.widgets) 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 (emfacilities.protocols.pynvml.c_nvmlUnitInfo_t attribute) ID_COLUMN (pyworkflow.gui.form.SubclassesTreeProvider attribute) (pyworkflow.gui.tree.ProjectRunsTreeProvider attribute) ifa_addr (emfacilities.protocols.getnifs.struct_ifaddrs attribute) ifa_data (emfacilities.protocols.getnifs.struct_ifaddrs attribute) ifa_flags (emfacilities.protocols.getnifs.struct_ifaddrs attribute) ifa_ifu (emfacilities.protocols.getnifs.struct_ifaddrs attribute) ifa_name (emfacilities.protocols.getnifs.struct_ifaddrs attribute) ifa_netmask (emfacilities.protocols.getnifs.struct_ifaddrs attribute) ifa_next (emfacilities.protocols.getnifs.struct_ifaddrs attribute) ifap_iter() (in module emfacilities.protocols.getnifs) ifNomask() (xmipp3.protocols.protocol_resolution_monogenic_signal.XmippProtMonoRes method) ifu_broadaddr (emfacilities.protocols.getnifs.union_ifa_ifu attribute) ifu_dstaddr (emfacilities.protocols.getnifs.union_ifa_ifu attribute) ignoreCopy() (pwem.protocols.protocol_import.micrographs.ProtImportMovies method) Image (class in pwem.objects.data) ImageBox (class in spider.viewers.viewer_classify) ImageDim (class in pwem.objects.data) ImageFileHandler (class in pwem.viewers.filehandlers) ImageHandler (class in pwem.emlib.image.image_handler) ImagePreview (class in pyworkflow.gui.matplotlib_image) ImagePreviewDialog (class in pwem.wizards.wizard) imageToRow() (in module cryosparc2.convert.convert) (in module relion.convert.convert_deprecated) (in module xmipp3.convert.convert) ImageView (class in pwem.viewers.views) imod (module) imod.bibtex (module) imod.constants (module) imod.file_handlers (module) imod.protocols (module) imod.protocols.protocol_applyTransformationMatrix (module) imod.protocols.protocol_auto3d (module) imod.protocols.protocol_base (module) imod.protocols.protocol_ctfCorrection (module) imod.protocols.protocol_ctfEstimation_automatic (module) imod.protocols.protocol_ctfEstimation_manual (module) imod.protocols.protocol_doseFilter (module) imod.protocols.protocol_etomo (module) imod.protocols.protocol_excludeViews (module) imod.protocols.protocol_fiducialAlignment (module) imod.protocols.protocol_fiducialModel (module) imod.protocols.protocol_goldBeadEraser (module) imod.protocols.protocol_goldBeadPicker3d (module) imod.protocols.protocol_importSetOfCTFTomoSeries (module) imod.protocols.protocol_importSetOfTM (module) imod.protocols.protocol_tomoNormalization (module) imod.protocols.protocol_tomoProjection (module) imod.protocols.protocol_tomoReconstruction (module) imod.protocols.protocol_tsNormalization (module) imod.protocols.protocol_xCorrPrealignment (module) imod.protocols.protocol_xRaysEraser (module) imod.utils (module) imod.viewers (module) imod.viewers.viewers (module) imod.viewers.views_tkinter_tree (module) ImodEtomoViewer (class in imod.viewers.viewers) ImodGenericTreeProvider (class in imod.viewers.views_tkinter_tree) ImodGenericViewer (class in imod.viewers.views_tkinter_tree) ImodHandler (class in imod.file_handlers) ImodListDialog (class in imod.viewers.views_tkinter_tree) ImodObjectView (class in imod.viewers.viewers) ImodSetOfLandmarkModelsView (class in imod.viewers.views_tkinter_tree) ImodSetOfTomogramsView (class in imod.viewers.views_tkinter_tree) ImodSetView (class in imod.viewers.views_tkinter_tree) ImodViewer (class in imod.viewers.viewers) IMPORT_COPY_FILES (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) IMPORT_FROM_AUTO (pwem.protocols.protocol_import.coordinates.ProtImportCoordinates attribute) (pwem.protocols.protocol_import.ctfs.ProtImportCTF 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 (continuousflex.protocols.pdb.protocol_convert_pdb.FlexProtConvertPdb attribute) (pwem.protocols.protocol_import.base.ProtImportFiles attribute) (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) (pwem.protocols.protocol_import.volumes.ProtImportPdb attribute) (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) (xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb 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_GENEBANK (pwem.protocols.protocol_import.sequence.ProtImportSequence attribute) IMPORT_FROM_GRIGORIEFF (pwem.protocols.protocol_import.ctfs.ProtImportCTF attribute) IMPORT_FROM_ID (continuousflex.protocols.pdb.protocol_convert_pdb.FlexProtConvertPdb attribute) (pwem.protocols.protocol_import.volumes.ProtImportPdb attribute) (xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb attribute) IMPORT_FROM_NUCLEOTIDE_FILES (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_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_LINK_ABS (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) IMPORT_LINK_REL (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) IMPORT_OBJ (continuousflex.protocols.pdb.protocol_convert_pdb.FlexProtConvertPdb attribute) (xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb attribute) (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) importAngles() (eman2.convert.dataimport.EmanImport method) (emantomo.convert.dataimport.EmanTomoImport method) importCoordinates() (appion.convert.dataimport.DogpickerImport method) (eman2.convert.dataimport.EmanImport method) (pwem.protocols.protocol_import.dataimport.ScipionImport method) (relion.convert.dataimport.RelionImport method) (xmipp3.convert.dataimport.XmippImport method) ImportCoordinates3D (class in deepfinder.protocols.protocol_import_coordinates) importCoordinates3D() (emantomo.convert.dataimport.EmanTomoImport method) (tomo.convert.convert.TomoImport method) ImportCoordinatesBoxSizeWizard (class in pwem.wizards.wizards) importCoordinatesStep() (deepfinder.protocols.protocol_import_coordinates.ImportCoordinates3D method) (tomo.protocols.protocol_import_coordinates.ProtImportCoordinates3D method) importCTF() (cistem.convert.dataimport.GrigorieffLabImportCTF method) (eman2.convert.dataimport.EmanImport method) (emantomo.convert.dataimport.EmanTomoImport method) (gctf.convert.dataimport.GctfImportCTF method) (xmipp3.convert.dataimport.XmippImport method) importCTFStep() (pwem.protocols.protocol_import.ctfs.ProtImportCTF method) importData() (emxlib.convert.dataimport.EmxImport method) (in module emxlib.convert.convert) importDynamoTomogramsStep() (dynamo.protocols.protocol_import_tomograms.DynamoImportTomograms method) importExts (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) importFormats (pwem.protocols.protocol_import.particles.ProtImportParticles attribute) importFromPlugin() (pyworkflow.plugin.Domain static method) 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() (emxlib.convert.dataimport.EmxImport method) (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) importModelStep() (sphire.protocols.protocol_cryolo_import.SphireProtCryoloImport method) (topaz.protocols.protocol_topaz_import.TopazProtImport method) ImportMoviesOutput (class in pwem.protocols.protocol_import.micrographs) ImportOriginTomoWizard (class in tomo.wizards) ImportOriginVolumeWizard (class in pwem.wizards.wizards) importParticles() (cistem.convert.dataimport.GrigorieffLabImportParticles method) (eman2.convert.dataimport.EmanImport method) (emxlib.convert.dataimport.EmxImport method) (pwem.protocols.protocol_import.dataimport.ScipionImport method) (relion.convert.dataimport.RelionImport 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) importSetOfCtfTomoSeries() (imod.protocols.protocol_importSetOfCTFTomoSeries.ProtImodImportSetOfCtfTomoSeries method) importStep() (tomo.protocols.protocol_ts_import.ProtImportTsBase method) importSubTomogramsStep() (dynamo.protocols.protocol_import_subtomos.DynamoImportSubtomos method) (tomo.protocols.protocol_import_subtomograms.ProtImportSubTomograms method) importTomogramsStep() (tomo.protocols.protocol_import_tomograms.ProtImportTomograms method) importVolumesStep() (pwem.protocols.protocol_import.volumes.ProtImportVolumes method) incomingDose (tomo.protocols.protocol_ts_import.ProtImportTsBase attribute) increment() (pyworkflow.object.Integer method) indent() (pyworkflow.mapper.xmlmapper.XmlMapper method) indentation (pyworkflow.utils.profiler.Timer attribute) indexes (pyworkflow.object.Set attribute) indexToAlphabet() (in module pwem.convert.sequence) INFILE1 (chimera.protocols.protocol_modeller_search.ChimeraModelFromTemplate attribute) INFILE2 (chimera.protocols.protocol_modeller_search.ChimeraModelFromTemplate attribute) InfluxHandler (class in pwperformance.loggers.influxdb) info() (emfacilities.protocols.protocol_monitor.Monitor method) (emfacilities.protocols.report_html.ReportHtml 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) initDictVesicles() (in module tomo.utils) initGPU() (in module emfacilities.protocols.protocol_monitor_system) initialize_PyQt() (tomo3D.viewers.viewer_triangulations.TriangulationPlot method) initializeLists() (in module xmipp3.protocols.protocol_projmatch.projmatch_initialize) initializeParams() (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method) initializePlot() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) (tomo3D.viewers.viewer_mrc.MrcPlot method) (tomo3D.viewers.viewer_triangulations.TriangulationPlot method) (tomo3D.viewers.viewer_vtk.VtkPlot method) initializeRejDict() (xmipp3.protocols.protocol_ctf_consensus.XmippProtCTFConsensus method) initializeStep() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method) initLoop() (emfacilities.protocols.protocol_monitor.Monitor method) (emfacilities.protocols.protocol_monitor_ctf.MonitorCTF method) (emfacilities.protocols.protocol_monitor_movie_gain.MonitorMovieGain method) (emfacilities.protocols.protocol_monitor_system.MonitorSystem 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_HELP (fsc3d.protocols.protocol_3dfsc.Prot3DFSC attribute) (resmap.protocols.protocol_resmap.ProtResMap attribute) INPUTARG (xmipp3.protocols.protocol_multireference_alignability.XmippProtMultiRefAlignability attribute) inputProtocolDict() (pyworkflow.protocol.protocol.Protocol method) insert() (pyworkflow.mapper.mapper.Mapper method) (pyworkflow.mapper.sqlite.SqliteFlatMapper method) (pyworkflow.mapper.sqlite.SqliteMapper method) (pyworkflow.mapper.xmlmapper.XmlMapper 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_heterogeneous.XmippProtReconstructHeterogeneous method) (xmipp3.protocols.protocol_reconstruct_highres.XmippProtReconstructHighRes method) insertLabel() (xmipp3.programs.ProgramDb method) insertMaskReferenceStep() (in module xmipp3.protocols.protocol_projmatch.projmatch_steps) insertNewCoorsSteps() (tomo3D.protocols.protocol_particle_pick_consensus.ProtTomoConsensusPicking method) (tomo3D.protocols.protocol_particle_pick_remove_duplicates.ProtTomoPickingRemoveDuplicates method) (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) insertObjectWithChilds() (pyworkflow.mapper.xmlmapper.XmlMapper method) insertOperation() (scipion.install.plugin_manager.OperationList method) insertProgram() (xmipp3.programs.ProgramDb 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) inside() (continuousflex.viewers.nma_gui.matplotlib_point_selector.PointSelector method) (continuousflex.viewers.nma_vol_gui.PointSelectorVol.PointSelectorVol method) inspectObj() (in module pyworkflow.gui.project.viewprotocols) 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) installDeepLearningToolkit() (in module xmipp3)

INSTALLED (pyworkflow.utils.properties.Icon attribute) (pyworkflow.utils.properties.PluginStates attribute) installed_item() (scipion.install.plugin_manager.PluginTree method) installPipModule() (scipion.install.plugin_funcs.PluginInfo method) installPluginMethods() (in module scipion.install.install_plugin) Instance (class in pwperformance.StaticVsInstanceMethod) instanceCreated() (in module pyworkflow.utils.profiler) instanceDestroyed() (in module pyworkflow.utils.profiler) instantiateClass() (in module tomo3D.viewers.viewer_triangulations) inStarName (pyseg.protocols.protocol_2d_classification.ProtPySegPlaneAlignClassification attribute) (pyseg.protocols.protocol_post_rec_particles.ProtPySegPostRecParticles attribute) (reliontomo.protocols.protocol_reconstruct_subtomo.ProtRelionSubTomoReconstruct attribute) Integer (class in pyworkflow.object) INTERP_CUBIC (xmipp3.protocols.protocol_movie_average.XmippProtMovieAverage attribute) (xmipp3.protocols.protocol_movie_correlation.XmippProtMovieCorr attribute) INTERP_LINEAR (xmipp3.protocols.protocol_movie_average.XmippProtMovieAverage attribute) (xmipp3.protocols.protocol_movie_correlation.XmippProtMovieCorr attribute) INTERP_MAP (xmipp3.protocols.protocol_movie_average.XmippProtMovieAverage attribute) (xmipp3.protocols.protocol_movie_correlation.XmippProtMovieCorr attribute) interpolateTiltSeries() (xmipptomo.protocols.protocol_misalignTS.XmippProtMisalignTiltSeries method) interpolRes() (xmipp3.viewers.viewer_resolution_fso.XmippProtFSOViewer method) intersectClasses() (tomo.protocols.protocol_consensus_classes_subtomo.ProtConsensusClassesSubtomo method) (xmipp3.protocols.protocol_consensus_classes3D.XmippProtConsensusClasses3D method) intersectsList (tomo.protocols.protocol_consensus_classes_subtomo.ProtConsensusClassesSubtomo attribute) (xmipp3.protocols.protocol_consensus_classes3D.XmippProtConsensusClasses3D attribute) INTERVAL (pyworkflow.utils.log.STATUS attribute) IntParam (class in pyworkflow.protocol.params) introduceRandomMisalignment() (xmipptomo.protocols.protocol_misalignTS.XmippProtMisalignTiltSeries method) inverse_Transformation() (in module tomo3D.utils) invert() (pwem.emlib.image.image_handler.ImageHandler method) (pwem.objects.data.Transform method) invert_array() (in module xmipp3.protocols.protocol_movie_gain) invertContrastStep() (dynamo.protocols.protocol_extraction.DynamoExtraction method) invertImage() (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) (tomo.objects.Coordinate3D method) IS_2D (cryosparc2.protocols.protocol_cryosparc2d.ProtCryo2D attribute) (relion.protocols.protocol_base.ProtRelionBase attribute) (relion.protocols.protocol_classify2d.ProtRelionClassify2D attribute) (relion.protocols.protocol_initialmodel.ProtRelionInitialModel attribute) IS_30() (reliontomo.Plugin class method) IS_3D_INIT (relion.protocols.protocol_base.ProtRelionBase attribute) (relion.protocols.protocol_initialmodel.ProtRelionInitialModel attribute) is_class_private_name() (in module pyworkflow.utils.echo) IS_CLASSIFY (relion.protocols.protocol_base.ProtRelionBase attribute) (relion.protocols.protocol_initialmodel.ProtRelionInitialModel attribute) (relion.protocols.protocol_refine3d.ProtRelionRefine3D attribute) (reliontomo.protocols.protocol_classify_3d_tomo.ProtRelionSubtomoClassif3D attribute) (reliontomo.protocols.protocol_refine_3d_tomo.ProtRelionSubtomoRefine3D attribute) is_classmethod() (in module pyworkflow.utils.echo) is_disabled() (scipion.install.plugin_manager.PluginTree method) is_enabled() (scipion.install.plugin_manager.PluginTree method) IS_GT31() (relion.Plugin class method) is_tool() (chimera.protocols.protocol_base.ChimeraProtBase method) (phenix.protocols.protocol_dock_in_map.PhenixProtRunDockInMap method) (phenix.protocols.protocol_emringer.PhenixProtRunEMRinger method) is_window_closed() (pwem.wizards.wizards_3d.mask_structure_wizard.MaskStructureWizard method) (pwem.wizards.wizards_3d.mask_volume_wizard.MaskVolumeWizard method) isAborted() (pyworkflow.protocol.protocol.Step method) isActive() (pyworkflow.protocol.protocol.Step method) isAFinalProtocol() (pyworkflow.gui.project.viewprotocols.ProtocolTreeConfig class method) 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) (tomo.protocols.protocol_ts_import.ProtImportTsBase method) isChild() (pyworkflow.protocol.protocol.Protocol method) isClosed() (pyworkflow.gui.plotter.Plotter method) isCompressed() (pwem.objects.data.Movie method) isContinued() (pyworkflow.protocol.protocol.Protocol method) isCryosparcRunning() (in module cryosparc2.utils) isDefault() (scipion.install.funcs.Target method) isDefocusUDeviationInRange() (tomo.objects.CTFTomo method) isDefocusVDeviationInRange() (tomo.objects.CTFTomo method) isDir() (pyworkflow.gui.browser.FileInfo method) isDisabled() (pwem.protocols.protocol_tests.ProtTests class method) (pyworkflow.protocol.protocol.Protocol class method) isDiscarded() (continuousflex.protocols.data.Point method) (xmipp3.utils.Point method) 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) (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) isFinished() (pyworkflow.protocol.protocol.Step method) isGoldStdProt() (spider.viewers.viewer_refinement.SpiderViewerRefinement 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) (tomo.protocols.protocol_ts_import.ProtImportTsBase method) isInteractive() (pyworkflow.protocol.protocol.Step method) isItemPresent() (xmipp3.protocols.protocol_classification_gpuCorr_full.HashTableDict method) (xmipp3.protocols.protocol_classification_gpuCorr_semi.HashTableDict method) isLaunched() (pyworkflow.protocol.protocol.Step method) isLink() (pyworkflow.gui.browser.FileInfo method) (pyworkflow.project.manager.ProjectInfo method) (pyworkflow.project.project.Project method) isModuleAFolder() (in module pyworkflow.utils.reflection) isModuleLoaded() (in module pyworkflow.utils.reflection) isNew() (pyworkflow.protocol.protocol.Protocol class method) isOddX() (pwem.objects.data.SetOfImages method) isovolumes() (tomo3D.viewers.viewer_mrc.MrcPlot method) isPhaseFlipped() (pwem.objects.data.SetOfImages method) isPlugin() (scipion.install.plugin_manager.PluginBrowser method) isPointer() (pyworkflow.object.Object method) (pyworkflow.protocol.params.DeprecatedParam method) (xmipp3.utils.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 (emfacilities.protocols.pynvml.c_nvmlAccountingStats_t attribute) isRunning() (pyworkflow.protocol.protocol.Step method) isSameFunction() (in module pyworkflow.utils.reflection) isSaved() (pyworkflow.protocol.protocol.Step method) isScheduled() (pyworkflow.protocol.protocol.Step method) isSelected() (continuousflex.protocols.data.Point method) (imod.viewers.views_tkinter_tree.ImodGenericTreeProvider method) (pyworkflow.gui.form.ScalarTreeProvider method) (pyworkflow.gui.form.SubclassesTreeProvider method) (pyworkflow.project.config.NodeConfig method) (tomo.viewers.views_tkinter_tree.CtfEstimationTreeProvider method) (tomo.viewers.views_tkinter_tree.TiltSeriesTreeProvider method) (xmipp3.utils.Point method) isSetOfVolumes() (xmipp3.protocols.protocol_mltomo.XmippProtMLTomo method) isSortingAscending() (pyworkflow.gui.tree.TreeProvider method) isStandardImage() (in module pyworkflow.gui.browser) isStreamClosed() (pyworkflow.object.Set method) isStreamOpen() (pyworkflow.object.Set method) isVersion() (eman2.Plugin class method) (emantomo.Plugin class method) isVersion118() (gctf.protocols.program_gctf.ProgramGctf class method) isVersionActive() (appion.Plugin class method) (atsas.Plugin class method) (bamfordlab.Plugin class method) (ccp4.Plugin class method) (chimera.Plugin class method) (continuousflex.Plugin class method) (jjsoft.Plugin class method) (localrec.Plugin class method) (locscale.Plugin class method) (phenix.Plugin class method) (xmipp2.Plugin class method) isVisible() (pyworkflow.project.config.NodeConfig method) isWaiting() (pyworkflow.protocol.protocol.Step method) isXmippCudaPresent() (in module xmipp3.base) Item (class in pyworkflow.gui.canvas) ITEM_PREFIX (pyworkflow.object.List attribute) ITEM_TYPE (deepfinder.objects.SetOfCoordinates3DWithScore attribute) (pwem.objects.data.SetOfAtomStructs attribute) (pwem.objects.data.SetOfCTF 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.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_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) (tomo.objects.CTFTomoSeries attribute) (tomo.objects.SetOfAverageSubTomograms attribute) (tomo.objects.SetOfCTFTomoSeries attribute) (tomo.objects.SetOfClassesSubTomograms attribute) (tomo.objects.SetOfCoordinates3D attribute) (tomo.objects.SetOfLandmarkModels attribute) (tomo.objects.SetOfMeshes attribute) (tomo.objects.SetOfSubTomograms attribute) (tomo.objects.SetOfTiltSeries attribute) (tomo.objects.SetOfTiltSeriesM attribute) (tomo.objects.SetOfTomoMasks attribute) (tomo.objects.SetOfTomograms attribute) (tomo.objects.TiltSeries attribute) (tomo.objects.TiltSeriesM attribute) itemConfig() (pyworkflow.gui.tree.BoundTree method) iterAll() (continuousflex.protocols.data.Data method) (xmipp3.utils.Data method) iterAllParams() (pyworkflow.protocol.params.Form method) iterAngles() (in module cryoef.convert) iterationStep() (xmipp3.protocols.protocol_classification_gpuCorr.XmippProtGpuCrrCL2D method) (xmipp3.protocols.protocol_classification_gpuCorr_full.XmippProtStrGpuCrrCL2D method) iterAttributes() (emxlib.utils.EmxObject method) iterBigFile() (in module pyworkflow.utils.path) iterChilds() (pyworkflow.utils.graph.Node method) iterChildsBreadth() (pyworkflow.utils.graph.Node method) iterClasses() (emxlib.utils.EmxData method) iterClassItems() (pwem.objects.data.SetOfClasses method) (tomo.objects.SetOfCTFTomoSeries method) (tomo.objects.SetOfTiltSeriesBase method) iterColumns() (pyworkflow.utils.dataset.Table method) iterCoordinates() (pwem.objects.data.SetOfCoordinates method) (tomo.objects.SetOfCoordinates3D method) iterCoords() (sphire.convert.CoordBoxReader method) iterDefinitionAttributes() (pyworkflow.protocol.protocol.Protocol method) iterDefinitionSections() (pyworkflow.protocol.protocol.Protocol method) iterFiles() (imod.protocols.protocol_base.ProtImodBase method) (pwem.protocols.protocol_import.base.ProtImportFiles method) iterForeignKeys() (emxlib.utils.EmxObject 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) (tomo.objects.SetOfCTFTomoSeries method) (tomo.objects.SetOfTiltSeriesBase method) iterLstFile() (in module eman2.convert.convert) (in module emantomo.convert.convert) 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) iterParticlesByMic() (cistem.protocols.protocol_refine2d.CistemProtRefine2D method) (in module eman2.convert.convert) iterPointerParams() (pyworkflow.protocol.params.Form method) iterPrimaryKeys() (emxlib.utils.EmxObject 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) iterSubtomogramsByVol() (in module emantomo.convert.convert) iterValues() (spider.utils.SpiderDocFile method) iterVolumeCoordinates() (tomo.objects.SetOfCoordinates3D method) iterVolumes() (tomo.objects.SetOfCoordinates3D method)

J

JAVA_HOME (pwem.Config attribute) JAVA_MAX_MEMORY (pwem.Config attribute) JJDenoiseIterationsWizard (class in jjsoft.wizards) jjsoft (module) jjsoft.bibtex (module) jjsoft.constants (module) jjsoft.protocols (module) jjsoft.protocols.protocol_align_ts (module) jjsoft.protocols.protocol_denoise_tomogram (module) jjsoft.protocols.protocol_motion_compensation (module) jjsoft.protocols.protocol_reconstruct_tomogram (module)

jjsoft.wizards (module) 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) jsonFilesFromSet() (in module emantomo.convert.convert) jsons2SetCoords3D() (in module emantomo.convert.convert) jsonToCtfModel() (in module eman2.convert.convert) (in module emantomo.convert.convert) justPredict() (xmipp3.protocols.protocol_screen_deepConsensus.XmippProtScreenDeepConsensus method)

K

keepColumns() (in module pwem.emlib.metadata.utils) KendersomBaseClassify (class in xmipp3.protocols.protocol_kerdensom) keyPressed() (pyworkflow.gui.project.viewprotocols.ProtocolsView method) KEYSYM (class in pyworkflow.utils.properties)

KickoffView (class in scipion.scripts.kickoff) KickoffWindow (class in scipion.scripts.kickoff) killJob() (in module cryosparc2.utils) killWithChilds() (in module pyworkflow.utils.process) kmeansClassifyStep() (xmipp3.protocols.protocol_classify_kmeans2d.XmippProtKmeansClassif2D method)

L

l1Cache (emfacilities.protocols.pynvml.c_nvmlEccErrorCounts_t attribute) l2Cache (emfacilities.protocols.pynvml.c_nvmlEccErrorCounts_t attribute) 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_BROWSE_ACTION (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_ACTION (pyworkflow.utils.properties.Message attribute) LABEL_CONTINUE_WORKFLOW (pyworkflow.utils.properties.Message attribute) LABEL_COPY (pyworkflow.utils.properties.Message attribute) LABEL_COPY_ACTION (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_ACTION (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_EDIT (pyworkflow.utils.properties.Message attribute) LABEL_EDIT_ACTION (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_LIST (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)