cellpack package

Subpackages

• cellpack.autopack package
  • Subpackages
    • cellpack.autopack.ingredient package
      • Submodules
      • cellpack.autopack.ingredient.Ingredient module
      • cellpack.autopack.ingredient.agent module
      • cellpack.autopack.ingredient.grow module
      • cellpack.autopack.ingredient.multi_cylinder module
      • cellpack.autopack.ingredient.multi_sphere module
      • cellpack.autopack.ingredient.single_cube module
      • cellpack.autopack.ingredient.single_cylinder module
      • cellpack.autopack.ingredient.single_sphere module
      • cellpack.autopack.ingredient.utils module
      • Module contents
    • cellpack.autopack.interface_objects package
      • Submodules
      • cellpack.autopack.interface_objects.database_ids module
      • cellpack.autopack.interface_objects.default_values module
      • cellpack.autopack.interface_objects.ingredient_types module
      • cellpack.autopack.interface_objects.meta_enum module
      • cellpack.autopack.interface_objects.packed_objects module
      • cellpack.autopack.interface_objects.partners module
      • cellpack.autopack.interface_objects.representations module
      • Module contents
    • cellpack.autopack.loaders package
      • Submodules
      • cellpack.autopack.loaders.analysis_config_loader module
      • cellpack.autopack.loaders.config_loader module
      • cellpack.autopack.loaders.migrate_v1_to_v2 module
      • cellpack.autopack.loaders.migrate_v2_to_v2_1 module
      • cellpack.autopack.loaders.recipe_loader module
      • cellpack.autopack.loaders.utils module
      • cellpack.autopack.loaders.v1_v2_attribute_changes module
      • Module contents
    • cellpack.autopack.upy package
      • Subpackages
      • Submodules
      • cellpack.autopack.upy.colors module
      • cellpack.autopack.upy.hostHelper module
      • Module contents
    • cellpack.autopack.writers package
      • Submodules
      • cellpack.autopack.writers.ImageWriter module
      • cellpack.autopack.writers.MarkdownWriter module
      • Module contents
  • Submodules
  • cellpack.autopack.AWSHandler module
    • AWSHandler
      • AWSHandler.create_presigned_url()
      • AWSHandler.download_file()
      • AWSHandler.get_aws_object_key()
      • AWSHandler.is_url_valid()
      • AWSHandler.save_file_and_get_url()
      • AWSHandler.upload_directory()
      • AWSHandler.upload_file()
  • cellpack.autopack.Analysis module
    • Analysis
      • Analysis.add_ingredient_positions_to_plot()
      • Analysis.build_grid()
      • Analysis.cartesian_to_sph()
      • Analysis.combine_results_from_ingredients()
      • Analysis.combine_results_from_seeds()
      • Analysis.create_report()
      • Analysis.doloop()
      • Analysis.getHaltonUnique()
      • Analysis.get_ingredient_key_from_object_or_comp_name()
      • Analysis.get_ingredient_radii()
      • Analysis.get_list_of_dims()
      • Analysis.get_minimum_expected_distance_from_recipe()
      • Analysis.get_number_of_ingredients_packed()
      • Analysis.get_obj_dict()
      • Analysis.get_packed_minimum_distance()
      • Analysis.get_partner_pair_dict()
      • Analysis.histogram()
      • Analysis.loadJSON()
      • Analysis.pack()
      • Analysis.pack_one_seed()
      • Analysis.plot()
      • Analysis.plot_distance_distribution()
      • Analysis.plot_occurence_distribution()
      • Analysis.plot_position_distribution()
      • Analysis.plot_position_distribution_total()
      • Analysis.process_ingredients_in_recipe()
      • Analysis.read_dict_from_glob_file()
      • Analysis.run_analysis_workflow()
      • Analysis.run_distance_analysis()
      • Analysis.run_partner_analysis()
      • Analysis.set_ingredient_color()
      • Analysis.simpleplot()
      • Analysis.update_distance_distribution_dictionaries()
      • Analysis.update_pairwise_distances()
      • Analysis.writeJSON()
  • cellpack.autopack.BaseGrid module
    • BaseGrid
      • BaseGrid.cartesian()
      • BaseGrid.computeExteriorVolume()
      • BaseGrid.computeGridNumberOfPoint()
      • BaseGrid.computeVolume()
      • BaseGrid.create_grid_point_positions()
      • BaseGrid.getCenter()
      • BaseGrid.getClosestFreeGridPoint()
      • BaseGrid.getClosestGridPoint()
      • BaseGrid.getDiagonal()
      • BaseGrid.getIJK()
      • BaseGrid.getPointFrom3D()
      • BaseGrid.getPointsInCube()
      • BaseGrid.getPointsInCubeFillBB()
      • BaseGrid.getPointsInSphere()
      • BaseGrid.getPositionPeridocity()
      • BaseGrid.getRadius()
      • BaseGrid.is_point_inside_bb()
      • BaseGrid.removeFreePoint()
      • BaseGrid.reorder_free_points()
      • BaseGrid.reset()
      • BaseGrid.restore()
      • BaseGrid.save()
      • BaseGrid.set_surfPtsBht()
      • BaseGrid.set_surfPtscht()
      • BaseGrid.setup()
      • BaseGrid.setupBoundaryPeriodicity()
      • BaseGrid.slow_box_fill()
      • BaseGrid.test_points_in_bb()
      • BaseGrid.updateDistances()
    • HaltonGrid
      • HaltonGrid.create3DPointLookup()
      • HaltonGrid.getNBgridPoints()
      • HaltonGrid.getPointFrom3D()
      • HaltonGrid.getScale()
    • gridPoint
  • cellpack.autopack.Compartment module
    • Compartment
      • Compartment.BuildGrid()
      • Compartment.BuildGridEnviroOnly()
      • Compartment.BuildGrid_bhtree()
      • Compartment.BuildGrid_binvox()
      • Compartment.BuildGrid_box()
      • Compartment.BuildGrid_kevin()
      • Compartment.BuildGrid_multisdf()
      • Compartment.BuildGrid_pyray()
      • Compartment.BuildGrid_ray()
      • Compartment.BuildGrid_scanline()
      • Compartment.BuildGrid_trimesh()
      • Compartment.BuildGrid_utsdf()
      • Compartment.buildMesh()
      • Compartment.buildSphere()
      • Compartment.build_grid_sphere()
      • Compartment.checkPointInsideBB()
      • Compartment.compute_volume_and_set_count()
      • Compartment.create3DPointLookup()
      • Compartment.createSurfacePoints()
      • Compartment.create_rbnode()
      • Compartment.create_voxelization()
      • Compartment.create_voxelized_mask()
      • Compartment.extendGridArrays()
      • Compartment.filter_surface_pts_to_fill_box()
      • Compartment.find_nearest()
      • Compartment.getBoundingBox()
      • Compartment.getCenter()
      • Compartment.getFaceNormals()
      • Compartment.getFacesNfromV()
      • Compartment.getInterpolatedNormal()
      • Compartment.getMesh()
      • Compartment.getMinMaxProteinSize()
      • Compartment.getRadius()
      • Compartment.getSizeXYZ()
      • Compartment.getSurfaceInnerPoints()
      • Compartment.getSurfaceInnerPoints_kevin()
      • Compartment.getSurfaceInnerPoints_sdf()
      • Compartment.getSurfaceInnerPoints_sdf_interpolate()
      • Compartment.getSurfacePoint()
      • Compartment.getVNfromF()
      • Compartment.getVertexNormals()
      • Compartment.get_bbox()
      • Compartment.get_normal_for_point()
      • Compartment.get_rb_model()
      • Compartment.inBox()
      • Compartment.inGrid()
      • Compartment.initialize_shape()
      • Compartment.is_point_inside_mesh()
      • Compartment.prepare_buildgrid_box()
      • Compartment.printFillInfo()
      • Compartment.readGridFromFile()
      • Compartment.reset()
      • Compartment.saveGridToFile()
      • Compartment.setCount()
      • Compartment.setGeomFaces()
      • Compartment.setInnerRecipe()
      • Compartment.setMesh()
      • Compartment.setNumber()
      • Compartment.setSurfaceRecipe()
      • Compartment.set_surface_distances()
      • Compartment.store_packed_object()
      • Compartment.transformMesh()
    • CompartmentList
      • CompartmentList.add_compartment()
  • cellpack.autopack.DBRecipeHandler module
    • CompositionDoc
      • CompositionDoc.DEFAULT_VALUES
      • CompositionDoc.KEY_TO_DICT_MAPPING
      • CompositionDoc.as_dict()
      • CompositionDoc.build_dependency_graph()
      • CompositionDoc.comp_upload_order()
      • CompositionDoc.get_reference_data()
      • CompositionDoc.get_reference_in_obj()
      • CompositionDoc.replace_region_references()
      • CompositionDoc.resolve_combined_gradient()
      • CompositionDoc.resolve_db_regions()
      • CompositionDoc.resolve_object_data()
    • DBMaintenance
      • DBMaintenance.cleanup_results()
      • DBMaintenance.readme_url()
    • DBRecipeLoader
      • DBRecipeLoader.collect_and_sort_data()
      • DBRecipeLoader.collect_docs_by_id()
      • DBRecipeLoader.compile_db_recipe_data()
      • DBRecipeLoader.prep_db_doc_for_download()
      • DBRecipeLoader.read_config()
      • DBRecipeLoader.remove_dedup_hash()
      • DBRecipeLoader.remove_empty()
      • DBRecipeLoader.validate_input_recipe_path()
    • DBUploader
      • DBUploader.prep_data_for_db()
      • DBUploader.update_outputs_directory()
      • DBUploader.upload_collections()
      • DBUploader.upload_compositions()
      • DBUploader.upload_config()
      • DBUploader.upload_data()
      • DBUploader.upload_gradients()
      • DBUploader.upload_job_status()
      • DBUploader.upload_objects()
      • DBUploader.upload_outputs_to_s3()
      • DBUploader.upload_packing_results_workflow()
      • DBUploader.upload_recipe()
      • DBUploader.upload_result_metadata()
      • DBUploader.upload_single_object()
    • DataDoc
      • DataDoc.generate_hash()
      • DataDoc.is_db_dict()
      • DataDoc.is_key()
      • DataDoc.is_nested_list()
      • DataDoc.is_obj()
    • GradientDoc
    • ObjectDoc
      • ObjectDoc.as_dict()
      • ObjectDoc.convert_positions_in_representation()
      • ObjectDoc.convert_representation()
    • ResultDoc
      • ResultDoc.handle_expired_results()
      • ResultDoc.validate_existence()
  • cellpack.autopack.Environment module
    • Environment
      • Environment.BuildCompartmentsGrids()
      • Environment.SetRBOptions()
      • Environment.SetSpringOptions()
      • Environment.addMeshRBOrganelle()
      • Environment.addRB()
      • Environment.add_seed_number_to_base_name()
      • Environment.applyStep()
      • Environment.buildGrid()
      • Environment.build_compartment_grids()
      • Environment.calc_pairwise_distances()
      • Environment.callFunction()
      • Environment.check_new_placement()
      • Environment.clean_grid_cache()
      • Environment.clear()
      • Environment.clearRBingredient()
      • Environment.collectResultPerIngredient()
      • Environment.compartment_id_for_nearest_grid_point()
      • Environment.convertPickleToText()
      • Environment.create_compartment()
      • Environment.create_ingredient()
      • Environment.create_objects()
      • Environment.create_voxelization()
      • Environment.delRB()
      • Environment.distance_check_failed()
      • Environment.dropOneIngr()
      • Environment.dropOneIngrJson()
      • Environment.exportToBD_BOX()
      • Environment.exportToReaDDy()
      • Environment.exportToTEM()
      • Environment.exportToTEM_SIM()
      • Environment.extend_bounding_box_for_compartments()
      • Environment.extractMeshComponent()
      • Environment.finishWithWater()
      • Environment.getActiveIng()
      • Environment.getIngrFromNameInRecipe()
      • Environment.getOneIngr()
      • Environment.getOneIngrJson()
      • Environment.getPointToDrop()
      • Environment.getRotTransRB()
      • Environment.getSortedActiveIngredients()
      • Environment.getTotalNbObject()
      • Environment.get_all_distances()
      • Environment.get_attributes_to_update()
      • Environment.get_bounding_box_limits()
      • Environment.get_closest_ingredients()
      • Environment.get_compartment_object_by_name()
      • Environment.get_distances()
      • Environment.get_distances_and_angles()
      • Environment.get_dpad()
      • Environment.get_ingredient_angles()
      • Environment.get_ingredient_by_name()
      • Environment.get_ingredients_in_tree()
      • Environment.get_size_of_bounding_box()
      • Environment.includeIngrRecipe()
      • Environment.includeIngrRecipes()
      • Environment.includeIngredientRecipe()
      • Environment.is_two_d()
      • Environment.linkTraj()
      • Environment.loadFreePoint()
      • Environment.loadResult()
      • Environment.load_asJson()
      • Environment.load_asTxt()
      • Environment.loopThroughIngr()
      • Environment.moveRBnode()
      • Environment.onePrevIngredient()
      • Environment.pack_grid()
      • Environment.pickIngredient()
      • Environment.prep_molecules_for_save()
      • Environment.printFillInfo()
      • Environment.readArraysFromFile()
      • Environment.removeOnePoint()
      • Environment.reportprogress()
      • Environment.reset()
      • Environment.resetIngrRecip()
      • Environment.resolve_gradient_data_objects()
      • Environment.restore()
      • Environment.restoreFreePoints()
      • Environment.restoreGridFromFile()
      • Environment.restore_grids_from_pickle()
      • Environment.restore_molecules_array()
      • Environment.runBullet()
      • Environment.saveGridLogsAsJson()
      • Environment.saveGridToFile()
      • Environment.save_grids_to_pickle()
      • Environment.save_result()
      • Environment.setExteriorRecipe()
      • Environment.setGeomFaces()
      • Environment.setSeed()
      • Environment.set_gradient()
      • Environment.set_partners_ingredient()
      • Environment.set_result_file_name()
      • Environment.setupOctree()
      • Environment.setupRBOptions()
      • Environment.sortIngredient()
      • Environment.store()
      • Environment.store_asJson()
      • Environment.timeFunction()
      • Environment.unlinkTraj()
      • Environment.update_after_place()
      • Environment.update_largest_smallest_size()
      • Environment.update_variable_ingredient_attributes()
      • Environment.writeArraysToFile()
    • random()
  • cellpack.autopack.FirebaseHandler module
    • FirebaseHandler
      • FirebaseHandler.check_doc_existence()
      • FirebaseHandler.create_path()
      • FirebaseHandler.create_timestamp()
      • FirebaseHandler.db_name()
      • FirebaseHandler.delete_doc()
      • FirebaseHandler.doc_id()
      • FirebaseHandler.doc_to_dict()
      • FirebaseHandler.get_all_docs()
      • FirebaseHandler.get_collection_id_from_path()
      • FirebaseHandler.get_creds()
      • FirebaseHandler.get_dev_creds()
      • FirebaseHandler.get_doc_by_id()
      • FirebaseHandler.get_doc_by_name()
      • FirebaseHandler.get_doc_by_ref()
      • FirebaseHandler.get_path_from_ref()
      • FirebaseHandler.get_staging_creds()
      • FirebaseHandler.get_username()
      • FirebaseHandler.get_value()
      • FirebaseHandler.is_firebase_obj()
      • FirebaseHandler.is_reference()
      • FirebaseHandler.set_doc()
      • FirebaseHandler.update_doc()
      • FirebaseHandler.update_elements_in_array()
      • FirebaseHandler.update_or_create()
      • FirebaseHandler.update_reference_on_doc()
      • FirebaseHandler.upload_doc()
      • FirebaseHandler.which_db()
      • FirebaseHandler.write_creds_path()
  • cellpack.autopack.GeometryTools module
    • GeometryTools
      • GeometryTools.GetDistance()
      • GeometryTools.LowerCircleFunction()
      • GeometryTools.LowerRectangleFunction()
      • GeometryTools.Resolution
      • GeometryTools.UpperCircleFunction()
      • GeometryTools.UpperRectangleFunction()
      • GeometryTools.calc_volume()
      • GeometryTools.check_rectangle_oustide()
      • GeometryTools.check_sphere_inside()
      • GeometryTools.getBoundary()
      • GeometryTools.get_rectangle_cercle_area()
      • GeometryTools.region_1()
      • GeometryTools.region_1_2_theta()
      • GeometryTools.region_2()
      • GeometryTools.region_2_integrand()
      • GeometryTools.region_3()
      • GeometryTools.region_3_integrand()
    • Rectangle
  • cellpack.autopack.Gradient module
    • Gradient
      • Gradient.build_axis_weight_map()
      • Gradient.build_directional_weight_map()
      • Gradient.build_radial_weight_map()
      • Gradient.build_surface_distance_weight_map()
      • Gradient.build_weight_map()
      • Gradient.create_voxelization()
      • Gradient.defaultFunction()
      • Gradient.getBinaryWeighted()
      • Gradient.getForwWeight()
      • Gradient.getLinearWeighted()
      • Gradient.getMaxWeight()
      • Gradient.getMinWeight()
      • Gradient.getRndWeighted()
      • Gradient.getSubWeighted()
      • Gradient.get_center()
      • Gradient.get_combined_gradient_weight()
      • Gradient.get_gauss_weights()
      • Gradient.normalize_vector()
      • Gradient.pickPoint()
      • Gradient.pick_point_for_ingredient()
      • Gradient.pick_point_from_weight()
      • Gradient.scale_between_0_and_1()
      • Gradient.set_weights_by_mode()
      • Gradient.update_ingredient_gradient()
    • random()
  • cellpack.autopack.Graphics module
    • AutopackViewer
      • AutopackViewer.SetHistoVol()
      • AutopackViewer.__init__()
      • AutopackViewer.addCompartmentFromGeom()
      • AutopackViewer.addIngredientFromGeom()
      • AutopackViewer.addMasterIngr()
      • AutopackViewer.appendIngrInstance()
      • AutopackViewer.buildIngrPrimitive()
      • AutopackViewer.callFunction()
      • AutopackViewer.checkCreateEmpty()
      • AutopackViewer.checkIngrPartnerProperties()
      • AutopackViewer.checkIngrSpheres()
      • AutopackViewer.clearAll()
      • AutopackViewer.clearFill()
      • AutopackViewer.clearIngr()
      • AutopackViewer.clearRecipe()
      • AutopackViewer.collectResult()
      • AutopackViewer.color()
      • AutopackViewer.colorByDistanceFrom()
      • AutopackViewer.colorByOrder()
      • AutopackViewer.colorPT()
      • AutopackViewer.createIngrMesh()
      • AutopackViewer.createOrganelMesh()
      • AutopackViewer.createTemplate()
      • AutopackViewer.createTemplateCompartment()
      • AutopackViewer.delIngr()
      • AutopackViewer.delIngredientGrow()
      • AutopackViewer.displayCompartment()
      • AutopackViewer.displayCompartmentPoints()
      • AutopackViewer.displayCompartments()
      • AutopackViewer.displayCompartmentsIngredients()
      • AutopackViewer.displayCompartmentsPoints()
      • AutopackViewer.displayCytoplasmIngredients()
      • AutopackViewer.displayDistance()
      • AutopackViewer.displayEnv()
      • AutopackViewer.displayFill()
      • AutopackViewer.displayFillBox()
      • AutopackViewer.displayFreePoints()
      • AutopackViewer.displayFreePointsAsPS()
      • AutopackViewer.displayGradient()
      • AutopackViewer.displayIngrCylinders()
      • AutopackViewer.displayIngrGrow()
      • AutopackViewer.displayIngrGrows()
      • AutopackViewer.displayIngrMesh()
      • AutopackViewer.displayIngrResults()
      • AutopackViewer.displayIngrSpheres()
      • AutopackViewer.displayIngredients()
      • AutopackViewer.displayInstancesIngredient()
      • AutopackViewer.displayLeafOctree()
      • AutopackViewer.displayOctree()
      • AutopackViewer.displayOctreeLeaf()
      • AutopackViewer.displayOneNodeOctree()
      • AutopackViewer.displayParticleVolumeDistance()
      • AutopackViewer.displayPoints()
      • AutopackViewer.displayPreFill()
      • AutopackViewer.displayRoot()
      • AutopackViewer.displaysubnode()
      • AutopackViewer.dspMesh()
      • AutopackViewer.dspSph()
      • AutopackViewer.exportAsIndexedMeshs()
      • AutopackViewer.exportIngredient()
      • AutopackViewer.exportRecipeIngredients()
      • AutopackViewer.hideIngrPrimitive()
      • AutopackViewer.prepareDynamic()
      • AutopackViewer.prepareIngredient()
      • AutopackViewer.prepareMaster()
      • AutopackViewer.printIngredients()
      • AutopackViewer.printOneIngr()
      • AutopackViewer.replaceIngrMesh()
      • AutopackViewer.showHide()
      • AutopackViewer.showIngrPrimitive()
      • AutopackViewer.timeFunction()
      • AutopackViewer.toggleOrganelMatr()
      • AutopackViewer.toggleOrganelMesh()
      • AutopackViewer.toggleOrganelSurf()
      • AutopackViewer.undspMesh()
      • AutopackViewer.undspSph()
    • ColladaExporter
  • cellpack.autopack.Grid module
    • Grid
      • Grid.create3DPointLookup()
      • Grid.getIJK()
      • Grid.reset()
      • Grid.restore()
      • Grid.save()
  • cellpack.autopack.IOutils module
    • ExportCollada
    • GrabResult
      • GrabResult.grab()
      • GrabResult.reset()
    • IOingredientTool
      • IOingredientTool.clean_arguments()
      • IOingredientTool.ingrJsonNode()
      • IOingredientTool.ingrPythonNode()
      • IOingredientTool.makeIngredient()
      • IOingredientTool.makeIngredientFromJson()
      • IOingredientTool.read()
      • IOingredientTool.set_recipe_ingredient()
    • addCompartments()
    • checkRotFormat()
    • format_time()
    • gatherResult()
    • getAllPosRot()
    • getStringValueOptions()
    • load_Json()
    • load_JsonString()
    • load_MixedasJson()
    • saveResultBinary()
    • saveResultBinaryDic()
    • save_asPython()
    • serializedFromResult()
    • serializedRecipe()
    • serializedRecipe_group()
    • serializedRecipe_group_dic()
    • setValueToPythonStr()
    • setupFromJsonDic()
    • toBinary()
    • updatePositionsRadii()
  • cellpack.autopack.MeshStore module
    • MeshStore
      • MeshStore.add_mesh_to_scene()
      • MeshStore.build_mesh()
      • MeshStore.calc_scaled_distances_for_positions()
      • MeshStore.contains_point()
      • MeshStore.contains_points_mesh()
      • MeshStore.create_mesh()
      • MeshStore.create_sphere()
      • MeshStore.create_sphere_data()
      • MeshStore.decompose_mesh()
      • MeshStore.get_centroid()
      • MeshStore.get_collada_material()
      • MeshStore.get_mesh()
      • MeshStore.get_mesh_filepath_and_extension()
      • MeshStore.get_midpoint()
      • MeshStore.get_normal()
      • MeshStore.get_nsphere()
      • MeshStore.get_object()
      • MeshStore.get_scaled_distances_between_surfaces()
      • MeshStore.get_smallest_radius()
      • MeshStore.norm()
      • MeshStore.normal_array()
      • MeshStore.normalize()
      • MeshStore.normalize_v3()
      • MeshStore.read_mesh_file()
  • cellpack.autopack.OutputSimularium module
  • cellpack.autopack.Recipe module
    • Recipe
      • Recipe.addIngredient()
      • Recipe.delIngredient()
      • Recipe.getMinMaxProteinSize()
      • Recipe.is_key()
      • Recipe.printFillInfo()
      • Recipe.resetIngrs()
      • Recipe.resolve_composition()
      • Recipe.setCount()
      • Recipe.sort()
    • random()
  • cellpack.autopack.Serializable module
    • sCompartment
      • sCompartment.addCompartment()
      • sCompartment.addIngredientGroup()
      • sCompartment.static_id
      • sCompartment.to_JSON()
    • sIngredient
      • sIngredient.static_id
      • sIngredient.to_JSON()
    • sIngredientFiber
      • sIngredientFiber.static_id
      • sIngredientFiber.to_JSON()
    • sIngredientGroup
      • sIngredientGroup.addIngredient()
      • sIngredientGroup.static_id
      • sIngredientGroup.to_JSON()
  • cellpack.autopack.binvox_rw module
    • Voxels
      • Voxels.cartesian()
      • Voxels.clone()
      • Voxels.getIndex()
      • Voxels.getIndexData()
      • Voxels.ijkToIndex()
      • Voxels.ijkToxyz()
      • Voxels.write()
      • Voxels.xyzToijk()
    • dense_to_sparse()
    • read()
    • read_as_3d_array()
    • read_as_coord_array()
    • read_header()
    • sparse_to_dense()
    • write()
  • cellpack.autopack.ldSequence module
    • HaltonSequence
    • SphereHalton()
    • cHaltonSequence3
      • cHaltonSequence3.inc()
      • cHaltonSequence3.reset()
    • halton()
    • halton2()
    • halton3()
    • halton_sequence()
    • haltonterm()
  • cellpack.autopack.octree module
    • OctNode
    • Octree
      • Octree.addNode()
      • Octree.findBranch()
      • Octree.findPosition()
      • Octree.insertNode()
  • cellpack.autopack.plotly_result module
    • PlotlyAnalysis
      • PlotlyAnalysis.add_circle()
      • PlotlyAnalysis.add_ingredient_positions()
      • PlotlyAnalysis.add_square()
      • PlotlyAnalysis.format_color()
      • PlotlyAnalysis.make_and_show_heatmap()
      • PlotlyAnalysis.make_grid_heatmap()
      • PlotlyAnalysis.show()
      • PlotlyAnalysis.transformPoints2D()
      • PlotlyAnalysis.update_title()
  • cellpack.autopack.randomRot module
    • RandomRot
      • RandomRot.get()
      • RandomRot.getOld()
      • RandomRot.quaternion_matrix()
      • RandomRot.random_quaternion()
      • RandomRot.random_rotation_matrix()
      • RandomRot.setSeed()
  • cellpack.autopack.ray module
    • Created on Saturday September 1 1:50:00 2012
    • dot()
    • f_dot_product()
    • f_ray_intersect_polyhedron()
    • findPointsCenter()
    • makeMarchingCube()
    • ray_intersect_polygon()
    • ray_intersect_polyhedron()
    • vcross()
    • vdiff()
    • vlen()
    • vnorm()
  • cellpack.autopack.trajectory module
    • Trajectory
      • Trajectory.applyState()
      • Trajectory.applyState_cb()
      • Trajectory.applyState_name()
      • Trajectory.applyState_primitive_name()
      • Trajectory.completeMapping()
      • Trajectory.generalApply()
      • Trajectory.getIngredientInstancePos()
      • Trajectory.makeIngrMapping()
      • Trajectory.reg
      • Trajectory.traj_type
    • dcdTrajectory
      • dcdTrajectory.dcd
      • dcdTrajectory.getPosAt()
      • dcdTrajectory.parse()
      • dcdTrajectory.traj_type
    • molbTrajectory
      • molbTrajectory.applyState_name()
      • molbTrajectory.applyState_primitive_name()
      • molbTrajectory.getPosAt()
      • molbTrajectory.parse()
      • molbTrajectory.parse_one_mol()
      • molbTrajectory.traj_type
    • xyzTrajectory
      • xyzTrajectory.getPosAt()
      • xyzTrajectory.getPosLine()
      • xyzTrajectory.parse()
      • xyzTrajectory.traj_type
  • cellpack.autopack.transformation module
    • Requirements
  • cellpack.autopack.utils module
    • check_paired_key()
    • cmp_to_key()
    • deep_merge()
    • expand_object_using_key()
    • get_distance()
    • get_distances_from_point()
    • get_max_value_from_distribution()
    • get_min_value_from_distribution()
    • get_paired_key()
    • get_seed_list()
    • get_value_from_distribution()
    • ingredient_compare0()
    • ingredient_compare1()
    • ingredient_compare2()
  • Module contents
    • Created on Fri Jul 20 23:53:00 2012
    • checkErrorInPath()
    • checkPath()
    • checkRecipeAvailable()
    • clearCaches()
    • convert_db_shortname_to_url()
    • download_file()
    • fixOnePath()
    • fixPath()
    • get_cache_location()
    • get_local_file_location()
    • is_full_url()
    • is_remote_path()
    • is_s3_url()
    • load_file()
    • make_directory_if_needed()
    • parse_s3_uri()
    • read_text_file()
    • resetDefault()
    • saveRecipeAvailable()
    • saveRecipeAvailableJSON()
    • updatePath()
    • updatePathJSON()
    • updateRecipAvailableXML()
    • updateReplacePath()
    • url_exists()
    • write_username_to_creds()
• cellpack.bin package
  • Submodules
  • cellpack.bin.analyze module
    • analyze()
    • main()
  • cellpack.bin.clean module
    • clean()
    • main()
  • cellpack.bin.cleanup_tasks module
    • run_cleanup()
  • cellpack.bin.get-pdb-offset module
  • cellpack.bin.pack module
    • main()
    • pack()
  • cellpack.bin.simularium_converter module
    • ConvertToSimularium
      • ConvertToSimularium.DEFAULT_GEO_TYPE
      • ConvertToSimularium.DEFAULT_INPUT_RECIPE
      • ConvertToSimularium.DEFAULT_OUTPUT_DIRECTORY
      • ConvertToSimularium.DEFAULT_PACKING_RESULT
      • ConvertToSimularium.DEFAULT_SCALE_FACTOR
      • ConvertToSimularium.fill_in_empty_fiber_data()
      • ConvertToSimularium.get_bounding_box()
      • ConvertToSimularium.get_euler()
      • ConvertToSimularium.get_euler_from_matrix()
      • ConvertToSimularium.get_euler_from_quat()
      • ConvertToSimularium.get_ingredient_data()
      • ConvertToSimularium.get_ingredient_display_data()
      • ConvertToSimularium.get_mesh_data()
      • ConvertToSimularium.get_positions_per_ingredient()
      • ConvertToSimularium.is_matrix()
      • ConvertToSimularium.process_one_ingredient()
      • ConvertToSimularium.unpack_curve()
      • ConvertToSimularium.unpack_positions()
    • main()
  • cellpack.bin.upload module
    • get_recipe_metadata()
    • main()
    • upload()
  • cellpack.bin.validate module
    • main()
    • validate()
  • Module contents

Module contents

Top-level package for cellPACK.

cellpack.get_module_version()