Python Module Index

a | b | c | d | e | f | g | i | 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_convertsymmetry
    atomstructutils.protocols.protocol_operate
    atomstructutils.viewers
    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.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_abinitio
    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_batch_cluster
    continuousflex.protocols.protocol_nma
    continuousflex.protocols.protocol_nma_alignment
    continuousflex.protocols.protocol_nma_base
    continuousflex.protocols.protocol_nma_choose
    continuousflex.protocols.protocol_nma_dimred
    continuousflex.protocols.protocol_structure_mapping
    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.plotter
    continuousflex.viewers.viewer_nma
    continuousflex.viewers.viewer_nma_alignment
    continuousflex.viewers.viewer_nma_dimred
    continuousflex.viewers.viewer_structure_mapping
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_local_ctf_refinement
    cryosparc2.protocols.protocol_cryosparc_local_refine
    cryosparc2.protocols.protocol_cryosparc_nonuniform_refine
    cryosparc2.protocols.protocol_cryosparc_part_subtract
    cryosparc2.protocols.protocol_cryosparc_sharppening
    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_segment
    deepfinder.protocols.protocol_target_generation
    deepfinder.protocols.protocol_train
    deepfinder.protocols.protocol_utilities
dynamo
    dynamo.bibtex
    dynamo.constants
    dynamo.convert
    dynamo.convert.convert
    dynamo.protocols
    dynamo.protocols.protocol_boxing
    dynamo.protocols.protocol_extraction
    dynamo.protocols.protocol_import_subtomos
    dynamo.protocols.protocol_models
    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_autopick_sparx
    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.protocols.protocol_tomo_boxing
    eman2.protocols.protocol_tomo_extraction
    eman2.protocols.protocol_tomo_initialmodel
    eman2.protocols.protocol_tomo_reconstruction
    eman2.protocols.protocol_tomo_subtomogram_refinement
    eman2.protocols.protocol_tomo_template_match
    eman2.viewers
    eman2.viewers.viewers
    eman2.viewers.viewers_data
    eman2.viewers.views_tkinter_tree
    eman2.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.protocols
    imod.protocols.protocol_applyTransformationMatrix
    imod.protocols.protocol_auto3d
    imod.protocols.protocol_ctfCorrecion
    imod.protocols.protocol_ctfEstimation
    imod.protocols.protocol_etomo
    imod.protocols.protocol_fiducialAlignment
    imod.protocols.protocol_tomoNormalization
    imod.protocols.protocol_tomoReconstruction
    imod.protocols.protocol_tsNormalization
    imod.protocols.protocol_xCorrPrealignment
    imod.utils
    imod.viewers
 
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.viewers
 
n
novactf
    novactf.bibtex
    novactf.constants
    novactf.protocols
    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_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_superpose_pdbs
    phenix.viewers.viewer_validation_cryoem
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_batch
    pwem.protocols.protocol_classes_consensus
    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_metadata_editor
    pwem.protocols.protocol_micrographs
    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_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.viewers_protocols
    pwem.viewers.views
    pwem.wizards
    pwem.wizards.wizard
    pwem.wizards.wizards
pyseg
    pyseg.bibtex
    pyseg.convert
    pyseg.protocols
    pyseg.protocols.protocol_import_starfile
    pyseg.wizards
pyworkflow
    pyworkflow.apps
    pyworkflow.apps.pw_manager
    pyworkflow.apps.pw_plot
    pyworkflow.apps.pw_project
    pyworkflow.apps.pw_protocol_list
    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.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.file_transfer
    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.remote
    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_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_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_sort
    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.viewers.viewer_sort
    relion.wizards
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.convert
    tomo.objects
    tomo.protocols
    tomo.protocols.protocol_alignment_assign_subtomo
    tomo.protocols.protocol_assign_tomo2subtomo
    tomo.protocols.protocol_base
    tomo.protocols.protocol_extract_coordinates
    tomo.protocols.protocol_import_coordinates
    tomo.protocols.protocol_import_subtomograms
    tomo.protocols.protocol_import_tomograms
    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
tomoj
    tomoj.bibtex
    tomoj.constants
    tomoj.protocols
    tomoj.protocols.protocol_xCorrPrealignment
topaz
    topaz.bibtex
    topaz.constants
    topaz.convert
    topaz.protocols
    topaz.protocols.protocol_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_angular_alignment_sph
    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_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_deepres
    xmipp3.protocols.protocol_resolution_directional
    xmipp3.protocols.protocol_resolution_fso
    xmipp3.protocols.protocol_resolution_monogenic_signal
    xmipp3.protocols.protocol_resolution_monotomo
    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_solid_angles
    xmipp3.protocols.protocol_split_volume
    xmipp3.protocols.protocol_split_volume_hierarchical_cluster
    xmipp3.protocols.protocol_structure_map_sph
    xmipp3.protocols.protocol_subtract_projection
    xmipp3.protocols.protocol_trigger_data
    xmipp3.protocols.protocol_validate_fscq
    xmipp3.protocols.protocol_validate_nontilt
    xmipp3.protocols.protocol_validate_overfitting
    xmipp3.protocols.protocol_volume_deform_sph
    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_consensus
    xmipp3.viewers.viewer_deep_micrograph_cleaner
    xmipp3.viewers.viewer_eliminate_empty_images
    xmipp3.viewers.viewer_extract_asymmetric_unit
    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_deepres
    xmipp3.viewers.viewer_resolution_directional
    xmipp3.viewers.viewer_resolution_fso
    xmipp3.viewers.viewer_resolution_monogenic_signal
    xmipp3.viewers.viewer_resolution_monotomo
    xmipp3.viewers.viewer_solid_angles
    xmipp3.viewers.viewer_split_volume
    xmipp3.viewers.viewer_structure_map_sph
    xmipp3.viewers.viewer_swarm
    xmipp3.viewers.viewer_validate_fscq
    xmipp3.viewers.viewer_validate_nontilt
    xmipp3.viewers.viewer_validate_overfitting
    xmipp3.viewers.viewer_volume_deform_sph
    xmipp3.viewers.viewer_volume_strain
    xmipp3.wizards
xmipptomo
    xmipptomo.bibtex
    xmipptomo.protocols
    xmipptomo.protocols.protocol_apply_alignment_subtomo
    xmipptomo.protocols.protocol_cltomo
    xmipptomo.protocols.protocol_connected_components
    xmipptomo.protocols.protocol_coords_roi
    xmipptomo.protocols.protocol_flexalign
    xmipptomo.protocols.protocol_misalignTS
    xmipptomo.protocols.protocol_phantom_subtomo
    xmipptomo.protocols.protocol_project_top
    xmipptomo.protocols.protocol_roiIJ
    xmipptomo.protocols.protocol_splitTS
    xmipptomo.protocols.protocol_subtomo_map_back
    xmipptomo.viewers
    xmipptomo.viewers.viewer_cltomo
    xmipptomo.wizards