Python Module Index

a | b | c | d | e | f | g | i | j | l | m | n | p | r | s | t | x


	a
	`appion`
	`appion.bibtex`
	`appion.constants`
	`appion.convert`
	`appion.convert.convert`
	`appion.convert.dataimport`
	`appion.protocols`
	`appion.protocols.protocol_dogpicker`
	`appion.wizards`
	`atomstructutils`
	`atomstructutils.bibtex`
	`atomstructutils.constants`
	`atomstructutils.protocols`
	`atomstructutils.protocols.protocol_average_subunits`
	`atomstructutils.protocols.protocol_convertsymmetry`
	`atomstructutils.protocols.protocol_operate`
	`atomstructutils.viewers`
	`atomstructutils.viewers.viewer`
	`atomstructutils.viewers.viewer_protocol_convertsymmetry`
	`atomstructutils.wizards`
	`atsas`
	`atsas.bibtex`
	`atsas.constants`
	`atsas.protocols`
	`atsas.protocols.protocol_pdb_to_saxs`
	`atsas.viewers`
	`atsas.viewers.viewer`

	b
	`bamfordlab`
	`bamfordlab.bibtex`
	`bamfordlab.constants`
	`bamfordlab.protocols`
	`bamfordlab.protocols.protocol_ethan_picking`
	`bamfordlab.wizards`
	`bsoft`
	`bsoft.bibtex`
	`bsoft.constants`
	`bsoft.convert`
	`bsoft.protocols`
	`bsoft.protocols.protocol_bfilter`
	`bsoft.protocols.protocol_blocres`
	`bsoft.protocols.protocol_particle_pick`
	`bsoft.viewers`
	`bsoft.viewers.bsoft_viewers`
	`bsoft.wizards`

	c
	`ccp4`
	`ccp4.bibtex`
	`ccp4.constants`
	`ccp4.convert`
	`ccp4.protocols`
	`ccp4.protocols.protocol_coot`
	`ccp4.protocols.protocol_refmac`
	`ccp4.protocols.refmac_template_map2mtz`
	`ccp4.protocols.refmac_template_refine`
	`ccp4.viewers`
	`ccp4.viewers.viewer_coot`
	`ccp4.viewers.viewer_refmac`
	`chimera`
	`chimera.bibtex`
	`chimera.constants`
	`chimera.convert`
	`chimera.editList`
	`chimera.getchimera`
	`chimera.protocols`
	`chimera.protocols.protocol_base`
	`chimera.protocols.protocol_contacts`
	`chimera.protocols.protocol_fit`
	`chimera.protocols.protocol_modeller_search`
	`chimera.protocols.protocol_operate`
	`chimera.protocols.protocol_restore`
	`chimera.protocols.protocol_subtraction_maps`
	`chimera.utils`
	`chimera.viewers`
	`chimera.viewers.viewer`
	`chimera.viewers.viewer_contacts`
	`chimera.wizards`
	`cistem`
	`cistem.bibtex`
	`cistem.constants`
	`cistem.convert`
	`cistem.convert.convert`
	`cistem.convert.dataimport`
	`cistem.protocols`
	`cistem.protocols.program_ctffind`
	`cistem.protocols.protocol_ctffind`
	`cistem.protocols.protocol_picking`
	`cistem.protocols.protocol_refine2d`
	`cistem.protocols.protocol_ts_ctffind`
	`cistem.protocols.protocol_unblur`
	`cistem.viewers`
	`cistem.wizards`
	`continuousflex`
	`continuousflex.bibtex`
	`continuousflex.constants`
	`continuousflex.protocols`
	`continuousflex.protocols.convert`
	`continuousflex.protocols.data`
	`continuousflex.protocols.pdb`
	`continuousflex.protocols.pdb.protocol_convert_pdb`
	`continuousflex.protocols.pdb.protocol_pseudoatoms`
	`continuousflex.protocols.pdb.protocol_pseudoatoms_base`
	`continuousflex.protocols.protocol_apply_volumeset_alignment`
	`continuousflex.protocols.protocol_batch_cluster`
	`continuousflex.protocols.protocol_batch_cluster_vol`
	`continuousflex.protocols.protocol_denoise_volumes`
	`continuousflex.protocols.protocol_image_synthesize`
	`continuousflex.protocols.protocol_missing_wedge_filling`
	`continuousflex.protocols.protocol_nma`
	`continuousflex.protocols.protocol_nma_alignment`
	`continuousflex.protocols.protocol_nma_alignment_vol`
	`continuousflex.protocols.protocol_nma_base`
	`continuousflex.protocols.protocol_nma_choose`
	`continuousflex.protocols.protocol_nma_dimred`
	`continuousflex.protocols.protocol_nma_dimred_vol`
	`continuousflex.protocols.protocol_pdb_dimred`
	`continuousflex.protocols.protocol_structure_mapping`
	`continuousflex.protocols.protocol_subtomogram_averaging`
	`continuousflex.protocols.protocol_subtomograms_classify`
	`continuousflex.protocols.protocol_subtomogrmas_synthesize`
	`continuousflex.protocols.utilities`
	`continuousflex.protocols.utilities.bm4d`
	`continuousflex.protocols.utilities.dynamo`
	`continuousflex.protocols.utilities.mwr`
	`continuousflex.protocols.utilities.mwr.utils`
	`continuousflex.protocols.utilities.mwr.utils.BM4D_v3p2`
	`continuousflex.protocols.utilities.mwr.utils.freezeColors`
	`continuousflex.protocols.utilities.mwr.utils.freezeColors.demo`
	`continuousflex.protocols.utilities.mwr.utils.freezeColors.demo.html`
	`continuousflex.protocols.utilities.mwr.utils.freezeColors.test`
	`continuousflex.protocols.utilities.mwr_wrapper`
	`continuousflex.protocols.utilities.spider_files3`
	`continuousflex.protocols.utilities.spider_matlab`
	`continuousflex.viewers`
	`continuousflex.viewers.nma_gui`
	`continuousflex.viewers.nma_gui.matplotlib_point_path`
	`continuousflex.viewers.nma_gui.matplotlib_point_selector`
	`continuousflex.viewers.nma_gui.tk_clustering`
	`continuousflex.viewers.nma_gui.tk_trajectories`
	`continuousflex.viewers.nma_plotter`
	`continuousflex.viewers.nma_vol_gui`
	`continuousflex.viewers.nma_vol_gui.PointPathVol`
	`continuousflex.viewers.nma_vol_gui.PointSelectorVol`
	`continuousflex.viewers.nma_vol_gui.tk_clustering_vol`
	`continuousflex.viewers.nma_vol_gui.tk_trajectories_vol`
	`continuousflex.viewers.plotter`
	`continuousflex.viewers.plotter_vol`
	`continuousflex.viewers.viewer_image_synthesize`
	`continuousflex.viewers.viewer_nma`
	`continuousflex.viewers.viewer_nma_alignment`
	`continuousflex.viewers.viewer_nma_alignment_vol`
	`continuousflex.viewers.viewer_nma_dimred`
	`continuousflex.viewers.viewer_nma_dimred_vol`
	`continuousflex.viewers.viewer_pdb_dimred`
	`continuousflex.viewers.viewer_structure_mapping`
	`continuousflex.viewers.viewer_subtomograms_classify`
	`continuousflex.viewers.viewer_subtomograms_synthesize`
	`cryocare`
	`cryocare.bibtex`
	`cryocare.constants`
	`cryocare.objects`
	`cryocare.protocols`
	`cryocare.protocols.protocol_load_model`
	`cryocare.protocols.protocol_predict`
	`cryocare.protocols.protocol_prepare_training_data`
	`cryocare.protocols.protocol_training`
	`cryocare.utils`
	`cryocare.wizards`
	`cryoef`
	`cryoef.bibtex`
	`cryoef.constants`
	`cryoef.convert`
	`cryoef.protocols`
	`cryoef.protocols.protocol_cryoef`
	`cryoef.viewers`
	`cryoef.wizards`
	`cryosparc2`
	`cryosparc2.bibtex`
	`cryosparc2.constants`
	`cryosparc2.convert`
	`cryosparc2.convert.convert`
	`cryosparc2.protocols`
	`cryosparc2.protocols.protocol_base`
	`cryosparc2.protocols.protocol_cryorefine`
	`cryosparc2.protocols.protocol_cryosparc2d`
	`cryosparc2.protocols.protocol_cryosparc_3D_classification`
	`cryosparc2.protocols.protocol_cryosparc_ab`
	`cryosparc2.protocols.protocol_cryosparc_global_ctf_refinement`
	`cryosparc2.protocols.protocol_cryosparc_helical_refinement`
	`cryosparc2.protocols.protocol_cryosparc_homogeneous_refine`
	`cryosparc2.protocols.protocol_cryosparc_local_ctf_refinement`
	`cryosparc2.protocols.protocol_cryosparc_naive_local_refine`
	`cryosparc2.protocols.protocol_cryosparc_new_local_refine`
	`cryosparc2.protocols.protocol_cryosparc_new_nonuniform_refine`
	`cryosparc2.protocols.protocol_cryosparc_nonuniform_refine`
	`cryosparc2.protocols.protocol_cryosparc_part_subtract`
	`cryosparc2.protocols.protocol_cryosparc_sharppening`
	`cryosparc2.protocols.protocol_cryosparc_symmetry_expansion`
	`cryosparc2.utils`
	`cryosparc2.viewers`
	`cryosparc2.viewers.viewer_2Dclassify`
	`cryosparc2.viewers.viewer_initialmodel`
	`cryosparc2.viewers.viewer_partsubtract`
	`cryosparc2.viewers.viewer_refinement`
	`cryosparc2.wizards`

	d
	`deepfinder`
	`deepfinder.bibtex`
	`deepfinder.constants`
	`deepfinder.convert`
	`deepfinder.objects`
	`deepfinder.protocols`
	`deepfinder.protocols.protocol_annotation`
	`deepfinder.protocols.protocol_base`
	`deepfinder.protocols.protocol_cluster`
	`deepfinder.protocols.protocol_import_coordinates`
	`deepfinder.protocols.protocol_load_training_model`
	`deepfinder.protocols.protocol_segment`
	`deepfinder.protocols.protocol_target_generation`
	`deepfinder.protocols.protocol_train`
	`deepfinder.protocols.protocol_utilities`
	`deepfinder.viewers`
	`deepfinder.viewers.particle_annotator_tomo_viewer`
	`deepfinder.viewers.particle_annotator_tree`
	`deepfinder.viewers.viewer_deepfinder`
	`dynamo`
	`dynamo.bibtex`
	`dynamo.constants`
	`dynamo.convert`
	`dynamo.convert.convert`
	`dynamo.protocols`
	`dynamo.protocols.protocol_bin_tomograms`
	`dynamo.protocols.protocol_boxing`
	`dynamo.protocols.protocol_extraction`
	`dynamo.protocols.protocol_import_subtomos`
	`dynamo.protocols.protocol_import_tomograms`
	`dynamo.protocols.protocol_model_workflow`
	`dynamo.protocols.protocol_subBoxing`
	`dynamo.protocols.protocol_subtomo_MRA`
	`dynamo.viewers`
	`dynamo.viewers.viewers_data`
	`dynamo.viewers.views_tkinter_tree`
	`dynamo.wizards`

	e
	`eman2`
	`eman2.bibtex`
	`eman2.constants`
	`eman2.convert`
	`eman2.convert.convert`
	`eman2.convert.dataimport`
	`eman2.protocols`
	`eman2.protocols.protocol_autopick_boxer`
	`eman2.protocols.protocol_boxing`
	`eman2.protocols.protocol_ctf`
	`eman2.protocols.protocol_initialmodel`
	`eman2.protocols.protocol_initialmodel_sgd`
	`eman2.protocols.protocol_reconstruct`
	`eman2.protocols.protocol_refine2d`
	`eman2.protocols.protocol_refine2d_bispec`
	`eman2.protocols.protocol_refineasy`
	`eman2.protocols.protocol_tiltvalidate`
	`eman2.viewers`
	`eman2.viewers.viewers`
	`emantomo`
	`emantomo.bibtex`
	`emantomo.constants`
	`emantomo.convert`
	`emantomo.convert.convert`
	`emantomo.convert.dataimport`
	`emantomo.protocols`
	`emantomo.protocols.protocol_align_ts`
	`emantomo.protocols.protocol_tomo_boxing`
	`emantomo.protocols.protocol_tomo_boxing_convnet`
	`emantomo.protocols.protocol_tomo_fill_mw`
	`emantomo.protocols.protocol_tomo_initialmodel`
	`emantomo.protocols.protocol_tomo_reconstruction`
	`emantomo.protocols.protocol_tomo_subtomogram_refinement`
	`emantomo.protocols.protocol_tomo_template_match`
	`emantomo.viewers`
	`emantomo.viewers.viewers`
	`emantomo.viewers.viewers_data`
	`emantomo.viewers.views_tkinter_tree`
	`emantomo.wizards`
	`emfacilities`
	`emfacilities.bibtex`
	`emfacilities.constants`
	`emfacilities.protocols`
	`emfacilities.protocols.getnifs`
	`emfacilities.protocols.protocol_monitor`
	`emfacilities.protocols.protocol_monitor_2d_streamer`
	`emfacilities.protocols.protocol_monitor_ctf`
	`emfacilities.protocols.protocol_monitor_movie_gain`
	`emfacilities.protocols.protocol_monitor_summary`
	`emfacilities.protocols.protocol_monitor_system`
	`emfacilities.protocols.pynvml`
	`emfacilities.protocols.report_html`
	`emfacilities.protocols.report_influx`
	`emfacilities.protocols.summary_provider`
	`emfacilities.protocols.transport`
	`emfacilities.viewers`
	`emfacilities.viewers.viewer_monitors`
	`emxlib`
	`emxlib.bibtex`
	`emxlib.constants`
	`emxlib.convert`
	`emxlib.convert.convert`
	`emxlib.convert.dataimport`
	`emxlib.protocols`
	`emxlib.protocols.protocol_export`
	`emxlib.utils`
	`emxlib.viewers`
	`emxlib.viewers.emxlib_viewers`

	f
	`fsc3d`
	`fsc3d.bibtex`
	`fsc3d.constants`
	`fsc3d.protocols`
	`fsc3d.protocols.protocol_3dfsc`
	`fsc3d.viewers`

	g
	`gautomatch`
	`gautomatch.bibtex`
	`gautomatch.constants`
	`gautomatch.convert`
	`gautomatch.protocols`
	`gautomatch.protocols.protocol_gautomatch`
	`gautomatch.run_gautomatch`
	`gautomatch.viewers`
	`gautomatch.wizards`
	`gctf`
	`gctf.bibtex`
	`gctf.constants`
	`gctf.convert`
	`gctf.convert.convert`
	`gctf.convert.dataimport`
	`gctf.protocols`
	`gctf.protocols.program_gctf`
	`gctf.protocols.protocol_gctf`
	`gctf.protocols.protocol_gctf_refine`
	`gctf.protocols.protocol_ts_gctf`
	`gctf.viewers`
	`gctf.wizards`

	i
	`imod`
	`imod.bibtex`
	`imod.constants`
	`imod.file_handlers`
	`imod.protocols`
	`imod.protocols.protocol_applyTransformationMatrix`
	`imod.protocols.protocol_auto3d`
	`imod.protocols.protocol_base`
	`imod.protocols.protocol_ctfCorrection`
	`imod.protocols.protocol_ctfEstimation_automatic`
	`imod.protocols.protocol_ctfEstimation_manual`
	`imod.protocols.protocol_doseFilter`
	`imod.protocols.protocol_etomo`
	`imod.protocols.protocol_excludeViews`
	`imod.protocols.protocol_fiducialAlignment`
	`imod.protocols.protocol_fiducialModel`
	`imod.protocols.protocol_goldBeadEraser`
	`imod.protocols.protocol_goldBeadPicker3d`
	`imod.protocols.protocol_importSetOfCTFTomoSeries`
	`imod.protocols.protocol_importSetOfTM`
	`imod.protocols.protocol_tomoNormalization`
	`imod.protocols.protocol_tomoProjection`
	`imod.protocols.protocol_tomoReconstruction`
	`imod.protocols.protocol_tsNormalization`
	`imod.protocols.protocol_xCorrPrealignment`
	`imod.protocols.protocol_xRaysEraser`
	`imod.utils`
	`imod.viewers`
	`imod.viewers.viewers`
	`imod.viewers.views_tkinter_tree`

	j
	`jjsoft`
	`jjsoft.bibtex`
	`jjsoft.constants`
	`jjsoft.protocols`
	`jjsoft.protocols.protocol_align_ts`
	`jjsoft.protocols.protocol_denoise_tomogram`
	`jjsoft.protocols.protocol_motion_compensation`
	`jjsoft.protocols.protocol_reconstruct_tomogram`
	`jjsoft.wizards`

	l
	`localrec`
	`localrec.bibtex`
	`localrec.constants`
	`localrec.convert`
	`localrec.progressbar`
	`localrec.protocols`
	`localrec.protocols.protocol_filter_subparticles`
	`localrec.protocols.protocol_localized`
	`localrec.protocols.protocol_localized_extraction`
	`localrec.protocols.protocol_localized_set_origin`
	`localrec.protocols.protocol_localized_stitch`
	`localrec.protocols.protocol_localized_subset`
	`localrec.utils`
	`localrec.viewers`
	`localrec.viewers.viewer`
	`locscale`
	`locscale.bibtex`
	`locscale.constants`
	`locscale.convert`
	`locscale.protocols`
	`locscale.protocols.protocol_locscale`

	m
	`motioncorr`
	`motioncorr.bibtex`
	`motioncorr.constants`
	`motioncorr.convert`
	`motioncorr.protocols`
	`motioncorr.protocols.protocol_motioncorr`
	`motioncorr.protocols.protocol_ts_motioncor`
	`motioncorr.viewers`

	n
	`novactf`
	`novactf.bibtex`
	`novactf.constants`
	`novactf.protocols`
	`novactf.protocols.protocol_tomoDefocus`
	`novactf.protocols.protocol_tomoReconstruction`

	p
	`phenix`
	`phenix.bibtex`
	`phenix.constants`
	`phenix.protocols`
	`phenix.protocols.protocol_dock_in_map`
	`phenix.protocols.protocol_emringer`
	`phenix.protocols.protocol_molprobity`
	`phenix.protocols.protocol_real_space_refine`
	`phenix.protocols.protocol_refinement_base`
	`phenix.protocols.protocol_search_fit`
	`phenix.protocols.protocol_superpose_pdbs`
	`phenix.protocols.protocol_validation_cryoem`
	`phenix.viewers`
	`phenix.viewers.viewer_dock_in_map`
	`phenix.viewers.viewer_emringer`
	`phenix.viewers.viewer_molprobity`
	`phenix.viewers.viewer_real_space_refine`
	`phenix.viewers.viewer_refinement_base`
	`phenix.viewers.viewer_search_fit`
	`phenix.viewers.viewer_superpose_pdbs`
	`phenix.viewers.viewer_validation_cryoem`
	`phenix.wizards`
	`pwem`
	`pwem.bibtex`
	`pwem.constants`
	`pwem.convert`
	`pwem.convert.atom_struct`
	`pwem.convert.headers`
	`pwem.convert.sequence`
	`pwem.convert.symmetry`
	`pwem.convert.transformations`
	`pwem.convert.utils`
	`pwem.emlib`
	`pwem.emlib.image`
	`pwem.emlib.image.image_handler`
	`pwem.emlib.lib`
	`pwem.emlib.metadata`
	`pwem.emlib.metadata.utils`
	`pwem.objects`
	`pwem.objects.data`
	`pwem.objects.data_tiltpairs`
	`pwem.protocols`
	`pwem.protocols.parallel`
	`pwem.protocols.protocol`
	`pwem.protocols.protocol_2d`
	`pwem.protocols.protocol_3d`
	`pwem.protocols.protocol_align_movies`
	`pwem.protocols.protocol_alignment_assign`
	`pwem.protocols.protocol_alignment_invertHand`
	`pwem.protocols.protocol_batch`
	`pwem.protocols.protocol_classes_selector`
	`pwem.protocols.protocol_create_stream_data`
	`pwem.protocols.protocol_ctf_assign`
	`pwem.protocols.protocol_export`
	`pwem.protocols.protocol_export.protocol_export_DB`
	`pwem.protocols.protocol_extract_coordinates`
	`pwem.protocols.protocol_import`
	`pwem.protocols.protocol_import.base`
	`pwem.protocols.protocol_import.coordinates`
	`pwem.protocols.protocol_import.ctfs`
	`pwem.protocols.protocol_import.dataimport`
	`pwem.protocols.protocol_import.images`
	`pwem.protocols.protocol_import.masks`
	`pwem.protocols.protocol_import.micrographs`
	`pwem.protocols.protocol_import.particles`
	`pwem.protocols.protocol_import.sequence`
	`pwem.protocols.protocol_import.volumes`
	`pwem.protocols.protocol_micrographs`
	`pwem.protocols.protocol_movie_eraser`
	`pwem.protocols.protocol_movies`
	`pwem.protocols.protocol_origin_sampling_volume`
	`pwem.protocols.protocol_particles`
	`pwem.protocols.protocol_particles_picking`
	`pwem.protocols.protocol_pdf_report`
	`pwem.protocols.protocol_set_editor`
	`pwem.protocols.protocol_set_filter`
	`pwem.protocols.protocol_sets`
	`pwem.protocols.protocol_tests`
	`pwem.protocols.protocol_tiltpairs`
	`pwem.utils`
	`pwem.viewers`
	`pwem.viewers.filehandlers`
	`pwem.viewers.plotter`
	`pwem.viewers.showj`
	`pwem.viewers.viewer_base`
	`pwem.viewers.viewer_chimera`
	`pwem.viewers.viewer_fsc`
	`pwem.viewers.viewer_localres`
	`pwem.viewers.viewer_pdf`
	`pwem.viewers.viewer_sequence`
	`pwem.viewers.viewer_vmd`
	`pwem.viewers.viewer_volumes`
	`pwem.viewers.viewers_data`
	`pwem.viewers.views`
	`pwem.wizards`
	`pwem.wizards.wizard`
	`pwem.wizards.wizards`
	`pwem.wizards.wizards_3d`
	`pwem.wizards.wizards_3d.callbacks`
	`pwem.wizards.wizards_3d.mask_structure_wizard`
	`pwem.wizards.wizards_3d.mask_volume_wizard`
	`pwperformance`
	`pwperformance.hassAttrVsTry`
	`pwperformance.loggers`
	`pwperformance.loggers.influxdb`
	`pwperformance.main`
	`pwperformance.StaticVsInstanceMethod`
	`pyseg`
	`pyseg.bibtex`
	`pyseg.constants`
	`pyseg.convert`
	`pyseg.protocols`
	`pyseg.protocols.protocol_2d_classification`
	`pyseg.protocols.protocol_fils`
	`pyseg.protocols.protocol_graphs`
	`pyseg.protocols.protocol_picking`
	`pyseg.protocols.protocol_post_rec_particles`
	`pyseg.protocols.protocol_pre_seg`
	`pyseg.utils`
	`pyseg.viewers`
	`pyseg.viewers.vesicle_graphs_fils_viewer`
	`pyseg.viewers.vesicle_visualization_tree`
	`pyseg.viewers.viewers_data`
	`pyworkflow`
	`pyworkflow.apps`
	`pyworkflow.apps.pw_manager`
	`pyworkflow.apps.pw_plot`
	`pyworkflow.apps.pw_project`
	`pyworkflow.apps.pw_protocol_list`
	`pyworkflow.apps.pw_protocol_mpirun`
	`pyworkflow.apps.pw_protocol_remote`
	`pyworkflow.apps.pw_protocol_run`
	`pyworkflow.apps.pw_run_tests`
	`pyworkflow.apps.pw_schedule_run`
	`pyworkflow.apps.pw_sleep`
	`pyworkflow.apps.pw_sync_data`
	`pyworkflow.apps.pw_viewer`
	`pyworkflow.config`
	`pyworkflow.constants`
	`pyworkflow.exceptions`
	`pyworkflow.gui`
	`pyworkflow.gui.browser`
	`pyworkflow.gui.canvas`
	`pyworkflow.gui.dialog`
	`pyworkflow.gui.form`
	`pyworkflow.gui.graph`
	`pyworkflow.gui.graph_layout`
	`pyworkflow.gui.gui`
	`pyworkflow.gui.matplotlib_image`
	`pyworkflow.gui.plotter`
	`pyworkflow.gui.project`
	`pyworkflow.gui.project.base`
	`pyworkflow.gui.project.constants`
	`pyworkflow.gui.project.labels`
	`pyworkflow.gui.project.project`
	`pyworkflow.gui.project.utils`
	`pyworkflow.gui.project.viewdata`
	`pyworkflow.gui.project.viewprojects`
	`pyworkflow.gui.project.viewprotocols`
	`pyworkflow.gui.text`
	`pyworkflow.gui.tooltip`
	`pyworkflow.gui.tree`
	`pyworkflow.gui.widgets`
	`pyworkflow.mapper`
	`pyworkflow.mapper.mapper`
	`pyworkflow.mapper.sqlite`
	`pyworkflow.mapper.sqlite_db`
	`pyworkflow.mapper.xmlmapper`
	`pyworkflow.object`
	`pyworkflow.plugin`
	`pyworkflow.project`
	`pyworkflow.project.config`
	`pyworkflow.project.manager`
	`pyworkflow.project.project`
	`pyworkflow.protocol`
	`pyworkflow.protocol.bibtex`
	`pyworkflow.protocol.constants`
	`pyworkflow.protocol.executor`
	`pyworkflow.protocol.hosts`
	`pyworkflow.protocol.launch`
	`pyworkflow.protocol.package`
	`pyworkflow.protocol.params`
	`pyworkflow.protocol.protocol`
	`pyworkflow.template`
	`pyworkflow.tests`
	`pyworkflow.tests.test_utils`
	`pyworkflow.tests.tests`
	`pyworkflow.utils`
	`pyworkflow.utils.dataset`
	`pyworkflow.utils.echo`
	`pyworkflow.utils.graph`
	`pyworkflow.utils.log`
	`pyworkflow.utils.mpi`
	`pyworkflow.utils.path`
	`pyworkflow.utils.process`
	`pyworkflow.utils.profiler`
	`pyworkflow.utils.progressbar`
	`pyworkflow.utils.properties`
	`pyworkflow.utils.reflection`
	`pyworkflow.utils.utils`
	`pyworkflow.utils.which`
	`pyworkflow.viewer`
	`pyworkflow.webservices`
	`pyworkflow.webservices.config`
	`pyworkflow.webservices.notifier`
	`pyworkflow.webservices.repository`
	`pyworkflow.wizard`

	r
	`relion`
	`relion.bibtex`
	`relion.constants`
	`relion.convert`
	`relion.convert.convert30`
	`relion.convert.convert31`
	`relion.convert.convert_base`
	`relion.convert.convert_coordinates`
	`relion.convert.convert_deprecated`
	`relion.convert.convert_utils`
	`relion.convert.dataimport`
	`relion.objects`
	`relion.protocols`
	`relion.protocols.protocol_assign_optic_groups`
	`relion.protocols.protocol_autopick`
	`relion.protocols.protocol_autopick_log`
	`relion.protocols.protocol_autopick_ref`
	`relion.protocols.protocol_base`
	`relion.protocols.protocol_bayesian_polishing`
	`relion.protocols.protocol_center_averages`
	`relion.protocols.protocol_classify2d`
	`relion.protocols.protocol_classify3d`
	`relion.protocols.protocol_compress_estimate_gain`
	`relion.protocols.protocol_compress_movies`
	`relion.protocols.protocol_create_mask3d`
	`relion.protocols.protocol_crop_resize`
	`relion.protocols.protocol_ctf_refinement`
	`relion.protocols.protocol_expand_symmetry`
	`relion.protocols.protocol_export_coords`
	`relion.protocols.protocol_export_ctf`
	`relion.protocols.protocol_export_particles`
	`relion.protocols.protocol_extract_particles`
	`relion.protocols.protocol_gentle_clean`
	`relion.protocols.protocol_initialmodel`
	`relion.protocols.protocol_localres`
	`relion.protocols.protocol_motioncor`
	`relion.protocols.protocol_multibody`
	`relion.protocols.protocol_postprocess`
	`relion.protocols.protocol_preprocess`
	`relion.protocols.protocol_reconstruct`
	`relion.protocols.protocol_refine3d`
	`relion.protocols.protocol_remove_views`
	`relion.protocols.protocol_subtract`
	`relion.protocols.protocol_symmetrize_volume`
	`relion.viewers`
	`relion.viewers.viewer_base`
	`relion.viewers.viewer_ctfrefine`
	`relion.viewers.viewer_locres`
	`relion.viewers.viewer_motioncor`
	`relion.viewers.viewer_polishing`
	`relion.viewers.viewer_postprocess`
	`relion.wizards`
	`reliontomo`
	`reliontomo.bibtex`
	`reliontomo.constants`
	`reliontomo.convert`
	`reliontomo.convert.convert30_tomo`
	`reliontomo.protocols`
	`reliontomo.protocols.protocol_base_tomo`
	`reliontomo.protocols.protocol_classify_3d_tomo`
	`reliontomo.protocols.protocol_ctf_3d_estimation`
	`reliontomo.protocols.protocol_reconstruct_subtomo`
	`reliontomo.protocols.protocol_refine_3d_tomo`
	`resmap`
	`resmap.bibtex`
	`resmap.constants`
	`resmap.protocols`
	`resmap.protocols.protocol_resmap`
	`resmap.viewers`
	`resmap.viewers.resmap_viewers`
	`resmap.wizards`

	s
	`scipion`
	`scipion.constants`
	`scipion.guiplugin`
	`scipion.install`
	`scipion.install.change_rpath`
	`scipion.install.clean`
	`scipion.install.find_deps`
	`scipion.install.funcs`
	`scipion.install.install_plugin`
	`scipion.install.plugin_funcs`
	`scipion.install.plugin_manager`
	`scipion.install.update_manager`
	`scipion.scripts`
	`scipion.scripts.config`
	`scipion.scripts.fontbrowser`
	`scipion.scripts.kickoff`
	`scipion.scripts.tutorial`
	`scipion.utils`
	`sidesplitter`
	`sidesplitter.bibtex`
	`sidesplitter.constants`
	`sidesplitter.convert`
	`sidesplitter.protocols`
	`sidesplitter.protocols.protocol_sidesplitter`
	`sphire`
	`sphire.bibtex`
	`sphire.constants`
	`sphire.convert`
	`sphire.objects`
	`sphire.protocols`
	`sphire.protocols.protocol_cryolo_import`
	`sphire.protocols.protocol_cryolo_picking`
	`sphire.protocols.protocol_cryolo_training`
	`sphire.protocols.protocol_janni_denoise`
	`spider`
	`spider.bibtex`
	`spider.constants`
	`spider.convert`
	`spider.objects`
	`spider.protocols`
	`spider.protocols.protocol_align_apsr`
	`spider.protocols.protocol_align_base`
	`spider.protocols.protocol_align_pairwise`
	`spider.protocols.protocol_base`
	`spider.protocols.protocol_ca_pca`
	`spider.protocols.protocol_classify_base`
	`spider.protocols.protocol_classify_diday`
	`spider.protocols.protocol_classify_kmeans`
	`spider.protocols.protocol_classify_ward`
	`spider.protocols.protocol_custommask`
	`spider.protocols.protocol_filters`
	`spider.protocols.protocol_projmatch`
	`spider.protocols.protocol_reconstruct`
	`spider.utils`
	`spider.viewers`
	`spider.viewers.viewer`
	`spider.viewers.viewer_capca`
	`spider.viewers.viewer_classify`
	`spider.viewers.viewer_refinement`
	`spider.wizards`

	t
	`tomo`
	`tomo.constants`
	`tomo.convert`
	`tomo.convert.convert`
	`tomo.objects`
	`tomo.protocols`
	`tomo.protocols.protocol_alignment_assign`
	`tomo.protocols.protocol_assign_tomo2subtomo`
	`tomo.protocols.protocol_assignTransformationTS`
	`tomo.protocols.protocol_base`
	`tomo.protocols.protocol_consensus_classes_subtomo`
	`tomo.protocols.protocol_ctf_validate`
	`tomo.protocols.protocol_extract_coordinates`
	`tomo.protocols.protocol_import_coordinates`
	`tomo.protocols.protocol_import_subtomograms`
	`tomo.protocols.protocol_import_tomograms`
	`tomo.protocols.protocol_split_evenodd_subtomos`
	`tomo.protocols.protocol_ts_base`
	`tomo.protocols.protocol_ts_correct_motion`
	`tomo.protocols.protocol_ts_estimate_ctf`
	`tomo.protocols.protocol_ts_import`
	`tomo.utils`
	`tomo.viewers`
	`tomo.viewers.viewer_tomograms`
	`tomo.viewers.viewers_data`
	`tomo.viewers.views`
	`tomo.viewers.views_tkinter_tree`
	`tomo.wizards`
	`tomo3D`
	`tomo3D.bibtex`
	`tomo3D.protocols`
	`tomo3D.protocols.protocol_mesh_normal`
	`tomo3D.protocols.protocol_particle_pick_consensus`
	`tomo3D.protocols.protocol_particle_pick_remove_duplicates`
	`tomo3D.utils`
	`tomo3D.viewers`
	`tomo3D.viewers.viewer_mrc`
	`tomo3D.viewers.viewer_triangulations`
	`tomo3D.viewers.viewer_vtk`
	`tomo3D.viewers.viewers_data`
	`tomo3D.viewers.views_tkinter_tree`
	`tomoj`
	`tomoj.bibtex`
	`tomoj.constants`
	`tomoj.protocols`
	`tomoj.protocols.protocol_xCorrPrealignment`
	`topaz`
	`topaz.bibtex`
	`topaz.constants`
	`topaz.convert`
	`topaz.objects`
	`topaz.protocols`
	`topaz.protocols.protocol_base`
	`topaz.protocols.protocol_topaz_import`
	`topaz.protocols.protocol_topaz_picking`
	`topaz.protocols.protocol_topaz_training`

	x
	`xmipp2`
	`xmipp2.bibtex`
	`xmipp2.constants`
	`xmipp2.convert`
	`xmipp2.convert.convert`
	`xmipp2.protocols`
	`xmipp2.protocols.protocol_mltomo`
	`xmipp2.viewers`
	`xmipp2.viewers.viewer`
	`xmipp2.viewers.viewer_MlTomo`
	`xmipp2.wizards`
	`xmipp3`
	`xmipp3.base`
	`xmipp3.bibtex`
	`xmipp3.constants`
	`xmipp3.convert`
	`xmipp3.convert.convert`
	`xmipp3.convert.dataimport`
	`xmipp3.convert.io_coordinates`
	`xmipp3.programs`
	`xmipp3.protocols`
	`xmipp3.protocols.protocol_align_volume`
	`xmipp3.protocols.protocol_align_volume_and_particles`
	`xmipp3.protocols.protocol_analyze_local_ctf`
	`xmipp3.protocols.protocol_apply_alignment`
	`xmipp3.protocols.protocol_apply_transformation_matrix`
	`xmipp3.protocols.protocol_assignment_tilt_pair`
	`xmipp3.protocols.protocol_break_symmetry`
	`xmipp3.protocols.protocol_center_particles`
	`xmipp3.protocols.protocol_cl2d`
	`xmipp3.protocols.protocol_cl2d_align`
	`xmipp3.protocols.protocol_classification_gpuCorr`
	`xmipp3.protocols.protocol_classification_gpuCorr_full`
	`xmipp3.protocols.protocol_classification_gpuCorr_semi`
	`xmipp3.protocols.protocol_classify_kmeans2d`
	`xmipp3.protocols.protocol_compare_angles`
	`xmipp3.protocols.protocol_compare_reprojections`
	`xmipp3.protocols.protocol_consensus_classes3D`
	`xmipp3.protocols.protocol_consensus_local_ctf`
	`xmipp3.protocols.protocol_convert_pdb`
	`xmipp3.protocols.protocol_create_gallery`
	`xmipp3.protocols.protocol_ctf_consensus`
	`xmipp3.protocols.protocol_ctf_correct_wiener2d`
	`xmipp3.protocols.protocol_ctf_defocus_group`
	`xmipp3.protocols.protocol_ctf_micrographs`
	`xmipp3.protocols.protocol_deep_align`
	`xmipp3.protocols.protocol_deep_denoising`
	`xmipp3.protocols.protocol_deep_micrograph_screen`
	`xmipp3.protocols.protocol_denoise_particles`
	`xmipp3.protocols.protocol_eliminate_empty_images`
	`xmipp3.protocols.protocol_enrich`
	`xmipp3.protocols.protocol_extract_asymmetric_unit`
	`xmipp3.protocols.protocol_extract_particles`
	`xmipp3.protocols.protocol_extract_particles_movies`
	`xmipp3.protocols.protocol_extract_particles_pairs`
	`xmipp3.protocols.protocol_generate_reprojections`
	`xmipp3.protocols.protocol_helical_parameters`
	`xmipp3.protocols.protocol_kerdensom`
	`xmipp3.protocols.protocol_local_ctf`
	`xmipp3.protocols.protocol_metaprotocol_create_output`
	`xmipp3.protocols.protocol_metaprotocol_create_subset`
	`xmipp3.protocols.protocol_metaprotocol_discrete_heterogeneity_scheduler`
	`xmipp3.protocols.protocol_metaprotocol_golden_highres`
	`xmipp3.protocols.protocol_ml2d`
	`xmipp3.protocols.protocol_mltomo`
	`xmipp3.protocols.protocol_movie_average`
	`xmipp3.protocols.protocol_movie_correlation`
	`xmipp3.protocols.protocol_movie_gain`
	`xmipp3.protocols.protocol_movie_max_shift`
	`xmipp3.protocols.protocol_movie_opticalflow`
	`xmipp3.protocols.protocol_movie_split_frames`
	`xmipp3.protocols.protocol_multiple_fscs`
	`xmipp3.protocols.protocol_multireference_alignability`
	`xmipp3.protocols.protocol_normalize_strain`
	`xmipp3.protocols.protocol_particle_boxsize`
	`xmipp3.protocols.protocol_particle_pick`
	`xmipp3.protocols.protocol_particle_pick_automatic`
	`xmipp3.protocols.protocol_particle_pick_consensus`
	`xmipp3.protocols.protocol_particle_pick_pairs`
	`xmipp3.protocols.protocol_particle_pick_remove_duplicates`
	`xmipp3.protocols.protocol_pick_noise`
	`xmipp3.protocols.protocol_postProcessing_deepPostProcessing`
	`xmipp3.protocols.protocol_preprocess`
	`xmipp3.protocols.protocol_preprocess.geometrical_mask`
	`xmipp3.protocols.protocol_preprocess.protocol_add_noise`
	`xmipp3.protocols.protocol_preprocess.protocol_create_mask2d`
	`xmipp3.protocols.protocol_preprocess.protocol_create_mask3d`
	`xmipp3.protocols.protocol_preprocess.protocol_crop_resize`
	`xmipp3.protocols.protocol_preprocess.protocol_filter`
	`xmipp3.protocols.protocol_preprocess.protocol_image_operate`
	`xmipp3.protocols.protocol_preprocess.protocol_mask`
	`xmipp3.protocols.protocol_preprocess.protocol_movie_resize`
	`xmipp3.protocols.protocol_preprocess.protocol_preprocess`
	`xmipp3.protocols.protocol_preprocess.protocol_process`
	`xmipp3.protocols.protocol_preprocess_micrographs`
	`xmipp3.protocols.protocol_projmatch`
	`xmipp3.protocols.protocol_projmatch.projmatch_form`
	`xmipp3.protocols.protocol_projmatch.projmatch_initialize`
	`xmipp3.protocols.protocol_projmatch.projmatch_steps`
	`xmipp3.protocols.protocol_projmatch.protocol_projmatch`
	`xmipp3.protocols.protocol_random_conical_tilt`
	`xmipp3.protocols.protocol_ransac`
	`xmipp3.protocols.protocol_reconstruct_fourier`
	`xmipp3.protocols.protocol_reconstruct_heterogeneous`
	`xmipp3.protocols.protocol_reconstruct_highres`
	`xmipp3.protocols.protocol_reconstruct_significant`
	`xmipp3.protocols.protocol_reconstruct_swarm`
	`xmipp3.protocols.protocol_resolution3d`
	`xmipp3.protocols.protocol_resolution_bfactor`
	`xmipp3.protocols.protocol_resolution_deepres`
	`xmipp3.protocols.protocol_resolution_directional`
	`xmipp3.protocols.protocol_resolution_fso`
	`xmipp3.protocols.protocol_resolution_monogenic_signal`
	`xmipp3.protocols.protocol_rotational_spectra`
	`xmipp3.protocols.protocol_rotational_symmetry`
	`xmipp3.protocols.protocol_screen_deepConsensus`
	`xmipp3.protocols.protocol_screen_deeplearning`
	`xmipp3.protocols.protocol_screen_particles`
	`xmipp3.protocols.protocol_shift_particles`
	`xmipp3.protocols.protocol_simulate_ctf`
	`xmipp3.protocols.protocol_solid_angles`
	`xmipp3.protocols.protocol_split_volume`
	`xmipp3.protocols.protocol_split_volume_hierarchical_cluster`
	`xmipp3.protocols.protocol_trigger_data`
	`xmipp3.protocols.protocol_validate_fscq`
	`xmipp3.protocols.protocol_validate_nontilt`
	`xmipp3.protocols.protocol_validate_overfitting`
	`xmipp3.protocols.protocol_volume_adjust_sub`
	`xmipp3.protocols.protocol_volume_consensus`
	`xmipp3.protocols.protocol_volume_local_sharpening`
	`xmipp3.protocols.protocol_volume_strain`
	`xmipp3.protocols.protocol_write_testC`
	`xmipp3.protocols.protocol_write_testP`
	`xmipp3.utils`
	`xmipp3.viewers`
	`xmipp3.viewers.plotter`
	`xmipp3.viewers.viewer`
	`xmipp3.viewers.viewer_analyze_local_ctf`
	`xmipp3.viewers.viewer_angular_alignment_sph`
	`xmipp3.viewers.viewer_cl2d`
	`xmipp3.viewers.viewer_ctf_consensus`
	`xmipp3.viewers.viewer_deep_align`
	`xmipp3.viewers.viewer_deep_consensus`
	`xmipp3.viewers.viewer_deep_micrograph_cleaner`
	`xmipp3.viewers.viewer_deepEMHancer`
	`xmipp3.viewers.viewer_eliminate_empty_images`
	`xmipp3.viewers.viewer_extract_asymmetric_unit`
	`xmipp3.viewers.viewer_local_sharpening`
	`xmipp3.viewers.viewer_metaprotocol_golden_highres`
	`xmipp3.viewers.viewer_ml2d`
	`xmipp3.viewers.viewer_mltomo`
	`xmipp3.viewers.viewer_movie_alignment`
	`xmipp3.viewers.viewer_normalize_strain`
	`xmipp3.viewers.viewer_projmatch`
	`xmipp3.viewers.viewer_ransac`
	`xmipp3.viewers.viewer_reconstruct_highres`
	`xmipp3.viewers.viewer_resolution3d`
	`xmipp3.viewers.viewer_resolution_bfactor`
	`xmipp3.viewers.viewer_resolution_deepres`
	`xmipp3.viewers.viewer_resolution_directional`
	`xmipp3.viewers.viewer_resolution_fso`
	`xmipp3.viewers.viewer_resolution_monogenic_signal`
	`xmipp3.viewers.viewer_solid_angles`
	`xmipp3.viewers.viewer_split_volume`
	`xmipp3.viewers.viewer_swarm`
	`xmipp3.viewers.viewer_validate_fscq`
	`xmipp3.viewers.viewer_validate_nontilt`
	`xmipp3.viewers.viewer_validate_overfitting`
	`xmipp3.viewers.viewer_volume_consensus`
	`xmipp3.viewers.viewer_volume_strain`
	`xmipp3.viewers.viewer_volume_subtraction`
	`xmipp3.wizards`
	`xmipptomo`
	`xmipptomo.bibtex`
	`xmipptomo.protocols`
	`xmipptomo.protocols.protocol_align_transform`
	`xmipptomo.protocols.protocol_apply_alignment_subtomo`
	`xmipptomo.protocols.protocol_applyAlignmentTS`
	`xmipptomo.protocols.protocol_cltomo`
	`xmipptomo.protocols.protocol_connected_components`
	`xmipptomo.protocols.protocol_coords_roi`
	`xmipptomo.protocols.protocol_fit_ellipsoid`
	`xmipptomo.protocols.protocol_flexalign`
	`xmipptomo.protocols.protocol_misalignTS`
	`xmipptomo.protocols.protocol_phantom_subtomo`
	`xmipptomo.protocols.protocol_project_top`
	`xmipptomo.protocols.protocol_resize_base`
	`xmipptomo.protocols.protocol_resize_tomograms`
	`xmipptomo.protocols.protocol_resizeTS`
	`xmipptomo.protocols.protocol_resolution_local_monotomo`
	`xmipptomo.protocols.protocol_roiIJ`
	`xmipptomo.protocols.protocol_rotate_astigmatism`
	`xmipptomo.protocols.protocol_score_coordinates`
	`xmipptomo.protocols.protocol_score_transform`
	`xmipptomo.protocols.protocol_splitTS`
	`xmipptomo.protocols.protocol_subtomo_map_back`
	`xmipptomo.protocols.protocol_subtraction_subtomo`
	`xmipptomo.utils`
	`xmipptomo.viewers`
	`xmipptomo.viewers.monotomo_tree_provider`
	`xmipptomo.viewers.viewer_cltomo`
	`xmipptomo.viewers.viewer_resolution_local_monotomo`
	`xmipptomo.wizards`