Index

A

ActinIngredient (class in cellpack.autopack.ingredient.grow) add() (cellpack.autopack.interface_objects.packed_objects.PackedObjects method) add_circle() (cellpack.autopack.plotly_result.PlotlyAnalysis method) add_compartment() (cellpack.autopack.Compartment.CompartmentList static method) add_compartment_to_scene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) add_grid_data_to_scene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) add_header() (cellpack.autopack.writers.MarkdownWriter.MarkdownWriter method) add_histogram() (cellpack.autopack.upy.simularium.plots.PlotData method) add_images() (cellpack.autopack.writers.MarkdownWriter.MarkdownWriter method) add_ingredient_positions() (cellpack.autopack.plotly_result.PlotlyAnalysis method) add_ingredient_positions_to_plot() (cellpack.autopack.Analysis.Analysis method) add_inline_image() (cellpack.autopack.writers.MarkdownWriter.MarkdownWriter method) add_instance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) add_line() (cellpack.autopack.writers.MarkdownWriter.MarkdownWriter method) add_list() (cellpack.autopack.writers.MarkdownWriter.MarkdownWriter method) add_mesh_to_scene() (cellpack.autopack.MeshStore.MeshStore method) add_new_instance_and_update_time() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) add_object_to_scene() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) add_partner() (cellpack.autopack.interface_objects.partners.Partners method) add_scatter() (cellpack.autopack.upy.simularium.plots.PlotData method) add_seed_number_to_base_name() (cellpack.autopack.Environment.Environment method) add_square() (cellpack.autopack.plotly_result.PlotlyAnalysis method) add_table() (cellpack.autopack.writers.MarkdownWriter.MarkdownWriter method) add_table_from_csv() (cellpack.autopack.writers.MarkdownWriter.MarkdownWriter method) addBone() (cellpack.autopack.upy.hostHelper.Helper method) addCameraToScene() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) addCompartment() (cellpack.autopack.Serializable.sCompartment method) addCompartmentFromGeom() (cellpack.autopack.Graphics.AutopackViewer method) addCompartments() (in module cellpack.autopack.IOutils) addConstraint() (cellpack.autopack.upy.hostHelper.Helper method) addIngredient() (cellpack.autopack.Recipe.Recipe method) (cellpack.autopack.Serializable.sIngredientGroup method) addIngredientFromGeom() (cellpack.autopack.Graphics.AutopackViewer method) addIngredientGroup() (cellpack.autopack.Serializable.sCompartment method) addLampToScene() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) addMasterIngr() (cellpack.autopack.Graphics.AutopackViewer method) addMaterial() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) addMaterialFromDic() (cellpack.autopack.upy.hostHelper.Helper method) addMeshEdge() (cellpack.autopack.upy.hostHelper.Helper method)

addMeshEdges() (cellpack.autopack.upy.hostHelper.Helper method) addMeshFace() (cellpack.autopack.upy.hostHelper.Helper method) addMeshFaces() (cellpack.autopack.upy.hostHelper.Helper method) addMeshRBOrganelle() (cellpack.autopack.Environment.Environment method) addMeshVertice() (cellpack.autopack.upy.hostHelper.Helper method) addMeshVertices() (cellpack.autopack.upy.hostHelper.Helper method) addNode() (cellpack.autopack.octree.Octree method) AddObject() (cellpack.autopack.upy.hostHelper.Helper method) addObjectToScene() (cellpack.autopack.upy.hostHelper.Helper method) addRB() (cellpack.autopack.Environment.Environment method) advance_randpoint_onsphere() (cellpack.autopack.upy.hostHelper.Helper method) Agent (class in cellpack.autopack.ingredient.agent) alignRotation() (cellpack.autopack.ingredient.Ingredient.Ingredient method) Analysis (class in cellpack.autopack.Analysis) AnalysisConfigLoader (class in cellpack.autopack.loaders.analysis_config_loader) analyze() (in module cellpack.bin.analyze) angle_between_vectors() (cellpack.autopack.upy.hostHelper.Helper method) animationStart() (cellpack.autopack.upy.hostHelper.Helper method) animationStop() (cellpack.autopack.upy.hostHelper.Helper method) appendIngrInstance() (cellpack.autopack.Graphics.AutopackViewer method) apply_rotation() (cellpack.autopack.ingredient.Ingredient.Ingredient method) ApplyMatrix() (cellpack.autopack.upy.hostHelper.Helper method) (in module cellpack.autopack.ingredient.utils) applyState() (cellpack.autopack.trajectory.Trajectory method) applyState_cb() (cellpack.autopack.trajectory.Trajectory method) applyState_name() (cellpack.autopack.trajectory.molbTrajectory method) (cellpack.autopack.trajectory.Trajectory method) applyState_primitive_name() (cellpack.autopack.trajectory.molbTrajectory method) (cellpack.autopack.trajectory.Trajectory method) applyStep() (cellpack.autopack.Environment.Environment method) ARGUMENTS (cellpack.autopack.ingredient.grow.GrowIngredient attribute) (cellpack.autopack.ingredient.Ingredient.Ingredient attribute) armature() (cellpack.autopack.upy.hostHelper.Helper method) as_dict() (cellpack.autopack.DBRecipeHandler.CompositionDoc method) (cellpack.autopack.DBRecipeHandler.DataDoc method) (cellpack.autopack.DBRecipeHandler.ObjectDoc method) assignMaterial() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) assignNewMaterial() (cellpack.autopack.upy.hostHelper.Helper method) attempt_to_pack_at_grid_location() (cellpack.autopack.ingredient.Ingredient.Ingredient method) AutopackViewer (class in cellpack.autopack.Graphics) AWS (cellpack.autopack.interface_objects.database_ids.DATABASE_IDS attribute) AWSHandler (class in cellpack.autopack.AWSHandler)

B

BaseGrid (class in cellpack.autopack.BaseGrid) BINARY (cellpack.autopack.interface_objects.gradient_data.PickModes attribute) BONES (cellpack.autopack.upy.hostHelper.Helper attribute) box() (cellpack.autopack.upy.hostHelper.Helper method) Box() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) box() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) build_axis_weight_map() (cellpack.autopack.Gradient.Gradient method) build_compartment_grids() (cellpack.autopack.Environment.Environment method) build_directional_weight_map() (cellpack.autopack.Gradient.Gradient method) build_grid() (cellpack.autopack.Analysis.Analysis method) build_grid_sphere() (cellpack.autopack.Compartment.Compartment method) build_mesh() (cellpack.autopack.MeshStore.MeshStore method) build_radial_weight_map() (cellpack.autopack.Gradient.Gradient method) build_surface_distance_weight_map() (cellpack.autopack.Gradient.Gradient method) build_weight_map() (cellpack.autopack.Gradient.Gradient method) BuildCompartmentsGrids() (cellpack.autopack.Environment.Environment method) BuildGrid() (cellpack.autopack.Compartment.Compartment method)

buildGrid() (cellpack.autopack.Environment.Environment method) BuildGrid_bhtree() (cellpack.autopack.Compartment.Compartment method) BuildGrid_binvox() (cellpack.autopack.Compartment.Compartment method) BuildGrid_box() (cellpack.autopack.Compartment.Compartment method) BuildGrid_kevin() (cellpack.autopack.Compartment.Compartment method) BuildGrid_multisdf() (cellpack.autopack.Compartment.Compartment method) BuildGrid_pyray() (cellpack.autopack.Compartment.Compartment method) BuildGrid_ray() (cellpack.autopack.Compartment.Compartment method) BuildGrid_scanline() (cellpack.autopack.Compartment.Compartment method) BuildGrid_trimesh() (cellpack.autopack.Compartment.Compartment method) BuildGrid_utsdf() (cellpack.autopack.Compartment.Compartment method) BuildGridEnviroOnly() (cellpack.autopack.Compartment.Compartment method) buildIngrPrimitive() (cellpack.autopack.Graphics.AutopackViewer method) buildMesh() (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.ingredient.Ingredient.Ingredient method) buildSphere() (cellpack.autopack.Compartment.Compartment method) bullet_checkCollision_mp() (in module cellpack.autopack.ingredient.utils)

C

calc_pairwise_distances() (cellpack.autopack.Environment.Environment method) calc_scaled_distances_for_positions() (cellpack.autopack.MeshStore.MeshStore static method) calc_volume() (cellpack.autopack.GeometryTools.GeometryTools method) callFunction() (cellpack.autopack.Environment.Environment method) (cellpack.autopack.Graphics.AutopackViewer method) CAM_OPTIONS (cellpack.autopack.upy.hostHelper.Helper attribute) cartesian() (cellpack.autopack.BaseGrid.BaseGrid method) (cellpack.autopack.binvox_rw.Voxels method) cartesian_to_sph() (cellpack.autopack.Analysis.Analysis static method) cellpack module cellpack.autopack module cellpack.autopack.Analysis module cellpack.autopack.AWSHandler module cellpack.autopack.BaseGrid module cellpack.autopack.binvox_rw module cellpack.autopack.Compartment module cellpack.autopack.DBRecipeHandler module cellpack.autopack.Environment module cellpack.autopack.FirebaseHandler module cellpack.autopack.GeometryTools module cellpack.autopack.Gradient module cellpack.autopack.Graphics module cellpack.autopack.Grid module cellpack.autopack.ingredient module cellpack.autopack.ingredient.agent module cellpack.autopack.ingredient.grow module cellpack.autopack.ingredient.Ingredient 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 cellpack.autopack.interface_objects module cellpack.autopack.interface_objects.database_ids module cellpack.autopack.interface_objects.default_values module cellpack.autopack.interface_objects.gradient_data 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 cellpack.autopack.IOutils module cellpack.autopack.ldSequence module cellpack.autopack.loaders module 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 cellpack.autopack.MeshStore module cellpack.autopack.octree module cellpack.autopack.plotly_result module cellpack.autopack.randomRot module cellpack.autopack.ray module cellpack.autopack.Recipe module cellpack.autopack.Serializable module cellpack.autopack.trajectory module cellpack.autopack.transformation module cellpack.autopack.upy module cellpack.autopack.upy.colors module cellpack.autopack.upy.hostHelper module cellpack.autopack.upy.simularium module cellpack.autopack.upy.simularium.plots module cellpack.autopack.upy.simularium.simularium_helper module cellpack.autopack.utils module cellpack.autopack.writers module cellpack.autopack.writers.ImageWriter module cellpack.autopack.writers.MarkdownWriter module cellpack.bin module cellpack.bin.analyze module cellpack.bin.clean module cellpack.bin.cleanup_tasks module cellpack.bin.pack module cellpack.bin.simularium_converter module

cellpack.bin.upload module center (cellpack.autopack.interface_objects.gradient_data.ModeOptions attribute) cHaltonSequence3 (class in cellpack.autopack.ldSequence) changeColor() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) changeColorO() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) changeMaterialProperty() (cellpack.autopack.upy.hostHelper.Helper method) changeObjColorMat() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) check_against_one_packed_ingr() (cellpack.autopack.ingredient.Ingredient.Ingredient method) check_and_replace_references() (cellpack.autopack.DBRecipeHandler.CompositionDoc method) check_new_placement() (cellpack.autopack.Environment.Environment method) check_paired_key() (in module cellpack.autopack.utils) check_rectangle_oustide() (cellpack.autopack.GeometryTools.GeometryTools method) check_required_attributes() (in module cellpack.autopack.loaders.migrate_v1_to_v2) check_sphere_inside() (cellpack.autopack.GeometryTools.GeometryTools method) checkCreateEmpty() (cellpack.autopack.Graphics.AutopackViewer method) checkCylCollisions() (cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr method) (cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr method) checkDistance() (cellpack.autopack.ingredient.Ingredient.Ingredient method) checkErrorInPath() (in module cellpack.autopack) checkIfUpdate() (cellpack.autopack.ingredient.Ingredient.Ingredient method) checkIngrPartnerProperties() (cellpack.autopack.Graphics.AutopackViewer method) checkIngrSpheres() (cellpack.autopack.Graphics.AutopackViewer method) checkIsMesh() (cellpack.autopack.upy.hostHelper.Helper method) checkName() (cellpack.autopack.upy.hostHelper.Helper method) checkPath() (in module cellpack.autopack) checkPointInsideBB() (cellpack.autopack.Compartment.Compartment method) checkRecipeAvailable() (in module cellpack.autopack) checkRotFormat() (in module cellpack.autopack.IOutils) Circle() (cellpack.autopack.upy.hostHelper.Helper method) clean() (in module cellpack.bin.clean) clean_arguments() (cellpack.autopack.IOutils.IOingredientTool static method) clean_grid_cache() (cellpack.autopack.Environment.Environment method) cleanup_results() (cellpack.autopack.DBRecipeHandler.DBMaintenance method) clear() (cellpack.autopack.Environment.Environment method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) clearAll() (cellpack.autopack.Graphics.AutopackViewer method) clearCaches() (in module cellpack.autopack) clearFill() (cellpack.autopack.Graphics.AutopackViewer method) clearIngr() (cellpack.autopack.Graphics.AutopackViewer method) clearRBingredient() (cellpack.autopack.Environment.Environment method) clearRecipe() (cellpack.autopack.Graphics.AutopackViewer method) clone() (cellpack.autopack.binvox_rw.Voxels method) close_partner_check() (cellpack.autopack.ingredient.Ingredient.Ingredient method) cmp_to_key() (in module cellpack.autopack.utils) ColladaExporter (class in cellpack.autopack.Graphics) collect_and_sort_data() (cellpack.autopack.DBRecipeHandler.DBRecipeLoader static method) collect_docs_by_id() (cellpack.autopack.DBRecipeHandler.DBRecipeLoader method) collectResult() (cellpack.autopack.Graphics.AutopackViewer method) collectResultPerIngredient() (cellpack.autopack.Environment.Environment method) collides_with_compartment() (cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr method) (cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr method) (cellpack.autopack.ingredient.single_cube.SingleCubeIngr method) (cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr method) (cellpack.autopack.ingredient.single_sphere.SingleSphereIngr method) collision_jitter() (cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr method) (cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr method) (cellpack.autopack.ingredient.single_cube.SingleCubeIngr method) (cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr method) (cellpack.autopack.ingredient.single_sphere.SingleSphereIngr method) color() (cellpack.autopack.Graphics.AutopackViewer method) colorByDistanceFrom() (cellpack.autopack.Graphics.AutopackViewer method) colorByOrder() (cellpack.autopack.Graphics.AutopackViewer method) colorMaterial() (cellpack.autopack.upy.hostHelper.Helper method) colorObject() (cellpack.autopack.upy.hostHelper.Helper method) colorPT() (cellpack.autopack.Graphics.AutopackViewer method) combine_results_from_ingredients() (cellpack.autopack.Analysis.Analysis method) combine_results_from_seeds() (cellpack.autopack.Analysis.Analysis method) combineDaeMeshData() (cellpack.autopack.upy.hostHelper.Helper method) Compartment (class in cellpack.autopack.Compartment) compartment_id_for_nearest_grid_point() (cellpack.autopack.Environment.Environment method) CompartmentList (class in cellpack.autopack.Compartment) compile_db_recipe_data() (cellpack.autopack.DBRecipeHandler.DBRecipeLoader static method) completeMapping() (cellpack.autopack.trajectory.Trajectory method) CompositionDoc (class in cellpack.autopack.DBRecipeHandler) compute_volume_and_set_count() (cellpack.autopack.Compartment.Compartment method) computeExteriorVolume() (cellpack.autopack.BaseGrid.BaseGrid method) computeGridNumberOfPoint() (cellpack.autopack.BaseGrid.BaseGrid method) computeVolume() (cellpack.autopack.BaseGrid.BaseGrid method) concatenate_image_data() (cellpack.autopack.writers.ImageWriter.ImageWriter method) concatObjectMatrix() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) ConfigLoader (class in cellpack.autopack.loaders.config_loader) constraintLookAt() (cellpack.autopack.upy.hostHelper.Helper method) contains_point() (cellpack.autopack.MeshStore.MeshStore method) contains_points_mesh() (cellpack.autopack.MeshStore.MeshStore method) convert() (in module cellpack.autopack.loaders.migrate_v1_to_v2) (in module cellpack.autopack.loaders.migrate_v2_to_v2_1) convert_db_shortname_to_url() (in module cellpack.autopack) convert_gradients() (in module cellpack.autopack.loaders.migrate_v2_to_v2_1) convert_partners() (in module cellpack.autopack.loaders.migrate_v2_to_v2_1) convert_positions_in_representation() (cellpack.autopack.DBRecipeHandler.ObjectDoc static method) convert_representation() (cellpack.autopack.DBRecipeHandler.ObjectDoc static method) convert_rotation_range() (in module cellpack.autopack.loaders.migrate_v1_to_v2) convertColor() (cellpack.autopack.upy.hostHelper.Helper method) convertPickleToText() (cellpack.autopack.Environment.Environment class method) ConvertToSimularium (class in cellpack.bin.simularium_converter) convolve_channel() (cellpack.autopack.writers.ImageWriter.ImageWriter static method) convolve_image() (cellpack.autopack.writers.ImageWriter.ImageWriter method) correctBB() (cellpack.autopack.ingredient.Ingredient.Ingredient method) create3DPointLookup() (cellpack.autopack.BaseGrid.HaltonGrid method) (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.Grid.Grid method) create_box_psf() (cellpack.autopack.writers.ImageWriter.ImageWriter static method) create_circular_mask() (cellpack.autopack.ingredient.single_sphere.SingleSphereIngr static method) create_compartment() (cellpack.autopack.Environment.Environment method) create_divergent_color_map_with_scaled_values() (in module cellpack.autopack.upy.colors) create_file_info_object_from_full_path() (in module cellpack.autopack.loaders.utils) create_gaussian_psf() (cellpack.autopack.writers.ImageWriter.ImageWriter static method) create_grid_point_positions() (cellpack.autopack.BaseGrid.BaseGrid method) create_ingredient() (cellpack.autopack.Environment.Environment method) create_mesh() (cellpack.autopack.MeshStore.MeshStore method) create_objects() (cellpack.autopack.Environment.Environment method) create_output_dir() (in module cellpack.autopack.loaders.utils) create_path() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) create_presigned_url() (cellpack.autopack.AWSHandler.AWSHandler method) create_rbnode() (cellpack.autopack.Compartment.Compartment method) create_report() (cellpack.autopack.Analysis.Analysis method) create_sphere() (cellpack.autopack.MeshStore.MeshStore method) create_sphere_data() (cellpack.autopack.MeshStore.MeshStore method) create_timestamp() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) create_voxelization() (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.Environment.Environment method) (cellpack.autopack.Gradient.Gradient method) (cellpack.autopack.ingredient.single_sphere.SingleSphereIngr method) create_voxelized_mask() (cellpack.autopack.Compartment.Compartment method) createColorsMat() (cellpack.autopack.upy.hostHelper.Helper method) createIngrMesh() (cellpack.autopack.Graphics.AutopackViewer method) createMaterial() (cellpack.autopack.upy.hostHelper.Helper method) createOrganelMesh() (cellpack.autopack.Graphics.AutopackViewer method) createsNmesh() (cellpack.autopack.upy.hostHelper.Helper method) createSpring() (cellpack.autopack.upy.hostHelper.Helper method) createSurfacePoints() (cellpack.autopack.Compartment.Compartment method) createTemplate() (cellpack.autopack.Graphics.AutopackViewer method) createTemplateCompartment() (cellpack.autopack.Graphics.AutopackViewer method) createTexturedMaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) CUBE (cellpack.autopack.interface_objects.gradient_data.WeightModes attribute) Cube() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) cube_surface_distance() (cellpack.autopack.ingredient.single_cube.SingleCubeIngr method) Cylinder() (cellpack.autopack.upy.hostHelper.Helper method) cylinder() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) CylinderHeadTails() (cellpack.autopack.upy.hostHelper.Helper method) Cylinders() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method)

D

DATABASE (cellpack.autopack.interface_objects.representations.Representations attribute) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute) DATABASE_IDS (class in cellpack.autopack.interface_objects.database_ids) DataDoc (class in cellpack.autopack.DBRecipeHandler) db_name() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) DBMaintenance (class in cellpack.autopack.DBRecipeHandler) DBRecipeLoader (class in cellpack.autopack.DBRecipeHandler) DBUploader (class in cellpack.autopack.DBRecipeHandler) dcd (cellpack.autopack.trajectory.dcdTrajectory attribute) dcdTrajectory (class in cellpack.autopack.trajectory) DEBUG (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute) decay_length (cellpack.autopack.interface_objects.gradient_data.WeightModeOptions attribute) Decompose4x4() (cellpack.autopack.upy.hostHelper.Helper method) decompose_mesh() (cellpack.autopack.MeshStore.MeshStore method) decomposeColladaGeom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) DecomposeMesh() (cellpack.autopack.ingredient.Ingredient.Ingredient method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) deep_merge() (in module cellpack.autopack.utils) default() (cellpack.autopack.writers.NumpyArrayEncoder method) DEFAULT_GEO_TYPE (cellpack.bin.simularium_converter.ConvertToSimularium attribute) DEFAULT_INPUT_RECIPE (cellpack.bin.simularium_converter.ConvertToSimularium attribute) DEFAULT_OUTPUT_DIRECTORY (cellpack.bin.simularium_converter.ConvertToSimularium attribute) DEFAULT_PACKING_RESULT (cellpack.bin.simularium_converter.ConvertToSimularium attribute) DEFAULT_SCALE_FACTOR (cellpack.bin.simularium_converter.ConvertToSimularium attribute) DEFAULT_VALUES (cellpack.autopack.DBRecipeHandler.CompositionDoc attribute) default_values (cellpack.autopack.interface_objects.gradient_data.GradientData attribute) (cellpack.autopack.loaders.analysis_config_loader.AnalysisConfigLoader attribute) (cellpack.autopack.loaders.config_loader.ConfigLoader attribute) (cellpack.autopack.loaders.recipe_loader.RecipeLoader attribute) defaultFunction() (cellpack.autopack.Gradient.Gradient method) delete_doc() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) deleteblist() (cellpack.autopack.ingredient.Ingredient.Ingredient method) deleteChildrens() (cellpack.autopack.upy.hostHelper.Helper method) deleteInstance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) deleteMeshEdges() (cellpack.autopack.upy.hostHelper.Helper method) deleteMeshFaces() (cellpack.autopack.upy.hostHelper.Helper method) deleteMeshVertices() (cellpack.autopack.upy.hostHelper.Helper method) deleteObject() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) delIngr() (cellpack.autopack.Graphics.AutopackViewer method) delIngredient() (cellpack.autopack.Recipe.Recipe method) delIngredientGrow() (cellpack.autopack.Graphics.AutopackViewer method) delRB() (cellpack.autopack.Environment.Environment method) dense_to_sparse() (in module cellpack.autopack.binvox_rw) dihedral() (cellpack.autopack.upy.hostHelper.Helper method) direction (cellpack.autopack.interface_objects.gradient_data.ModeOptions attribute) displayCompartment() (cellpack.autopack.Graphics.AutopackViewer method) displayCompartmentPoints() (cellpack.autopack.Graphics.AutopackViewer method) displayCompartments() (cellpack.autopack.Graphics.AutopackViewer method)

displayCompartmentsIngredients() (cellpack.autopack.Graphics.AutopackViewer method) displayCompartmentsPoints() (cellpack.autopack.Graphics.AutopackViewer method) displayCytoplasmIngredients() (cellpack.autopack.Graphics.AutopackViewer method) displayDistance() (cellpack.autopack.Graphics.AutopackViewer method) displayEnv() (cellpack.autopack.Graphics.AutopackViewer method) displayFill() (cellpack.autopack.Graphics.AutopackViewer method) displayFillBox() (cellpack.autopack.Graphics.AutopackViewer method) displayFreePoints() (cellpack.autopack.Graphics.AutopackViewer method) displayFreePointsAsPS() (cellpack.autopack.Graphics.AutopackViewer method) displayGradient() (cellpack.autopack.Graphics.AutopackViewer method) displayIngrCylinders() (cellpack.autopack.Graphics.AutopackViewer method) displayIngredients() (cellpack.autopack.Graphics.AutopackViewer method) displayIngrGrow() (cellpack.autopack.Graphics.AutopackViewer method) displayIngrGrows() (cellpack.autopack.Graphics.AutopackViewer method) displayIngrMesh() (cellpack.autopack.Graphics.AutopackViewer method) displayIngrResults() (cellpack.autopack.Graphics.AutopackViewer method) displayIngrSpheres() (cellpack.autopack.Graphics.AutopackViewer method) displayInstancesIngredient() (cellpack.autopack.Graphics.AutopackViewer method) displayLeafOctree() (cellpack.autopack.Graphics.AutopackViewer method) displayOctree() (cellpack.autopack.Graphics.AutopackViewer method) displayOctreeLeaf() (cellpack.autopack.Graphics.AutopackViewer method) displayOneNodeOctree() (cellpack.autopack.Graphics.AutopackViewer method) displayParticleVolumeDistance() (cellpack.autopack.Graphics.AutopackViewer method) displayPoints() (cellpack.autopack.Graphics.AutopackViewer method) displayPreFill() (cellpack.autopack.Graphics.AutopackViewer method) displayRoot() (cellpack.autopack.Graphics.AutopackViewer method) displaysubnode() (cellpack.autopack.Graphics.AutopackViewer method) distance (cellpack.autopack.interface_objects.gradient_data.InvertOptions attribute) distance_check_failed() (cellpack.autopack.Environment.Environment method) distanceFunction() (cellpack.autopack.interface_objects.partners.Partner method) DistributionOptions (class in cellpack.autopack.ingredient.Ingredient) DistributionTypes (class in cellpack.autopack.ingredient.Ingredient) doc_id() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) doc_to_dict() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) Dodecahedron() (cellpack.autopack.upy.hostHelper.Helper method) dodecahedron() (cellpack.autopack.upy.hostHelper.Helper method) doloop() (cellpack.autopack.Analysis.Analysis method) dot() (in module cellpack.autopack.ray) (in module cellpack.autopack.upy.hostHelper) download_file() (cellpack.autopack.AWSHandler.AWSHandler method) (in module cellpack.autopack) drawGradientLine() (cellpack.autopack.upy.hostHelper.Helper method) drawPtCol() (cellpack.autopack.upy.hostHelper.Helper method) dropOneIngr() (cellpack.autopack.Environment.Environment class method) dropOneIngrJson() (cellpack.autopack.Environment.Environment method) dspMesh() (cellpack.autopack.Graphics.AutopackViewer method) dspSph() (cellpack.autopack.Graphics.AutopackViewer method) dupliVert (cellpack.autopack.upy.hostHelper.Helper attribute)

E

EMPTY (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute) Environment (class in cellpack.autopack.Environment) eulerToMatrix() (cellpack.autopack.upy.hostHelper.Helper method) expand_object_using_key() (in module cellpack.autopack.utils) EXPONENTIAL (cellpack.autopack.interface_objects.gradient_data.WeightModes attribute) export_image() (cellpack.autopack.writers.ImageWriter.ImageWriter method) exportAsIndexedMeshs() (cellpack.autopack.Graphics.AutopackViewer method) ExportCollada (class in cellpack.autopack.IOutils)

exportIngredient() (cellpack.autopack.Graphics.AutopackViewer method) exportRecipeIngredients() (cellpack.autopack.Graphics.AutopackViewer method) exportToBD_BOX() (cellpack.autopack.Environment.Environment method) exportToReaDDy() (cellpack.autopack.Environment.Environment method) exportToTEM() (cellpack.autopack.Environment.Environment method) exportToTEM_SIM() (cellpack.autopack.Environment.Environment method) extend_bounding_box_for_compartments() (cellpack.autopack.Environment.Environment method) extendGridArrays() (cellpack.autopack.Compartment.Compartment method) extractMeshComponent() (cellpack.autopack.Environment.Environment method)

F

f_dot_product() (in module cellpack.autopack.ray) f_ray_intersect_polyhedron() (in module cellpack.autopack.ray) far_enough_from_surfaces() (cellpack.autopack.ingredient.Ingredient.Ingredient method) fill_in_empty_fiber_data() (cellpack.bin.simularium_converter.ConvertToSimularium method) fillTriangleColor() (cellpack.autopack.upy.hostHelper.Helper method) filter_surface_pts_to_fill_box() (cellpack.autopack.Compartment.Compartment method) find_nearest() (cellpack.autopack.Compartment.Compartment method) findBranch() (cellpack.autopack.octree.Octree method) findClosestPoint() (cellpack.autopack.upy.hostHelper.Helper method) findPointsCenter() (in module cellpack.autopack.ray) findPosition() (cellpack.autopack.octree.Octree method)

finishWithWater() (cellpack.autopack.Environment.Environment method) FIREBASE (cellpack.autopack.interface_objects.database_ids.DATABASE_IDS attribute) FirebaseHandler (class in cellpack.autopack.FirebaseHandler) fit_view3D() (cellpack.autopack.upy.hostHelper.Helper method) FixNormals() (cellpack.autopack.upy.hostHelper.Helper method) fixOnePath() (in module cellpack.autopack) fixPath() (in module cellpack.autopack) format_color() (cellpack.autopack.plotly_result.PlotlyAnalysis static method) format_rgb_color() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper static method) frameAdvanced() (cellpack.autopack.upy.hostHelper.Helper method) FromVec() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method)

G

gatherResult() (in module cellpack.autopack.IOutils) gblob (cellpack.autopack.interface_objects.gradient_data.ModeOptions attribute) generalApply() (cellpack.autopack.trajectory.Trajectory method) Geom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) GeometryTools (class in cellpack.autopack.GeometryTools) get() (cellpack.autopack.randomRot.RandomRot method) get_active() (cellpack.autopack.interface_objects.representations.Representations method) get_active_data() (cellpack.autopack.interface_objects.representations.Representations method) get_adjusted_position() (cellpack.autopack.interface_objects.representations.Representations method) get_all() (cellpack.autopack.interface_objects.packed_objects.PackedObjects method) get_all_distances() (cellpack.autopack.Environment.Environment method) get_all_docs() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) get_all_ingredients() (cellpack.autopack.loaders.recipe_loader.RecipeLoader method) get_all_positions_to_check() (cellpack.autopack.ingredient.Ingredient.Ingredient method) get_alternate_position() (cellpack.autopack.ingredient.grow.GrowIngredient method) get_alternate_position_p() (cellpack.autopack.ingredient.grow.GrowIngredient method) get_and_store_v2_object() (in module cellpack.autopack.loaders.migrate_v1_to_v2) get_attributes_to_update() (cellpack.autopack.Environment.Environment static method) get_aws_object_key() (cellpack.autopack.AWSHandler.AWSHandler method) get_bbox() (cellpack.autopack.Compartment.Compartment method) get_bounding_box() (cellpack.bin.simularium_converter.ConvertToSimularium method) get_bounding_box_limits() (cellpack.autopack.Environment.Environment method) get_cache_location() (in module cellpack.autopack) get_center() (cellpack.autopack.Gradient.Gradient method) get_centroid() (cellpack.autopack.MeshStore.MeshStore method) get_closest_ingredients() (cellpack.autopack.Environment.Environment method) get_collada_material() (cellpack.autopack.MeshStore.MeshStore static method) get_collection_id_from_path() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) get_combined_gradient_weight() (cellpack.autopack.Gradient.Gradient static method) get_compartment() (cellpack.autopack.ingredient.Ingredient.Ingredient method) (cellpack.autopack.interface_objects.packed_objects.PackedObjects method) get_compartment_object_by_name() (cellpack.autopack.Environment.Environment method) get_creds() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) get_cuttoff_value() (cellpack.autopack.ingredient.Ingredient.Ingredient method) (cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr method) (cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr method) get_deepest_level() (cellpack.autopack.interface_objects.representations.Representations method) get_dev_creds() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) get_display_data() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) get_distance() (in module cellpack.autopack.utils) get_distances() (cellpack.autopack.Environment.Environment method) get_distances_and_angles() (cellpack.autopack.Environment.Environment method) get_distances_from_point() (in module cellpack.autopack.utils) get_doc_by_id() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) get_doc_by_name() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) get_doc_by_ref() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) get_dpad() (cellpack.autopack.Environment.Environment method) get_encapsulating_radii() (cellpack.autopack.interface_objects.packed_objects.PackedObjects method) get_euler() (cellpack.bin.simularium_converter.ConvertToSimularium method) get_euler_from_matrix() (cellpack.bin.simularium_converter.ConvertToSimularium method) get_euler_from_quat() (cellpack.bin.simularium_converter.ConvertToSimularium method) get_gauss_weights() (cellpack.autopack.Gradient.Gradient method) get_ingredient_angles() (cellpack.autopack.Environment.Environment method) get_ingredient_by_name() (cellpack.autopack.Environment.Environment method) get_ingredient_data() (cellpack.bin.simularium_converter.ConvertToSimularium method) get_ingredient_display_data() (cellpack.bin.simularium_converter.ConvertToSimularium method) get_ingredient_key_from_object_or_comp_name() (cellpack.autopack.Analysis.Analysis method) get_ingredient_radii() (cellpack.autopack.Analysis.Analysis method) get_ingredients() (cellpack.autopack.interface_objects.packed_objects.PackedObjects method) get_ingredients_in_tree() (cellpack.autopack.Environment.Environment method) get_list_of_dims() (cellpack.autopack.Analysis.Analysis static method) get_list_of_free_indices() (cellpack.autopack.ingredient.Ingredient.Ingredient method) get_local_file_location() (in module cellpack.autopack) get_max_value_from_distribution() (in module cellpack.autopack.utils) get_mesh() (cellpack.autopack.MeshStore.MeshStore method) get_mesh_data() (cellpack.bin.simularium_converter.ConvertToSimularium static method) get_mesh_filepath_and_extension() (cellpack.autopack.MeshStore.MeshStore static method) get_mesh_format() (cellpack.autopack.interface_objects.representations.Representations method) get_mesh_name() (cellpack.autopack.interface_objects.representations.Representations method) get_mesh_path() (cellpack.autopack.interface_objects.representations.Representations method) get_midpoint() (cellpack.autopack.MeshStore.MeshStore static method) get_min_max_radius() (cellpack.autopack.interface_objects.representations.Representations method) get_min_value_from_distribution() (in module cellpack.autopack.utils) get_minimum_expected_distance_from_recipe() (cellpack.autopack.Analysis.Analysis method) get_module_version() (in module cellpack) get_new_distance_values() (cellpack.autopack.ingredient.grow.GrowIngredient method) (cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr method) (cellpack.autopack.ingredient.single_cube.SingleCubeIngr method) (cellpack.autopack.ingredient.single_sphere.SingleSphereIngr method) get_new_distances_and_inside_points() (cellpack.autopack.ingredient.Ingredient.Ingredient method) get_new_jitter_location_and_rotation() (cellpack.autopack.ingredient.Ingredient.Ingredient method) get_new_pos() (cellpack.autopack.ingredient.Ingredient.Ingredient method) get_noise() (cellpack.autopack.upy.hostHelper.Helper method) get_normal() (cellpack.autopack.MeshStore.MeshStore method) get_normal_for_point() (cellpack.autopack.Compartment.Compartment method) get_nsphere() (cellpack.autopack.MeshStore.MeshStore method) get_number_of_ingredients_packed() (cellpack.autopack.Analysis.Analysis method) get_obj_dict() (cellpack.autopack.Analysis.Analysis method) get_object() (cellpack.autopack.MeshStore.MeshStore method) get_packed_minimum_distance() (cellpack.autopack.Analysis.Analysis method) get_paired_key() (in module cellpack.autopack.utils) get_partner_by_ingr_name() (cellpack.autopack.interface_objects.partners.Partners method) get_partner_pair_dict() (cellpack.autopack.Analysis.Analysis method) get_partners() (cellpack.autopack.ingredient.Ingredient.Ingredient method) get_path_from_ref() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) get_pdb_path() (cellpack.autopack.interface_objects.representations.Representations method) get_point() (cellpack.autopack.interface_objects.partners.Partner method) get_positions() (cellpack.autopack.interface_objects.packed_objects.PackedObjects method) (cellpack.autopack.interface_objects.representations.Representations method) get_positions_for_ingredient() (cellpack.autopack.interface_objects.packed_objects.PackedObjects method) get_positions_per_ingredient() (cellpack.bin.simularium_converter.ConvertToSimularium method) get_radii() (cellpack.autopack.interface_objects.packed_objects.PackedObjects method) (cellpack.autopack.interface_objects.representations.Representations method) get_radius() (cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr method) (cellpack.autopack.ingredient.single_sphere.SingleSphereIngr method) get_rb_model() (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.ingredient.Ingredient.Ingredient method) get_rbNodes() (cellpack.autopack.ingredient.Ingredient.Ingredient method) get_recipe_metadata() (in module cellpack.bin.upload) get_rectangle_cercle_area() (cellpack.autopack.GeometryTools.GeometryTools method) get_reference_data() (cellpack.autopack.DBRecipeHandler.CompositionDoc static method) get_reference_in_obj() (cellpack.autopack.DBRecipeHandler.CompositionDoc static method) get_reflected_point() (in module cellpack.autopack.ingredient.utils) get_representations() (in module cellpack.autopack.loaders.migrate_v1_to_v2) get_rotation() (cellpack.autopack.ingredient.Ingredient.Ingredient method) get_rotations_for_ingredient() (cellpack.autopack.interface_objects.packed_objects.PackedObjects method) get_scaled_distances_between_surfaces() (cellpack.autopack.MeshStore.MeshStore method) get_seed_list() (in module cellpack.autopack.utils) get_signed_distance() (cellpack.autopack.ingredient.grow.GrowIngredient method) (cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr method) (cellpack.autopack.ingredient.single_cube.SingleCubeIngr method) (cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr method) (cellpack.autopack.ingredient.single_sphere.SingleSphereIngr method) get_size_of_bounding_box() (cellpack.autopack.Environment.Environment method) get_smallest_radius() (cellpack.autopack.MeshStore.MeshStore method) get_staging_creds() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) get_username() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) get_value() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) get_value_from_distribution() (in module cellpack.autopack.utils) get_weights_by_distance() (cellpack.autopack.ingredient.agent.Agent method) getA() (cellpack.autopack.upy.hostHelper.Helper method) GetAbsPosUntilRoot() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getActiveIng() (cellpack.autopack.Environment.Environment method) getAllMaterials() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getAllPosRot() (in module cellpack.autopack.IOutils) getAngleAxis() (cellpack.autopack.upy.hostHelper.Helper method) getAxisRotation() (cellpack.autopack.ingredient.Ingredient.Ingredient method) getBiasedRotation() (cellpack.autopack.ingredient.Ingredient.Ingredient method) getBigBB() (cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr method) (cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr method) getBinaryWeighted() (cellpack.autopack.Gradient.Gradient method) getBoundary() (cellpack.autopack.GeometryTools.GeometryTools method) getBoundingBox() (cellpack.autopack.Compartment.Compartment method) getBoxSize() (cellpack.autopack.upy.hostHelper.Helper method) getCenter() (cellpack.autopack.BaseGrid.BaseGrid method) (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.upy.hostHelper.Helper method)

getChilds() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getClosestFreeGridPoint() (cellpack.autopack.BaseGrid.BaseGrid method) getClosestGridPoint() (cellpack.autopack.BaseGrid.BaseGrid method) getColladaMaterial() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getCornerPointCube() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getCurrentScene() (cellpack.autopack.upy.hostHelper.Helper class method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getCurrentSceneName() (cellpack.autopack.upy.hostHelper.Helper class method) getCurrentSelection() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getData() (cellpack.autopack.ingredient.Ingredient.Ingredient method) getDiagonal() (cellpack.autopack.BaseGrid.BaseGrid method) getDihedral() (in module cellpack.autopack.ingredient.utils) GetDistance() (cellpack.autopack.GeometryTools.GeometryTools method) getEncapsulatingRadius() (cellpack.autopack.ingredient.Ingredient.Ingredient method) getFace() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getFaceEdges() (cellpack.autopack.upy.hostHelper.Helper method) getFaceNormals() (cellpack.autopack.Compartment.Compartment method) getFaceNormalsArea() (cellpack.autopack.upy.hostHelper.Helper method) getFaces() (cellpack.autopack.upy.hostHelper.Helper method) getFacesfromV() (cellpack.autopack.upy.hostHelper.Helper method) getFacesNfromV() (cellpack.autopack.Compartment.Compartment method) getFirstPoint() (cellpack.autopack.ingredient.grow.GrowIngredient method) getForwWeight() (cellpack.autopack.Gradient.Gradient method) getHaltonUnique() (cellpack.autopack.Analysis.Analysis method) getHClass() (in module cellpack.autopack.upy) getHelperClass() (in module cellpack.autopack.upy) getIJK() (cellpack.autopack.BaseGrid.BaseGrid method) (cellpack.autopack.Grid.Grid method) getImage() (cellpack.autopack.upy.hostHelper.Helper method) getIndex() (cellpack.autopack.binvox_rw.Voxels method) getIndexData() (cellpack.autopack.binvox_rw.Voxels method) getIngredientInstancePos() (cellpack.autopack.trajectory.Trajectory method) getIngredientsInBox() (cellpack.autopack.ingredient.Ingredient.Ingredient method) getIngrFromNameInRecipe() (cellpack.autopack.Environment.Environment method) getInterpolatedNormal() (cellpack.autopack.Compartment.Compartment method) getInterpolatedSphere() (cellpack.autopack.ingredient.grow.GrowIngredient method) getJtransRot() (cellpack.autopack.ingredient.grow.GrowIngredient method) getJtransRot_r() (cellpack.autopack.ingredient.grow.GrowIngredient method) getLayers() (cellpack.autopack.upy.hostHelper.Helper method) getLinearWeighted() (cellpack.autopack.Gradient.Gradient method) getListCompFromMask() (cellpack.autopack.ingredient.Ingredient.Ingredient method) getMasterInstance() (cellpack.autopack.upy.hostHelper.Helper method) getMaterial() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getMaterialName() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getMaterialObject() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getMaterialProperty() (cellpack.autopack.upy.hostHelper.Helper method) getMaxJitter() (cellpack.autopack.ingredient.Ingredient.Ingredient method) getMaxWeight() (cellpack.autopack.Gradient.Gradient method) getMesh() (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.ingredient.Ingredient.Ingredient method) (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getMeshEdge() (cellpack.autopack.upy.hostHelper.Helper method) getMeshEdges() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getMeshFaces() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getMeshNormales() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getMeshVertice() (cellpack.autopack.upy.hostHelper.Helper method) getMeshVertices() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getMinMaxProteinSize() (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.Recipe.Recipe method) getMinWeight() (cellpack.autopack.Gradient.Gradient method) getName() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getNBgridPoints() (cellpack.autopack.BaseGrid.HaltonGrid method) getNextPoint() (cellpack.autopack.ingredient.grow.GrowIngredient method) getNextPtIndCyl() (cellpack.autopack.ingredient.grow.GrowIngredient method) getNormals() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getNormedVector() (in module cellpack.autopack.ingredient.utils) getNormedVectorOnes() (in module cellpack.autopack.ingredient.utils) getNormedVectorU() (in module cellpack.autopack.ingredient.utils) getObject() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getObjectName() (cellpack.autopack.upy.hostHelper.Helper method) getOld() (cellpack.autopack.randomRot.RandomRot method) getOneIngr() (cellpack.autopack.Environment.Environment class method) getOneIngrJson() (cellpack.autopack.Environment.Environment method) getOrder() (cellpack.autopack.upy.hostHelper.Helper method) getParticles() (cellpack.autopack.upy.hostHelper.Helper method) getParticulesPosition() (cellpack.autopack.upy.hostHelper.Helper method) getPointFrom3D() (cellpack.autopack.BaseGrid.BaseGrid method) (cellpack.autopack.BaseGrid.HaltonGrid method) getPointsInCube() (cellpack.autopack.BaseGrid.BaseGrid method) getPointsInCubeFillBB() (cellpack.autopack.BaseGrid.BaseGrid method) getPointsInSphere() (cellpack.autopack.BaseGrid.BaseGrid method) getPointToDrop() (cellpack.autopack.Environment.Environment method) getPosAt() (cellpack.autopack.trajectory.dcdTrajectory method) (cellpack.autopack.trajectory.molbTrajectory method) (cellpack.autopack.trajectory.xyzTrajectory method) getPositionPeridocity() (cellpack.autopack.BaseGrid.BaseGrid method) getPosLine() (cellpack.autopack.trajectory.xyzTrajectory method) getPosUntilRoot() (cellpack.autopack.upy.hostHelper.Helper method) getProperty() (cellpack.autopack.upy.hostHelper.Helper method) getPropertyObject() (cellpack.autopack.upy.hostHelper.Helper method) getRadius() (cellpack.autopack.BaseGrid.BaseGrid method) (cellpack.autopack.Compartment.Compartment method) getRamp() (in module cellpack.autopack.upy.colors) getRndWeighted() (cellpack.autopack.Gradient.Gradient method) getRotTransRB() (cellpack.autopack.Environment.Environment method) getScale() (cellpack.autopack.BaseGrid.HaltonGrid method) (cellpack.autopack.upy.hostHelper.Helper method) getSize() (cellpack.autopack.upy.hostHelper.Helper method) getSizeXYZ() (cellpack.autopack.Compartment.Compartment method) getSortedActiveIngredients() (cellpack.autopack.Environment.Environment method) getStringValueOptions() (in module cellpack.autopack.IOutils) getSubWeighted() (cellpack.autopack.Gradient.Gradient method) (cellpack.autopack.ingredient.agent.Agent method) getSurfaceInnerPoints() (cellpack.autopack.Compartment.Compartment method) getSurfaceInnerPoints_kevin() (cellpack.autopack.Compartment.Compartment method) getSurfaceInnerPoints_sdf() (cellpack.autopack.Compartment.Compartment method) getSurfaceInnerPoints_sdf_interpolate() (cellpack.autopack.Compartment.Compartment method) getSurfacePoint() (cellpack.autopack.Compartment.Compartment method) getTotalNbObject() (cellpack.autopack.Environment.Environment method) getTransformation() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getTranslation() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getTubeProperties() (cellpack.autopack.upy.hostHelper.Helper method) getTubePropertiesMatrix() (cellpack.autopack.upy.hostHelper.Helper method) getType() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getUV() (cellpack.autopack.upy.hostHelper.Helper method) getUVs() (cellpack.autopack.upy.hostHelper.Helper method) getV3() (cellpack.autopack.ingredient.grow.GrowIngredient method) getVertexNormals() (cellpack.autopack.Compartment.Compartment method) getVisibility() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) getVNfromF() (cellpack.autopack.Compartment.Compartment method) GITHUB (cellpack.autopack.interface_objects.database_ids.DATABASE_IDS attribute) grab() (cellpack.autopack.IOutils.GrabResult method) GrabResult (class in cellpack.autopack.IOutils) Gradient (class in cellpack.autopack.Gradient) gradient_list_to_dict() (cellpack.autopack.DBRecipeHandler.CompositionDoc static method) GradientData (class in cellpack.autopack.interface_objects.gradient_data) GradientDoc (class in cellpack.autopack.DBRecipeHandler) GradientModes (class in cellpack.autopack.interface_objects.gradient_data) Grid (class in cellpack.autopack.Grid) gridPoint (class in cellpack.autopack.BaseGrid) GROW (cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE attribute) grow() (cellpack.autopack.ingredient.grow.GrowIngredient method) grow_place() (cellpack.autopack.ingredient.grow.GrowIngredient method) GrowIngredient (class in cellpack.autopack.ingredient.grow)

H

halton() (in module cellpack.autopack.ldSequence) halton2() (in module cellpack.autopack.ldSequence) halton3() (in module cellpack.autopack.ldSequence) halton_sequence() (in module cellpack.autopack.ldSequence) HaltonGrid (class in cellpack.autopack.BaseGrid) HaltonSequence (class in cellpack.autopack.ldSequence) haltonterm() (in module cellpack.autopack.ldSequence) handle_expired_results() (cellpack.autopack.DBRecipeHandler.ResultDoc method) handle_real_time_visualization() (cellpack.autopack.ingredient.Ingredient.Ingredient method) handlers() (cellpack.autopack.interface_objects.database_ids.DATABASE_IDS class method)

has_mesh() (cellpack.autopack.ingredient.Ingredient.Ingredient method) (cellpack.autopack.interface_objects.representations.Representations method) has_pdb() (cellpack.autopack.ingredient.Ingredient.Ingredient method) (cellpack.autopack.interface_objects.representations.Representations method) Helper (class in cellpack.autopack.upy.hostHelper) Hexahedron() (cellpack.autopack.upy.hostHelper.Helper method) hexahedron() (cellpack.autopack.upy.hostHelper.Helper method) hexToRgb() (in module cellpack.autopack.upy.colors) hideIngrPrimitive() (cellpack.autopack.Graphics.AutopackViewer method) histogram() (cellpack.autopack.Analysis.Analysis method) host (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute)

I

Icosahedron() (cellpack.autopack.upy.hostHelper.Helper method) icosahedron() (cellpack.autopack.upy.hostHelper.Helper method) ijkToIndex() (cellpack.autopack.binvox_rw.Voxels method) ijkToxyz() (cellpack.autopack.binvox_rw.Voxels method) IK (cellpack.autopack.upy.hostHelper.Helper attribute) ImageWriter (class in cellpack.autopack.writers.ImageWriter) inBox() (cellpack.autopack.Compartment.Compartment method) inc() (cellpack.autopack.ldSequence.cHaltonSequence3 method) includeIngredientRecipe() (cellpack.autopack.Environment.Environment method) includeIngrRecipe() (cellpack.autopack.Environment.Environment method) includeIngrRecipes() (cellpack.autopack.Environment.Environment method) increment_static() (cellpack.autopack.upy.simularium.simularium_helper.Instance method) increment_static_objects() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) increment_time() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) IndexedPolgonsToTriPoints() (cellpack.autopack.upy.hostHelper.Helper method) IndexedPolygons() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) Ingredient (class in cellpack.autopack.ingredient.Ingredient) ingredient_compare0() (in module cellpack.autopack.utils) ingredient_compare1() (in module cellpack.autopack.utils) ingredient_compare2() (in module cellpack.autopack.utils) INGREDIENT_TYPE (class in cellpack.autopack.interface_objects.ingredient_types) IngredientInstanceDrop (class in cellpack.autopack.ingredient.Ingredient) inGrid() (cellpack.autopack.Compartment.Compartment method) ingrJsonNode() (cellpack.autopack.IOutils.IOingredientTool method) (cellpack.autopack.writers.IOingredientTool method) ingrPythonNode() (cellpack.autopack.IOutils.IOingredientTool method) init_scene_with_objects() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) initialize_mesh() (cellpack.autopack.ingredient.Ingredient.Ingredient method) (cellpack.autopack.ingredient.multi_cylinder.MultiCylindersIngr method) (cellpack.autopack.ingredient.single_cylinder.SingleCylinderIngr method) (cellpack.autopack.ingredient.single_sphere.SingleSphereIngr method) initialize_shape() (cellpack.autopack.Compartment.Compartment method)

Inner_Grid_Methods (class in cellpack.autopack.loaders.config_loader) insertNode() (cellpack.autopack.octree.Octree method) INSTANCE (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute) Instance (class in cellpack.autopack.upy.simularium.simularium_helper) instancePolygon() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) instancesCylinder() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) instancesSphere() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) instancesToCollada() (cellpack.autopack.upy.hostHelper.Helper method) InvertOptions (class in cellpack.autopack.interface_objects.gradient_data) IOingredientTool (class in cellpack.autopack.IOutils) (class in cellpack.autopack.writers) is_db_dict() (cellpack.autopack.DBRecipeHandler.DataDoc static method) is_fiber() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper static method) is_firebase_obj() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) is_full_url() (in module cellpack.autopack) is_key() (cellpack.autopack.DBRecipeHandler.DataDoc static method) (cellpack.autopack.Recipe.Recipe static method) is_matrix() (cellpack.bin.simularium_converter.ConvertToSimularium method) is_member() (cellpack.autopack.interface_objects.meta_enum.MetaEnum class method) is_nested_list() (cellpack.autopack.DBRecipeHandler.DataDoc static method) is_obj() (cellpack.autopack.DBRecipeHandler.DataDoc static method) is_partner() (cellpack.autopack.interface_objects.partners.Partners method) is_point_in_correct_region() (cellpack.autopack.ingredient.Ingredient.Ingredient method) is_point_inside_bb() (cellpack.autopack.BaseGrid.BaseGrid method) is_point_inside_mesh() (cellpack.autopack.Compartment.Compartment method) is_reference() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) is_remote_path() (in module cellpack.autopack) is_s3_url() (in module cellpack.autopack) is_two_d() (cellpack.autopack.Environment.Environment method) is_url_valid() (cellpack.autopack.AWSHandler.AWSHandler method) isIndexedPolyon() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) isSphere() (cellpack.autopack.upy.hostHelper.Helper method)

J

JITTER (cellpack.autopack.loaders.config_loader.Place_Methods attribute) jitter_place() (cellpack.autopack.ingredient.Ingredient.Ingredient method)

jitterPosition() (cellpack.autopack.ingredient.Ingredient.Ingredient method) JoinsObjects() (cellpack.autopack.upy.hostHelper.Helper method)

K

KEY_TO_DICT_MAPPING (cellpack.autopack.DBRecipeHandler.CompositionDoc attribute)

L

Labels() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) LIGHT_OPTIONS (cellpack.autopack.upy.hostHelper.Helper attribute) LINEAR (cellpack.autopack.interface_objects.gradient_data.PickModes attribute) (cellpack.autopack.interface_objects.gradient_data.WeightModes attribute) linkTraj() (cellpack.autopack.Environment.Environment method) LIST (cellpack.autopack.ingredient.Ingredient.DistributionTypes attribute) LIST_VALUES (cellpack.autopack.ingredient.Ingredient.DistributionOptions attribute) load_asJson() (cellpack.autopack.Environment.Environment method) load_asTxt() (cellpack.autopack.Environment.Environment method) load_file() (in module cellpack.autopack)

load_Json() (in module cellpack.autopack.IOutils) load_JsonString() (in module cellpack.autopack.IOutils) load_MixedasJson() (in module cellpack.autopack.IOutils) load_object_from_pickle() (in module cellpack.autopack.utils) loadFreePoint() (cellpack.autopack.Environment.Environment method) loadJSON() (cellpack.autopack.Analysis.Analysis method) loadResult() (cellpack.autopack.Environment.Environment method) lookForNeighbours() (cellpack.autopack.ingredient.Ingredient.Ingredient method) loopThroughIngr() (cellpack.autopack.Environment.Environment method) LowerCircleFunction() (cellpack.autopack.GeometryTools.GeometryTools method) LowerRectangleFunction() (cellpack.autopack.GeometryTools.GeometryTools method)

M

main() (in module cellpack.bin.analyze) (in module cellpack.bin.clean) (in module cellpack.bin.pack) (in module cellpack.bin.simularium_converter) (in module cellpack.bin.upload) make_and_show_heatmap() (cellpack.autopack.plotly_result.PlotlyAnalysis method) make_directory_if_needed() (in module cellpack.autopack) make_grid_heatmap() (cellpack.autopack.plotly_result.PlotlyAnalysis method) makeIngredient() (cellpack.autopack.IOutils.IOingredientTool method) makeIngredientFromJson() (cellpack.autopack.IOutils.IOingredientTool method) makeIngrMapping() (cellpack.autopack.trajectory.Trajectory method) makeMarchingCube() (in module cellpack.autopack.ray) makeTexture() (cellpack.autopack.upy.hostHelper.Helper method) map_colors() (in module cellpack.autopack.upy.colors) MarkdownWriter (class in cellpack.autopack.writers.MarkdownWriter) mask_sphere_points() (cellpack.autopack.ingredient.grow.GrowIngredient method) mask_sphere_points_angle() (cellpack.autopack.ingredient.grow.GrowIngredient method) mask_sphere_points_boundary() (cellpack.autopack.ingredient.grow.GrowIngredient method) mask_sphere_points_dihedral() (cellpack.autopack.ingredient.grow.GrowIngredient method) mask_sphere_points_ingredients() (cellpack.autopack.ingredient.grow.GrowIngredient method) mask_sphere_points_vector() (cellpack.autopack.ingredient.grow.GrowIngredient method) matrixToFacesMesh() (cellpack.autopack.upy.hostHelper.Helper method) matrixToVNMesh() (cellpack.autopack.upy.hostHelper.Helper method) MAX (cellpack.autopack.ingredient.Ingredient.DistributionOptions attribute) (cellpack.autopack.interface_objects.gradient_data.PickModes attribute) MEAN (cellpack.autopack.ingredient.Ingredient.DistributionOptions attribute) measure_distance() (cellpack.autopack.upy.hostHelper.Helper method) merge_place_results() (cellpack.autopack.ingredient.Ingredient.Ingredient method) MESH (cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE attribute) MeshStore (class in cellpack.autopack.MeshStore) metaballs() (cellpack.autopack.upy.hostHelper.Helper method) MetaEnum (class in cellpack.autopack.interface_objects.meta_enum) MidPoint() (cellpack.autopack.upy.hostHelper.Helper method) migrate_ingredient() (in module cellpack.autopack.loaders.migrate_v1_to_v2) MIN (cellpack.autopack.ingredient.Ingredient.DistributionOptions attribute) (cellpack.autopack.interface_objects.gradient_data.PickModes attribute) ModeOptions (class in cellpack.autopack.interface_objects.gradient_data) module cellpack cellpack.autopack cellpack.autopack.Analysis cellpack.autopack.AWSHandler cellpack.autopack.BaseGrid cellpack.autopack.binvox_rw cellpack.autopack.Compartment cellpack.autopack.DBRecipeHandler cellpack.autopack.Environment cellpack.autopack.FirebaseHandler cellpack.autopack.GeometryTools cellpack.autopack.Gradient cellpack.autopack.Graphics cellpack.autopack.Grid cellpack.autopack.ingredient cellpack.autopack.ingredient.agent cellpack.autopack.ingredient.grow cellpack.autopack.ingredient.Ingredient cellpack.autopack.ingredient.multi_cylinder cellpack.autopack.ingredient.multi_sphere cellpack.autopack.ingredient.single_cube cellpack.autopack.ingredient.single_cylinder cellpack.autopack.ingredient.single_sphere cellpack.autopack.ingredient.utils cellpack.autopack.interface_objects cellpack.autopack.interface_objects.database_ids cellpack.autopack.interface_objects.default_values cellpack.autopack.interface_objects.gradient_data cellpack.autopack.interface_objects.ingredient_types cellpack.autopack.interface_objects.meta_enum cellpack.autopack.interface_objects.packed_objects cellpack.autopack.interface_objects.partners cellpack.autopack.interface_objects.representations cellpack.autopack.IOutils cellpack.autopack.ldSequence cellpack.autopack.loaders cellpack.autopack.loaders.analysis_config_loader cellpack.autopack.loaders.config_loader cellpack.autopack.loaders.migrate_v1_to_v2 cellpack.autopack.loaders.migrate_v2_to_v2_1 cellpack.autopack.loaders.recipe_loader cellpack.autopack.loaders.utils cellpack.autopack.loaders.v1_v2_attribute_changes cellpack.autopack.MeshStore cellpack.autopack.octree cellpack.autopack.plotly_result cellpack.autopack.randomRot cellpack.autopack.ray cellpack.autopack.Recipe cellpack.autopack.Serializable cellpack.autopack.trajectory cellpack.autopack.transformation cellpack.autopack.upy cellpack.autopack.upy.colors cellpack.autopack.upy.hostHelper cellpack.autopack.upy.simularium cellpack.autopack.upy.simularium.plots cellpack.autopack.upy.simularium.simularium_helper cellpack.autopack.utils cellpack.autopack.writers cellpack.autopack.writers.ImageWriter cellpack.autopack.writers.MarkdownWriter cellpack.bin cellpack.bin.analyze cellpack.bin.clean cellpack.bin.cleanup_tasks cellpack.bin.pack cellpack.bin.simularium_converter cellpack.bin.upload

molbTrajectory (class in cellpack.autopack.trajectory) move() (cellpack.autopack.upy.simularium.simularium_helper.Instance method) move_object() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) moveRBnode() (cellpack.autopack.Environment.Environment method) MULTI_CYLINDER (cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE attribute) MULTI_SPHERE (cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE attribute) MultiCylindersIngr (class in cellpack.autopack.ingredient.multi_cylinder) MultiSphereIngr (class in cellpack.autopack.ingredient.multi_sphere)

N

newEmpty() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) newInstance() (cellpack.autopack.upy.hostHelper.Helper method) nodeToGeom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) norm() (cellpack.autopack.MeshStore.MeshStore static method) (cellpack.autopack.upy.hostHelper.Helper method) NORMAL (cellpack.autopack.ingredient.Ingredient.DistributionTypes attribute) normal_array() (cellpack.autopack.MeshStore.MeshStore static method) (cellpack.autopack.upy.hostHelper.Helper method)

normalize() (cellpack.autopack.MeshStore.MeshStore static method) (cellpack.autopack.upy.hostHelper.Helper method) normalize_v3() (cellpack.autopack.MeshStore.MeshStore static method) (cellpack.autopack.upy.hostHelper.Helper method) normalize_vector() (cellpack.autopack.Gradient.Gradient method) np_check_collision() (cellpack.autopack.ingredient.Ingredient.Ingredient method) NumpyArrayEncoder (class in cellpack.autopack.writers)

O

object (cellpack.autopack.interface_objects.gradient_data.ModeOptions attribute) ObjectDoc (class in cellpack.autopack.DBRecipeHandler) ObjectsSelection() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) Octahedron() (cellpack.autopack.upy.hostHelper.Helper method) octahedron() (cellpack.autopack.upy.hostHelper.Helper method) OctNode (class in cellpack.autopack.octree)

Octree (class in cellpack.autopack.octree) oneColladaGeom() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) oneCylinder() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) oneJitter() (cellpack.autopack.ingredient.Ingredient.Ingredient method) oneMetaBall() (cellpack.autopack.upy.hostHelper.Helper method) onePrevIngredient() (cellpack.autopack.Environment.Environment method) open_in_simularium() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper static method)

P

pack() (cellpack.autopack.Analysis.Analysis method) (in module cellpack.bin.pack) pack_at_grid_pt_location() (cellpack.autopack.ingredient.Ingredient.Ingredient method) (cellpack.autopack.ingredient.multi_sphere.MultiSphereIngr method) pack_grid() (cellpack.autopack.Environment.Environment method) pack_one_seed() (cellpack.autopack.Analysis.Analysis method) PackedObject (class in cellpack.autopack.interface_objects.packed_objects) PackedObjects (class in cellpack.autopack.interface_objects.packed_objects) parse() (cellpack.autopack.trajectory.dcdTrajectory method) (cellpack.autopack.trajectory.molbTrajectory method) (cellpack.autopack.trajectory.xyzTrajectory method) parse_one_mol() (cellpack.autopack.trajectory.molbTrajectory method) parse_s3_uri() (in module cellpack.autopack) particle() (cellpack.autopack.upy.hostHelper.Helper method) Partner (class in cellpack.autopack.interface_objects.partners) Partners (class in cellpack.autopack.interface_objects.partners) pathDeform() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) pb (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute) perturbAxis() (cellpack.autopack.ingredient.Ingredient.Ingredient method) pick_alternate() (cellpack.autopack.ingredient.grow.GrowIngredient method) pick_partner_grid_index() (cellpack.autopack.ingredient.agent.Agent method) pick_point_for_ingredient() (cellpack.autopack.Gradient.Gradient static method) pick_point_from_weight() (cellpack.autopack.Gradient.Gradient static method) pick_random_alternate() (cellpack.autopack.ingredient.grow.GrowIngredient method) pickAlternateHalton() (cellpack.autopack.ingredient.grow.GrowIngredient method) pickHalton() (cellpack.autopack.ingredient.grow.GrowIngredient method) pickIngredient() (cellpack.autopack.Environment.Environment method) PickModes (class in cellpack.autopack.interface_objects.gradient_data) pickPoint() (cellpack.autopack.Gradient.Gradient method) pickRandomSphere() (cellpack.autopack.ingredient.grow.GrowIngredient method) place() (cellpack.autopack.ingredient.Ingredient.Ingredient method) place_alternate() (cellpack.autopack.ingredient.grow.GrowIngredient method) place_alternate_p() (cellpack.autopack.ingredient.grow.GrowIngredient method) Place_Methods (class in cellpack.autopack.loaders.config_loader) place_object() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method)

plane() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) Platonic() (cellpack.autopack.upy.hostHelper.Helper method) plot() (cellpack.autopack.Analysis.Analysis method) plot_distance_distribution() (cellpack.autopack.Analysis.Analysis method) plot_occurence_distribution() (cellpack.autopack.Analysis.Analysis method) plot_position_distribution() (cellpack.autopack.Analysis.Analysis method) plot_position_distribution_total() (cellpack.autopack.Analysis.Analysis method) PlotData (class in cellpack.autopack.upy.simularium.plots) PlotlyAnalysis (class in cellpack.autopack.plotly_result) point_is_available() (cellpack.autopack.ingredient.Ingredient.Ingredient method) PointCloudObject() (cellpack.autopack.upy.hostHelper.Helper method) Points() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) POLYGON (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute) Polylines() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) post_and_open_file() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) power (cellpack.autopack.interface_objects.gradient_data.WeightModeOptions attribute) POWER (cellpack.autopack.interface_objects.gradient_data.WeightModes attribute) prep_data_for_db() (cellpack.autopack.DBRecipeHandler.DBUploader static method) prep_db_doc_for_download() (cellpack.autopack.DBRecipeHandler.DBRecipeLoader method) prep_molecules_for_save() (cellpack.autopack.Environment.Environment method) prepare_alternates() (cellpack.autopack.ingredient.grow.GrowIngredient method) prepare_alternates_proba() (cellpack.autopack.ingredient.grow.GrowIngredient method) prepare_buildgrid_box() (cellpack.autopack.Compartment.Compartment method) prepareDynamic() (cellpack.autopack.Graphics.AutopackViewer method) prepareIngredient() (cellpack.autopack.Graphics.AutopackViewer method) prepareMaster() (cellpack.autopack.Graphics.AutopackViewer method) printFillInfo() (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.Environment.Environment method) (cellpack.autopack.Recipe.Recipe method) printIngredients() (cellpack.autopack.Graphics.AutopackViewer method) printOneIngr() (cellpack.autopack.Graphics.AutopackViewer method) process_ingredients_in_recipe() (cellpack.autopack.Analysis.Analysis method) process_one_ingredient() (cellpack.bin.simularium_converter.ConvertToSimularium method) progressBar() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method)

Q

quaternion_matrix() (cellpack.autopack.randomRot.RandomRot method)

R

RADIAL (cellpack.autopack.interface_objects.gradient_data.GradientModes attribute) radius (cellpack.autopack.interface_objects.gradient_data.ModeOptions attribute) random() (in module cellpack.autopack.Environment) (in module cellpack.autopack.Gradient) (in module cellpack.autopack.ingredient.agent) (in module cellpack.autopack.ingredient.grow) (in module cellpack.autopack.ingredient.Ingredient) (in module cellpack.autopack.Recipe) random_quaternion() (cellpack.autopack.randomRot.RandomRot method) random_rotation_matrix() (cellpack.autopack.randomRot.RandomRot method) randomize_rotation() (cellpack.autopack.ingredient.Ingredient.Ingredient method) randomize_translation() (cellpack.autopack.ingredient.Ingredient.Ingredient method) RandomRot (class in cellpack.autopack.randomRot) randpoint_onsphere() (cellpack.autopack.upy.hostHelper.Helper method) ray_intersect_polygon() (in module cellpack.autopack.ray) ray_intersect_polyhedron() (in module cellpack.autopack.ray) raycast() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) raycast_test() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) RAYTRACE (cellpack.autopack.loaders.config_loader.Inner_Grid_Methods attribute) read() (cellpack.autopack.IOutils.IOingredientTool method) (cellpack.autopack.upy.hostHelper.Helper method) (in module cellpack.autopack.binvox_rw) read_as_3d_array() (in module cellpack.autopack.binvox_rw) read_as_coord_array() (in module cellpack.autopack.binvox_rw) read_dict_from_glob_file() (cellpack.autopack.Analysis.Analysis method) read_header() (in module cellpack.autopack.binvox_rw) read_json_file() (in module cellpack.autopack.loaders.utils) read_mesh_file() (cellpack.autopack.MeshStore.MeshStore method) read_text_file() (in module cellpack.autopack) readArraysFromFile() (cellpack.autopack.Environment.Environment method) readGridFromFile() (cellpack.autopack.Compartment.Compartment method) readme_url() (cellpack.autopack.DBRecipeHandler.DBMaintenance method) readMeshFromFile() (cellpack.autopack.upy.hostHelper.Helper method) recalc_normals() (cellpack.autopack.upy.hostHelper.Helper method) Recipe (class in cellpack.autopack.Recipe) RecipeLoader (class in cellpack.autopack.loaders.recipe_loader) Rectangle (class in cellpack.autopack.GeometryTools) RedWhiteBlueRamp() (in module cellpack.autopack.upy.colors) REG (cellpack.autopack.interface_objects.gradient_data.PickModes attribute) reg (cellpack.autopack.trajectory.Trajectory attribute) region_1() (cellpack.autopack.GeometryTools.GeometryTools method) region_1_2_theta() (cellpack.autopack.GeometryTools.GeometryTools method) region_2() (cellpack.autopack.GeometryTools.GeometryTools method) region_2_integrand() (cellpack.autopack.GeometryTools.GeometryTools method) region_3() (cellpack.autopack.GeometryTools.GeometryTools method) region_3_integrand() (cellpack.autopack.GeometryTools.GeometryTools method) reject() (cellpack.autopack.ingredient.Ingredient.Ingredient method) remove_from_realtime_display() (cellpack.autopack.ingredient.Ingredient.Ingredient method) remove_nans() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper static method) removeFreePoint() (cellpack.autopack.BaseGrid.BaseGrid method) removeOnePoint() (cellpack.autopack.Environment.Environment method) reorder_free_points() (cellpack.autopack.BaseGrid.BaseGrid static method) reParent() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method)

replaceIngrMesh() (cellpack.autopack.Graphics.AutopackViewer method) reporthook() (cellpack.autopack.upy.hostHelper.Helper method) reportprogress() (cellpack.autopack.Environment.Environment method) Representations (class in cellpack.autopack.interface_objects.representations) rerieveAxis() (cellpack.autopack.upy.hostHelper.Helper method) reset() (cellpack.autopack.BaseGrid.BaseGrid method) (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.Environment.Environment method) (cellpack.autopack.Grid.Grid method) (cellpack.autopack.ingredient.grow.GrowIngredient method) (cellpack.autopack.ingredient.Ingredient.Ingredient method) (cellpack.autopack.IOutils.GrabResult method) (cellpack.autopack.ldSequence.cHaltonSequence3 method) resetDefault() (in module cellpack.autopack) resetIngrRecip() (cellpack.autopack.Environment.Environment method) resetIngrs() (cellpack.autopack.Recipe.Recipe method) resetLastPoint() (cellpack.autopack.ingredient.grow.GrowIngredient method) resetProgressBar() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) resetSphereDistribution() (cellpack.autopack.ingredient.grow.GrowIngredient method) resetTransformation() (cellpack.autopack.upy.hostHelper.Helper method) Resolution (cellpack.autopack.GeometryTools.GeometryTools attribute) resolve_combined_gradient() (cellpack.autopack.DBRecipeHandler.CompositionDoc static method) resolve_composition() (cellpack.autopack.Recipe.Recipe static method) resolve_db_regions() (cellpack.autopack.DBRecipeHandler.CompositionDoc method) resolve_gradient_data_objects() (cellpack.autopack.Environment.Environment method) resolve_inheritance() (cellpack.autopack.loaders.recipe_loader.RecipeLoader static method) resolve_local_regions() (cellpack.autopack.DBRecipeHandler.CompositionDoc method) resolve_object_data() (cellpack.autopack.DBRecipeHandler.CompositionDoc method) restore() (cellpack.autopack.BaseGrid.BaseGrid method) (cellpack.autopack.Environment.Environment method) (cellpack.autopack.Grid.Grid method) restore_grids_from_pickle() (cellpack.autopack.Environment.Environment method) restore_molecules_array() (cellpack.autopack.Environment.Environment method) restoreEditMode() (cellpack.autopack.upy.hostHelper.Helper method) restoreFreePoints() (cellpack.autopack.Environment.Environment method) restoreGridFromFile() (cellpack.autopack.Environment.Environment method) ResultDoc (class in cellpack.autopack.DBRecipeHandler) retrieveColorMat() (cellpack.autopack.upy.hostHelper.Helper method) retrieveHost() (in module cellpack.autopack.upy) return_object_value() (cellpack.autopack.writers.Writer static method) rigid_place() (cellpack.autopack.ingredient.Ingredient.Ingredient method) RND (cellpack.autopack.interface_objects.gradient_data.PickModes attribute) rotate_about_axis() (cellpack.autopack.upy.hostHelper.Helper method) rotateObj() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) rotatePoint() (cellpack.autopack.upy.hostHelper.Helper method) rotation_matrix() (cellpack.autopack.upy.hostHelper.Helper class method) rotax() (in module cellpack.autopack.ingredient.utils) rotVectToVect() (cellpack.autopack.upy.hostHelper.Helper method) (in module cellpack.autopack.ingredient.utils) run_analysis_workflow() (cellpack.autopack.Analysis.Analysis method) run_cleanup() (in module cellpack.bin.cleanup_tasks) run_distance_analysis() (cellpack.autopack.Analysis.Analysis method) run_partner_analysis() (cellpack.autopack.Analysis.Analysis method) runBullet() (cellpack.autopack.Environment.Environment method)

S

save() (cellpack.autopack.BaseGrid.BaseGrid method) (cellpack.autopack.Grid.Grid method) (cellpack.autopack.writers.Writer method) save_as_simularium() (cellpack.autopack.writers.Writer method) save_asPython() (in module cellpack.autopack.IOutils) save_file_and_get_url() (cellpack.autopack.AWSHandler.AWSHandler method) save_grids_to_pickle() (cellpack.autopack.Environment.Environment method) save_Mixed_asJson() (cellpack.autopack.writers.Writer method) save_result() (cellpack.autopack.Environment.Environment method) saveDejaVuMesh() (cellpack.autopack.upy.hostHelper.Helper class method) saveGridLogsAsJson() (cellpack.autopack.Environment.Environment method) saveGridToFile() (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.Environment.Environment method) saveObjMesh() (cellpack.autopack.upy.hostHelper.Helper class method) saveRecipeAvailable() (in module cellpack.autopack) saveRecipeAvailableJSON() (in module cellpack.autopack) saveResultBinary() (in module cellpack.autopack.IOutils) saveResultBinaryDic() (in module cellpack.autopack.IOutils) scalar() (cellpack.autopack.upy.hostHelper.Helper method) scale_between_0_and_1() (cellpack.autopack.Gradient.Gradient static method) scale_distance_between (cellpack.autopack.interface_objects.gradient_data.ModeOptions attribute) scaleObj() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) SCANLINE (cellpack.autopack.loaders.config_loader.Inner_Grid_Methods attribute) sCompartment (class in cellpack.autopack.Serializable) selectEdge() (cellpack.autopack.upy.hostHelper.Helper method) selectEdges() (cellpack.autopack.upy.hostHelper.Helper method) selectFace() (cellpack.autopack.upy.hostHelper.Helper method) selectFaces() (cellpack.autopack.upy.hostHelper.Helper method) selectVertice() (cellpack.autopack.upy.hostHelper.Helper method) selectVertices() (cellpack.autopack.upy.hostHelper.Helper method) serializedFromResult() (in module cellpack.autopack.IOutils) serializedRecipe() (in module cellpack.autopack.IOutils) serializedRecipe_group() (in module cellpack.autopack.IOutils) serializedRecipe_group_dic() (in module cellpack.autopack.IOutils) set_active() (cellpack.autopack.interface_objects.representations.Representations method) set_doc() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) set_gradient() (cellpack.autopack.Environment.Environment method) set_ingredient() (cellpack.autopack.interface_objects.partners.Partner method) set_ingredient_color() (cellpack.autopack.Analysis.Analysis method) set_mode_properties() (cellpack.autopack.interface_objects.gradient_data.GradientData method) set_object_static() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) set_partners_ingredient() (cellpack.autopack.Environment.Environment method) set_recipe_ingredient() (cellpack.autopack.IOutils.IOingredientTool method) set_result_file_name() (cellpack.autopack.Environment.Environment method) set_sphere_positions() (cellpack.autopack.interface_objects.representations.Representations method) set_static() (cellpack.autopack.upy.simularium.simularium_helper.Instance method) set_surface_distances() (cellpack.autopack.Compartment.Compartment method) set_surfPtsBht() (cellpack.autopack.BaseGrid.BaseGrid method) set_surfPtscht() (cellpack.autopack.BaseGrid.BaseGrid method) set_weights_by_mode() (cellpack.autopack.Gradient.Gradient method) setCount() (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.Recipe.Recipe method) setCurrentSelection() (cellpack.autopack.upy.hostHelper.Helper method) setExteriorRecipe() (cellpack.autopack.Environment.Environment method) setFrame() (cellpack.autopack.upy.hostHelper.Helper method) setGeomFaces() (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.Environment.Environment method) SetHistoVol() (cellpack.autopack.Graphics.AutopackViewer method) setInnerRecipe() (cellpack.autopack.Compartment.Compartment method) setInstance() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) setKeyFrame() (cellpack.autopack.upy.hostHelper.Helper method) setLayers() (cellpack.autopack.upy.hostHelper.Helper method) setMesh() (cellpack.autopack.Compartment.Compartment method) setMeshEdge() (cellpack.autopack.upy.hostHelper.Helper method) setMeshEdges() (cellpack.autopack.upy.hostHelper.Helper method) setMeshFace() (cellpack.autopack.upy.hostHelper.Helper method) setMeshFaces() (cellpack.autopack.upy.hostHelper.Helper method) setMeshVertice() (cellpack.autopack.upy.hostHelper.Helper method) setMeshVertices() (cellpack.autopack.upy.hostHelper.Helper method) setName() (cellpack.autopack.upy.hostHelper.Helper method) setNumber() (cellpack.autopack.Compartment.Compartment method) setObjectMatrix() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) setParticulesPosition() (cellpack.autopack.upy.hostHelper.Helper method)

setProperty() (cellpack.autopack.upy.hostHelper.Helper method) setPropertyObject() (cellpack.autopack.upy.hostHelper.Helper method) SetRBOptions() (cellpack.autopack.Environment.Environment method) setRigidBody() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) setSeed() (cellpack.autopack.Environment.Environment method) (cellpack.autopack.randomRot.RandomRot method) setSoftBody() (cellpack.autopack.upy.hostHelper.Helper method) SetSpringOptions() (cellpack.autopack.Environment.Environment method) setSurfaceRecipe() (cellpack.autopack.Compartment.Compartment method) setTilling() (cellpack.autopack.ingredient.Ingredient.Ingredient method) setTransformation() (cellpack.autopack.upy.hostHelper.Helper method) setTranslation() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) setup() (cellpack.autopack.BaseGrid.BaseGrid method) setupBoundaryPeriodicity() (cellpack.autopack.BaseGrid.BaseGrid method) setupFromJsonDic() (in module cellpack.autopack.IOutils) setupOctree() (cellpack.autopack.Environment.Environment method) setupRBOptions() (cellpack.autopack.Environment.Environment method) setUV() (cellpack.autopack.upy.hostHelper.Helper method) setUVs() (cellpack.autopack.upy.hostHelper.Helper method) setValueToJsonNode() (cellpack.autopack.writers.Writer static method) setValueToPythonStr() (in module cellpack.autopack.IOutils) setViewer() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) setViewport() (cellpack.autopack.upy.hostHelper.Helper method) SHALLOW_MATCH (cellpack.autopack.DBRecipeHandler.CompositionDoc attribute) should_write() (cellpack.autopack.DBRecipeHandler.CompositionDoc method) (cellpack.autopack.DBRecipeHandler.DataDoc method) (cellpack.autopack.DBRecipeHandler.GradientDoc method) (cellpack.autopack.DBRecipeHandler.ObjectDoc method) show() (cellpack.autopack.plotly_result.PlotlyAnalysis method) showHide() (cellpack.autopack.Graphics.AutopackViewer method) showIngrPrimitive() (cellpack.autopack.Graphics.AutopackViewer method) simpleplot() (cellpack.autopack.Analysis.Analysis method) simulariumHelper (class in cellpack.autopack.upy.simularium.simularium_helper) SINGLE_CUBE (cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE attribute) SINGLE_CYLINDER (cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE attribute) SINGLE_SPHERE (cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE attribute) SingleCubeIngr (class in cellpack.autopack.ingredient.single_cube) SingleCylinderIngr (class in cellpack.autopack.ingredient.single_cylinder) SingleSphereIngr (class in cellpack.autopack.ingredient.single_sphere) sIngredient (class in cellpack.autopack.Serializable) sIngredientFiber (class in cellpack.autopack.Serializable) sIngredientGroup (class in cellpack.autopack.Serializable) slow_box_fill() (cellpack.autopack.BaseGrid.BaseGrid method) sort() (cellpack.autopack.Recipe.Recipe method) sort_values() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper static method) sortIngredient() (cellpack.autopack.Environment.Environment method) sparse_to_dense() (in module cellpack.autopack.binvox_rw) SPHERE (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute) Sphere() (cellpack.autopack.upy.hostHelper.Helper method) sphere() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) SphereHalton() (in module cellpack.autopack.ldSequence) Spheres() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) SPHERES_SST (cellpack.autopack.loaders.config_loader.Place_Methods attribute) spheres_SST_place() (cellpack.autopack.ingredient.Ingredient.Ingredient method) SPLINE (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute) spline() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) split_ingredient_data() (in module cellpack.autopack.loaders.migrate_v1_to_v2) SQUARE (cellpack.autopack.interface_objects.gradient_data.WeightModes attribute) static_id (cellpack.autopack.ingredient.Ingredient.Ingredient attribute) (cellpack.autopack.Serializable.sCompartment attribute) (cellpack.autopack.Serializable.sIngredient attribute) (cellpack.autopack.Serializable.sIngredientFiber attribute) (cellpack.autopack.Serializable.sIngredientGroup attribute) STD (cellpack.autopack.ingredient.Ingredient.DistributionOptions attribute) store() (cellpack.autopack.Environment.Environment method) store_asJson() (cellpack.autopack.Environment.Environment method) store_metadata() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper static method) store_packed_object() (cellpack.autopack.Compartment.Compartment method) (cellpack.autopack.ingredient.Ingredient.Ingredient method) store_result_file() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper static method) SUB (cellpack.autopack.interface_objects.gradient_data.PickModes attribute) SURFACE (cellpack.autopack.interface_objects.gradient_data.GradientModes attribute) swap() (cellpack.autopack.ingredient.Ingredient.Ingredient method)

T

test_points_in_bb() (cellpack.autopack.BaseGrid.BaseGrid method) testForEscape() (cellpack.autopack.upy.hostHelper.Helper method) Tetrahedron() (cellpack.autopack.upy.hostHelper.Helper method) tetrahedron() (cellpack.autopack.upy.hostHelper.Helper method) Text() (cellpack.autopack.upy.hostHelper.Helper method) TextureFaceCoordintesToVertexCoordinates() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) ThreeColorRamp() (in module cellpack.autopack.upy.colors) timeFunction() (cellpack.autopack.Environment.Environment method) (cellpack.autopack.Graphics.AutopackViewer method) to_JSON() (cellpack.autopack.Serializable.sCompartment method) (cellpack.autopack.Serializable.sIngredient method) (cellpack.autopack.Serializable.sIngredientFiber method) (cellpack.autopack.Serializable.sIngredientGroup method) toBinary() (in module cellpack.autopack.IOutils) toggle() (cellpack.autopack.upy.hostHelper.Helper method) toggleDisplay() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) toggleEditMode() (cellpack.autopack.upy.hostHelper.Helper method) toggleOrganelMatr() (cellpack.autopack.Graphics.AutopackViewer method) toggleOrganelMesh() (cellpack.autopack.Graphics.AutopackViewer method) toggleOrganelSurf() (cellpack.autopack.Graphics.AutopackViewer method) toggleXray() (cellpack.autopack.upy.hostHelper.Helper method)

ToMat() (cellpack.autopack.upy.hostHelper.Helper method) ToVec() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) traj_type (cellpack.autopack.trajectory.dcdTrajectory attribute) (cellpack.autopack.trajectory.molbTrajectory attribute) (cellpack.autopack.trajectory.Trajectory attribute) (cellpack.autopack.trajectory.xyzTrajectory attribute) Trajectory (class in cellpack.autopack.trajectory) transformMesh() (cellpack.autopack.Compartment.Compartment method) transformNode() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) transformPoints() (cellpack.autopack.ingredient.Ingredient.Ingredient method) transformPoints2D() (cellpack.autopack.plotly_result.PlotlyAnalysis method) transformPoints_mult() (cellpack.autopack.ingredient.Ingredient.Ingredient method) translateObj() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) transpose_image_for_projection() (cellpack.autopack.writers.ImageWriter.ImageWriter static method) transposeMatrix() (cellpack.autopack.upy.hostHelper.Helper method) triangulate() (cellpack.autopack.upy.hostHelper.Helper method) triangulateFace() (cellpack.autopack.upy.hostHelper.Helper method) triangulateFaceArray() (cellpack.autopack.upy.hostHelper.Helper method) TRIMESH (cellpack.autopack.loaders.config_loader.Inner_Grid_Methods attribute) TwoColorRamp() (in module cellpack.autopack.upy.colors)

U

undspMesh() (cellpack.autopack.Graphics.AutopackViewer method) undspSph() (cellpack.autopack.Graphics.AutopackViewer method) UNIFORM (cellpack.autopack.ingredient.Ingredient.DistributionTypes attribute) unit_vector() (cellpack.autopack.upy.hostHelper.Helper class method) unlinkTraj() (cellpack.autopack.Environment.Environment method) unpack_curve() (cellpack.bin.simularium_converter.ConvertToSimularium method) unpack_positions() (cellpack.bin.simularium_converter.ConvertToSimularium method) update() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) update_after_place() (cellpack.autopack.Environment.Environment method) update_data_tree() (cellpack.autopack.ingredient.Ingredient.Ingredient method) update_display_rt() (cellpack.autopack.ingredient.Ingredient.Ingredient method) update_distance_distribution_dictionaries() (cellpack.autopack.Analysis.Analysis method) update_doc() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) update_elements_in_array() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) update_ingredient_gradient() (cellpack.autopack.Gradient.Gradient static method) update_ingredient_size() (cellpack.autopack.ingredient.Ingredient.Ingredient method) update_instance_positions_and_rotations() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) update_largest_smallest_size() (cellpack.autopack.Environment.Environment method) update_or_create() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) update_pairwise_distances() (cellpack.autopack.Analysis.Analysis method) update_reference() (cellpack.autopack.DBRecipeHandler.CompositionDoc static method) update_reference_on_doc() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) update_spline() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) update_title() (cellpack.autopack.plotly_result.PlotlyAnalysis method) update_variable_ingredient_attributes() (cellpack.autopack.Environment.Environment method) updateAppli() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) updateArmature() (cellpack.autopack.upy.hostHelper.Helper method) updateBox() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) updateDistances() (cellpack.autopack.BaseGrid.BaseGrid static method) updateFromBB() (cellpack.autopack.ingredient.grow.ActinIngredient method)

updateGrid() (cellpack.autopack.ingredient.grow.GrowIngredient method) updateMasterInstance() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) updateMesh() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) updateParticles() (cellpack.autopack.upy.hostHelper.Helper method) updatePath() (in module cellpack.autopack) updatePathDeform() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) updatePathJSON() (in module cellpack.autopack) updatePoly() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) updatePositionsRadii() (in module cellpack.autopack.IOutils) (in module cellpack.autopack.writers) updateRecipAvailableXML() (in module cellpack.autopack) updateReplacePath() (in module cellpack.autopack) updateSpring() (cellpack.autopack.upy.hostHelper.Helper method) updateTubeMesh() (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) updateTubeObjs() (cellpack.autopack.upy.hostHelper.Helper method) upload() (in module cellpack.bin.upload) upload_collections() (cellpack.autopack.DBRecipeHandler.DBUploader method) upload_compositions() (cellpack.autopack.DBRecipeHandler.DBUploader method) upload_data() (cellpack.autopack.DBRecipeHandler.DBUploader method) upload_doc() (cellpack.autopack.FirebaseHandler.FirebaseHandler method) upload_file() (cellpack.autopack.AWSHandler.AWSHandler method) upload_gradients() (cellpack.autopack.DBRecipeHandler.DBUploader method) upload_objects() (cellpack.autopack.DBRecipeHandler.DBUploader method) upload_recipe() (cellpack.autopack.DBRecipeHandler.DBUploader method) upload_result_metadata() (cellpack.autopack.DBRecipeHandler.DBUploader method) upload_single_object() (cellpack.autopack.DBRecipeHandler.DBUploader method) UpperCircleFunction() (cellpack.autopack.GeometryTools.GeometryTools method) UpperRectangleFunction() (cellpack.autopack.GeometryTools.GeometryTools method) url_exists() (in module cellpack.autopack) use_mesh() (cellpack.autopack.ingredient.Ingredient.Ingredient method) use_pdb() (cellpack.autopack.ingredient.Ingredient.Ingredient method)

V

validate_distribution_options() (cellpack.autopack.ingredient.Ingredient.Ingredient static method) validate_existence() (cellpack.autopack.DBRecipeHandler.ResultDoc method) validate_gradient_data() (cellpack.autopack.interface_objects.gradient_data.GradientData method) validate_ingredient_info() (cellpack.autopack.ingredient.Ingredient.Ingredient static method) validate_input_recipe_path() (cellpack.autopack.DBRecipeHandler.DBRecipeLoader method) validate_invert_settings() (cellpack.autopack.interface_objects.gradient_data.GradientData method) validate_mode_settings() (cellpack.autopack.interface_objects.gradient_data.GradientData method) validate_weight_mode_settings() (cellpack.autopack.interface_objects.gradient_data.GradientData method) values() (cellpack.autopack.interface_objects.meta_enum.MetaEnum class method) vcross() (in module cellpack.autopack.ray) (in module cellpack.autopack.upy.hostHelper)

vdiff() (in module cellpack.autopack.ray) (in module cellpack.autopack.upy.hostHelper) vdistance() (in module cellpack.autopack.upy.hostHelper) VECTOR (cellpack.autopack.interface_objects.gradient_data.GradientModes attribute) vector_norm() (cellpack.autopack.upy.hostHelper.Helper method) VERBOSE (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute) viewer (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper attribute) vlen() (in module cellpack.autopack.ray) (in module cellpack.autopack.upy.hostHelper) vnorm() (in module cellpack.autopack.ray) (in module cellpack.autopack.upy.hostHelper) Voxels (class in cellpack.autopack.binvox_rw)

W

walkLattice() (cellpack.autopack.ingredient.grow.GrowIngredient method) walkLatticeSurface() (cellpack.autopack.ingredient.grow.GrowIngredient method) walkSphere() (cellpack.autopack.ingredient.grow.GrowIngredient method) weight (cellpack.autopack.interface_objects.gradient_data.InvertOptions attribute) WeightModeOptions (class in cellpack.autopack.interface_objects.gradient_data) WeightModes (class in cellpack.autopack.interface_objects.gradient_data) which_db() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) with_colon() (cellpack.autopack.interface_objects.database_ids.DATABASE_IDS class method) write() (cellpack.autopack.binvox_rw.Voxels method) (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method) (cellpack.autopack.writers.IOingredientTool method) (in module cellpack.autopack.binvox_rw)

write_creds_path() (cellpack.autopack.FirebaseHandler.FirebaseHandler static method) write_file() (cellpack.autopack.writers.MarkdownWriter.MarkdownWriter method) write_json_file() (in module cellpack.autopack.loaders.utils) write_username_to_creds() (in module cellpack.autopack) writeArraysToFile() (cellpack.autopack.Environment.Environment method) writeDX() (cellpack.autopack.upy.hostHelper.Helper class method) writeJSON() (cellpack.autopack.Analysis.Analysis method) writeMeshToFile() (cellpack.autopack.upy.hostHelper.Helper class method) Writer (class in cellpack.autopack.writers) writeToFile() (cellpack.autopack.upy.hostHelper.Helper method) (cellpack.autopack.upy.simularium.simularium_helper.simulariumHelper method)

X

X (cellpack.autopack.interface_objects.gradient_data.GradientModes attribute)

xyzToijk() (cellpack.autopack.binvox_rw.Voxels method) xyzTrajectory (class in cellpack.autopack.trajectory)

Y

Y (cellpack.autopack.interface_objects.gradient_data.GradientModes attribute)

Z

Z (cellpack.autopack.interface_objects.gradient_data.GradientModes attribute)