[ccpem_pipeliner.jobs]
acedrg.create_ligand = pipeliner.jobs.ccpem.acedrg_job:AceDRGCreateLigand
ccpem_utils.atomic_model_utilities.shift_origin_nstart = pipeliner.jobs.ccpem.model_shift_job:ModelShift
ccpem_utils.map_utilities.crop_pad_mask_map = pipeliner.jobs.ccpem.map_crop_pad_mask_job:CropPadMap
ccpem_utils.map_utilities.shift_origin_nstart = pipeliner.jobs.ccpem.map_shift_job:MapShift
checkmysequence.atomic_model_validation = pipeliner.jobs.other.checkmysequence_job:ModelSequenceValidate
cinderella.select.class_averages = pipeliner.jobs.other.cinderella_job:CinderellaPredict
cinderella.select.class_averages.train = pipeliner.jobs.other.cinderella_job:CinderellaTrain
confidencemap.map_analysis = pipeliner.jobs.ccpem.confidence_map_job:ConfidenceMap
cryodann.select.particles = pipeliner.jobs.ccpem.cryodann_job:CryoDANN
cryodrgn.abinit_het = pipeliner.jobs.ccpem.cryodrgn_abinit_het_job:CryodrgnAbinitHetJob
cryodrgn.abinit_homo = pipeliner.jobs.ccpem.cryodrgn_abinit_homo_job:CryodrgnAbinitHomoJob
cryodrgn.filter = pipeliner.jobs.ccpem.cryodrgn_filter_job:CryodrgnFilterJob
cryodrgn.train_vae = pipeliner.jobs.ccpem.cryodrgn_train_vae_job:CryodrgnTrainVAEJob
cryoef.map_analysis = pipeliner.jobs.other.cryoef_job:CryoEF
cryolo.autopick = pipeliner.jobs.other.cryolo_job:CrYOLOAutopickSPA
cryolo.autopick.tomo = pipeliner.jobs.other.cryolo_job:CrYOLOAutopickTomo
cryovae.image_analysis = pipeliner.jobs.ccpem.cryovae_job:CryoVAE
doppio.manualpick.edit = pipeliner.jobs.doppio.doppio_edit_picks_job:DoppioEditPicks
doublehelix.atomic_model_utilities.assign_sequence = pipeliner.jobs.other.doublehelix_job:ModelSequenceAssignNA
dpiscore.interface_validation = pipeliner.jobs.ccpem.dpi_score_job:DPIscore
dynamight = pipeliner.jobs.relion.dynamight_job:DynamightContinuousHeterogeneity
em_placement.atomic_model_fit = pipeliner.jobs.ccpem.em_placement_job:EMPlacement
emda.mask_creation.half_maps = pipeliner.jobs.other.emda_map_mask_job:EmdaMapMask
emdb_validation_analysis.map_model_validation = pipeliner.jobs.other.emdb_validation_analysis_job:MapModelValidate
emplace_local.atomic_model_fit = pipeliner.jobs.ccpem.emplace_local_job:EMPlaceLocal
eulermate.import.coordinates = pipeliner.jobs.tomography.other.tomo_eulermate_job:EulermateJob
findmysequence.atomic_model_utilities.assign_sequence = pipeliner.jobs.other.findmysequence_job:ModelSequenceAssign
flex_em.atomic_model_refine = pipeliner.jobs.ccpem.flex_em_job:FlexEM
gemmi.atomic_model_utilities.model_to_map = pipeliner.jobs.ccpem.gemmi_model_to_map_job:GemmiModelToMap
gemmi.atomic_model_utilities.process_model = pipeliner.jobs.ccpem.gemmi_process_model_job:GemmiProcessModel
icebreaker.micrograph_analysis.enhancecontrast = pipeliner.jobs.other.icebreaker_job:IceBreakerFlatten
icebreaker.micrograph_analysis.micrographs = pipeliner.jobs.other.icebreaker_job:IceBreakerGroupMics
icebreaker.micrograph_analysis.particles = pipeliner.jobs.other.icebreaker_job:IceBreakerGroupParts
icebreaker.micrograph_analysis.summary = pipeliner.jobs.other.icebreaker_job:IceBreakerFiveFigureSummary
lafter.postprocess.local_denoising = pipeliner.jobs.ccpem.lafter_job:LafterJob
locscale.postprocess.local_sharpening = pipeliner.jobs.ccpem.locscale_job:LocalSharpen
ltm.create.mask = pipeliner.jobs.tomography.other.tomo_create_mask_job:LtmCreateMaskJob
ltm.create.template = pipeliner.jobs.tomography.other.tomo_create_template_job:LtmCreateTemplateJob
ltm.extract.peaks = pipeliner.jobs.tomography.other.tomo_ltm_job:LtmExtractPeaksJob
ltm.halftomo.localcc = pipeliner.jobs.tomography.other.tomo_ltm_job:LtmHalfTomoLocalCCJob
ltm.template.match = pipeliner.jobs.tomography.other.tomo_ltm_job:LtmJob
metalcoord.create_restraints = pipeliner.jobs.ccpem.metalcoord_job:MetalCoord
modelangelo = pipeliner.jobs.relion.modelangelo_job:ModelAngelo
modelcraft.atomic_model_build = pipeliner.jobs.ccpem.modelcraft_job:ModelCraftJob
molprobity.atomic_model_validation.geometry = pipeliner.jobs.ccpem.molprobity_job:ValidateGeometry
molrep.atomic_model_fit = pipeliner.jobs.ccpem.molrep_job:MolrepJob
moorhen.atomic_model_refine = pipeliner.jobs.other.moorhen_job:MoorhenJob
parakeet.simulate = pipeliner.jobs.ccpem.parakeet_job:ParakeetJob
pipeliner.atomic_model_validation = pipeliner.jobs.ccpem.model_validation_job:ModelValidate
pipeliner.deposition.empiar = pipeliner.jobs.other.empiar_deposition_job:EmpiarDepositionJob
pipeliner.fetch.alphafold = pipeliner.jobs.other.fetch_mapmodel_job:FetchAlphaFold
pipeliner.fetch.emdb = pipeliner.jobs.other.fetch_mapmodel_job:FetchEmdb
pipeliner.fetch.pdb = pipeliner.jobs.other.fetch_mapmodel_job:FetchPdb
pipeliner.fetch.sequence = pipeliner.jobs.other.fetch_mapmodel_job:FetchFasta
pipeliner.image_analysis.average_particle_ps = pipeliner.jobs.other.average_particle_ps_job:AvgPartPS
pipeliner.run_external_program = pipeliner.jobs.other.pipeliner_run_external_program_job:PipelinerExternal
pipeliner.select.autoselect3d = pipeliner.jobs.other.autoselect_class3d_job:AutoSelect3D
pipeliner.select.classes = pipeliner.jobs.other.pipeliner_class_select_job:PipelinerClassSelect
pipeliner.select.random_sample = pipeliner.jobs.other.random_sample_job:RandomSampleStarfile
pipeliner.workflow.import_external = pipeliner.jobs.other.external_import_job:ExternalWorkflowImportJob
privateer.atomic_model_validation.glycans = pipeliner.jobs.ccpem.privateer_job:PrivateerValidate
process_predicted_model.atomic_model_utilities = pipeliner.jobs.ccpem.process_predicted_model_job:ProcessPredictedModel
proshade.map_analysis.symmetry = pipeliner.jobs.ccpem.proshade_job:ProShadeJobSym
proshade.map_utilities.overlay = pipeliner.jobs.ccpem.proshade_job:ProShadeJobOverlay
prosmart.create_restraints = pipeliner.jobs.ccpem.prosmart_job:ProSmart
refmac_servalcat.atomic_model_refine = pipeliner.jobs.ccpem.refmac_servalcat_job:Refine
relion.aligntiltseries.aretomo = pipeliner.jobs.tomography.relion_tomo.tomo_align_job:AreTomoJob
relion.aligntiltseries.imod_fiducial = pipeliner.jobs.tomography.relion_tomo.tomo_align_job:ImodAlignFiducialJob
relion.aligntiltseries.imod_patchtrack = pipeliner.jobs.tomography.relion_tomo.tomo_align_job:ImodAlignPatchTrackJob
relion.autopick.log = pipeliner.jobs.relion.autopick_job:RelionAutoPickLoG
relion.autopick.log.helical = pipeliner.jobs.relion.autopick_job:RelionAutoPickLogHelical
relion.autopick.ref2d = pipeliner.jobs.relion.autopick_job:RelionAutoPickRef2D
relion.autopick.ref2d.helical = pipeliner.jobs.relion.autopick_job:RelionAutoPickRef2DHelical
relion.autopick.ref3d = pipeliner.jobs.relion.autopick_job:RelionAutoPickRef3D
relion.autopick.ref3d.helical = pipeliner.jobs.relion.autopick_job:RelionAutoPickRef3DHelical
relion.autopick.topaz.pick = pipeliner.jobs.relion.autopick_job:RelionAutoPickTopaz
relion.autopick.topaz.pick.helical = pipeliner.jobs.relion.autopick_job:RelionAutoPickTopazHelical
relion.autopick.topaz.train = pipeliner.jobs.relion.autopick_job:RelionAutoPickTopazTrain
relion.class2d.em = pipeliner.jobs.relion.class2D_job:RelionClass2DEM
relion.class2d.em.helical = pipeliner.jobs.relion.class2D_job:RelionClass2DHelicalEM
relion.class2d.vdam = pipeliner.jobs.relion.class2D_job:RelionClass2DVDAM
relion.class2d.vdam.helical = pipeliner.jobs.relion.class2D_job:RelionClass2DHelicalVDAM
relion.class3d = pipeliner.jobs.relion.class3D_job:RelionClass3D
relion.class3d.helical = pipeliner.jobs.relion.class3D_job:RelionClass3DHelical
relion.class3d.helical.multiref = pipeliner.jobs.relion.class3D_job:RelionClass3DHelicalMulti
relion.class3d.multiref = pipeliner.jobs.relion.class3D_job:RelionClass3DMulti
relion.class3d.tomo = pipeliner.jobs.tomography.relion_tomo.tomo_class3D_job:TomoRelionClass3DJob
relion.ctffind.ctffind4 = pipeliner.jobs.relion.ctffind_job:RelionCtfFindCtffind4
relion.ctffind.gctf = pipeliner.jobs.relion.ctffind_job:RelionCtfFindGctf
relion.ctffind.tomo.ctffind4 = pipeliner.jobs.tomography.relion_tomo.tomo_ctffind_job:TomoRelionCtfFindCtffind4
relion.ctfrefine = pipeliner.jobs.relion.ctfrefine_job:RelionCtfRefine
relion.ctfrefinetomo = pipeliner.jobs.tomography.relion_tomo.tomo_ctfrefine_job:TomoRelionCtfRefine
relion.denoisetomo = pipeliner.jobs.tomography.relion_tomo.tomo_cryocare_job:RelionDenoiseJob
relion.denoisetomo.train = pipeliner.jobs.tomography.relion_tomo.tomo_cryocare_job:RelionDenoiseTrainJob
relion.excludetilts = pipeliner.jobs.tomography.relion_tomo.tomo_exclude_tilt_series_job:RelionExcludeTiltSeries
relion.external = pipeliner.jobs.relion.external_job:RelionExternal
relion.extract = pipeliner.jobs.relion.extract_job:RelionExtract
relion.extract.helical = pipeliner.jobs.relion.extract_job:RelionExtractHelical
relion.framealigntomo = pipeliner.jobs.tomography.relion_tomo.tomo_bayesianpolish_job:TomoRelionBayesPolishJob
relion.image_analysis.symmetry_expansion = pipeliner.jobs.relion.symmetry_expansion_job:RelionSymmetryExpansion
relion.import = pipeliner.jobs.relion.import_job:RelionImportOther
relion.import.coordinates = pipeliner.jobs.relion.import_job:RelionImportCoords
relion.import.movies = pipeliner.jobs.relion.import_job:RelionImportMovies
relion.importtomo = pipeliner.jobs.tomography.relion_tomo.tomo_import_job:RelionImportTiltSeriesMovies
relion.importtomo.coordinates = pipeliner.jobs.tomography.relion_tomo.tomo_import_job:RelionImportCoordinates
relion.initialmodel = pipeliner.jobs.relion.initialmodel_job:InimodelJob
relion.initialmodel.tomo = pipeliner.jobs.tomography.relion_tomo.tomo_initialmodel_job:RelionTomoInimodelJob
relion.joinstar.micrographs = pipeliner.jobs.relion.joinstar_job:RelionJoinStarMicrographs
relion.joinstar.movies = pipeliner.jobs.relion.joinstar_job:RelionJoinStarMovies
relion.joinstar.particles = pipeliner.jobs.relion.joinstar_job:RelionJoinStarParticles
relion.joinstar.tomograms = pipeliner.jobs.tomography.relion_tomo.tomo_join_tomogram_starfiles:RelionJoinStarTomograms
relion.localres.own = pipeliner.jobs.relion.localres_job:RelionLocalResOwn
relion.localres.resmap = pipeliner.jobs.relion.localres_job:RelionLocalResResMap
relion.manualpick = pipeliner.jobs.relion.manualpick_job:RelionManualPick
relion.manualpick.helical = pipeliner.jobs.relion.manualpick_job:RelionManualPickHelical
relion.map_utilities.align_symmetry = pipeliner.jobs.relion.align_symmetry_job:RelionAlignSymmetry
relion.map_utilities.apply_bfactor = pipeliner.jobs.relion.apply_bfactor_job:RelionApplyBFactor
relion.map_utilities.apply_symmetry = pipeliner.jobs.relion.apply_symmetry_job:RelionApplySymmetry
relion.map_utilities.filter_map = pipeliner.jobs.relion.filter_map_job:RelionFilterMap
relion.map_utilities.flip_handedness = pipeliner.jobs.relion.flip_map_job:RelionFlipMap
relion.map_utilities.rebox_rescale_map = pipeliner.jobs.relion.rebox_rescale_map_job:RelionReboxRescaleMap
relion.maskcreate = pipeliner.jobs.relion.maskcreate_job:RelionMaskCreate
relion.motioncorr.motioncor2 = pipeliner.jobs.relion.motioncorr_job:RelionMotionCorrMotionCor2
relion.motioncorr.own = pipeliner.jobs.relion.motioncorr_job:RelionMotionCorrOwn
relion.motioncorr.tomo.motioncor2 = pipeliner.jobs.tomography.relion_tomo.tomo_motioncorr_job:TomoRelionMotionCorrMotionCor2
relion.motioncorr.tomo.own = pipeliner.jobs.tomography.relion_tomo.tomo_motioncorr_job:TomoRelionMotionCorrOwn
relion.multibody.flexanalysis = pipeliner.jobs.relion.multibody_job:RelionMultiBodyFlexAnalysis
relion.multibody.refine = pipeliner.jobs.relion.multibody_job:RelionMultiBodyRefine
relion.picktomo = pipeliner.jobs.tomography.relion_tomo.tomo_napari_picker_job:RelionTomoNapariPickJob
relion.polish = pipeliner.jobs.relion.bayesianpolish_job:RelionPolishParticles
relion.polish.train = pipeliner.jobs.relion.bayesianpolish_job:RelionPolishTrain
relion.postprocess = pipeliner.jobs.relion.postprocess_job:PostprocessJob
relion.pseudosubtomo = pipeliner.jobs.tomography.relion_tomo.tomo_pseudosubtomo_job:RelionPseudoSubtomoJob
relion.reconstruct = pipeliner.jobs.relion.reconstruct_job:RelionReconstruct
relion.reconstructparticletomo = pipeliner.jobs.tomography.relion_tomo.tomo_reconstructparticle_job:RelionReconstructParticleJob
relion.reconstructtomograms = pipeliner.jobs.tomography.relion_tomo.tomo_reconstruct_job:RelionTomoReconstructJob
relion.refine3d = pipeliner.jobs.relion.refine3D_job:RelionRefine3D
relion.refine3d.helical = pipeliner.jobs.relion.refine3D_job:RelionRefine3DHelical
relion.refine3d.tomo = pipeliner.jobs.tomography.relion_tomo.tomo_refine3D_job:TomoRelionRefine3D
relion.refine3d.tomo.helical = pipeliner.jobs.tomography.relion_tomo.tomo_refine3D_job:TomoRelionRefine3DHelical
relion.reproject = pipeliner.jobs.relion.reproject_job:ReprojectJob
relion.select.class2dauto = pipeliner.jobs.relion.select_job:RelionSelectClass2DAuto
relion.select.discard = pipeliner.jobs.relion.select_job:RelionSelectDiscard
relion.select.interactive = pipeliner.jobs.relion.select_job:RelionSelectInteractive
relion.select.onvalue = pipeliner.jobs.relion.select_job:RelionSelectOnValue
relion.select.removeduplicates = pipeliner.jobs.relion.select_job:RelionSelectRemoveDuplicates
relion.select.split = pipeliner.jobs.relion.select_job:RelionSelectSplit
relion.subtract = pipeliner.jobs.relion.subtract_job:RelionSubtract
relion.subtract.revert = pipeliner.jobs.relion.subtract_job:RelionSubtractRevert
repic.autopick.consensus = pipeliner.jobs.other.repic_job:REPICJob
ribfind.atomic_model_split.rigid_body = pipeliner.jobs.ccpem.ribfind_job:RigidBodySplit
servalcat.atomic_model_refine = pipeliner.jobs.ccpem.servalcat_refine_job:ServalcatRefine
servalcat.difference_map = pipeliner.jobs.ccpem.servalcat_difference_map_job:DifferenceMap
servalcat.map_utilities.trim = pipeliner.jobs.ccpem.servalcat_trim_job:ServalcatTrimJob
servalcat.mask_creation.mask_from_model = pipeliner.jobs.ccpem.servalcat_mask_from_model_job:ServalcatMaskFromModel
slicendice.atomic_model_split = pipeliner.jobs.ccpem.slice_job:Slice
tempy.atomic_model_validation.map_fit = pipeliner.jobs.ccpem.tempy_scores_job:TEMPyMapFit
tempy_reff.atomic_model_refine.flexible_fit = pipeliner.jobs.other.tempy_reff_flexfit_job:FlexfitRefine
tempy_reff.atomic_model_refine.gmm = pipeliner.jobs.other.tempy_reff_gmm_job:GMMRefine

[console_scripts]
pipeliner = pipeliner.api.command_line:main
pipeliner.bfactor_plot = pipeliner.tools.bfactor_plot.bfactor_plot:main
pipeliner.check_setup = pipeliner.scripts.check_setup:main
pipeliner.make_project_tutorial = pipeliner.scripts.make_project_tutorial:main
pipeliner.recover_project = pipeliner.scripts.recover_project:main
pipeliner.regenerate_results = pipeliner.scripts.regenerate_results:main
pipeliner.update_metadata_schema = pipeliner.scripts.update_pipeliner_metadata_schema:main
pipeliner.update_nodes = pipeliner.scripts.update_nodes:main
