In this appendix we present alphabetical list of member functions and objects of the SteppableBasePy class from which all steppables should inherit:
add_free_floating_sbml - adds free floating SBML solver object to the simulation
add_new_plot_window - adds new plot windows to the Player display
add_sbml_to_cell - attaches SBML solver object to individual cell
add_sbml_to_cell_ids - attaches SBML solver object to individual cells with specified ids
add_sbml_to_cell_types - attaches SBML solver object to cells with specified types
adhesionFlexPlugin - a reference to C++ AdhesionFlexPlugin object. None if plugin not used.
are_cells_different - function determining if two cell objects are indeed different objects
boundaryMonitorPlugin - a reference to C++ BoundaryMonitorPlugin object. None if plugin not used
boundaryPixelTrackerPlugin - a reference to C++ BoundaryPixelTrackerPlugin object. None if plugin not used
build_wall - builds wall of cells (They have to be of cell type which has Freeze attribute set in the Cell Type Plugin) around the lattice
cell_field - reference to cell field.
cell_list - cell list. Allows iteration over all cells in the simulation
cell_list_by_type - function that creates on the fly a list of cells of given cell types.
cellOrientationPlugin - a reference to C++ CellOrientationPlugin object. None if plugin not used
cellTypeMonitorPlugin - a reference to C++ CellTypeMonitorPlugin object. None if plugin not used
centerOfMassPlugin - a reference to C++ CenterOfMassPlugin object. None if plugin not used
change_number_of_work_nodes - function that allows changing number of worknodes use dby the simulation
check_if_in_the_lattice - convenience function that determines if 3D point is within lattice boundaries
chemotaxisPlugin - a reference to C++ ChemotaxisPlugin object. None if plugin not used
cleanDeadCells - function that calls step function from VolumetrackerPlugin to remove dead cell. Advanced use only. Deprecated in CC3D 4.x
cleaverMeshDumper - a reference to C++ CleaverMeshDumper object. None if module not used. Experimental. Deprecated in CC3D 4.0.0
clone_attributes - copies all attributes from source cell to target cell. Typically used in mitosis. Allows specification of attributes that should not be copied.
clone_parent_2_child - used in mitosis plugin. Copies all parent cell attributes to the child cell.
clone_cluster_attributes - typically used in mitosis with compartmentalized cells. Copies attributes from cell in a source cluster to corresponging cell in the target cluster. Allows specification of attributes that should not be copied
clone_parent_cluster_2_child_cluster - used in mitosis with compartmentalized cells. Copies all attributes from cell in a parent cluster to corresponging cell in the child cluster
cluster_list - Python-iterable list of clusters. ObsoleteclusterSurfacePlugin- a reference to C++ ClusterSurfacePlugin object. None if module not used.clusterSurfaceTrackerPlugin- a reference to C++ ClusterSurfaceTrackerPlugin object. None if module not used.clusters- Python-iterable list of clusters.connectivityGlobalPlugin- a reference to C++ ConnectivityGlobalPlugin object. None if module not used.connectivityLocalFlexPlugin- a reference to C++ ConnectivityLocalFlexPlugin object. None if module not used.contactLocalFlexPlugin- a reference to C++ ContactLocalFlexPlugin object. None if module not used.contactLocalProductPlugin- a reference to C++ ContactLocalProductPlugin object. None if module not used.contactMultiCadPlugin- a reference to C++ ContactMultiCadPlugin object. None if module not used.contactOrientationPlugin- a reference to C++ ContactOrientationPlugin object. None if module not used.copy_sbml_simulators- function that copies SBML Solver objects from one cell to anothercreate_scalar_field_cell_level_py- function creating cell-level scalar field for Player visualization.create_scalar_field_py- function creating pixel-based scalar field for Player visualization.create_vector_field_cell_level_py- function creating cell-level vector field for Player visualization.create_vector_field_py-- function creating pixel-based vector field for Player visualization.delete_cell- function deleting cell.delete_free_floating_sbml- function deleting free floarting SBML Solver object with a given name.delete_sbml_from_cell- function deleting SBML Solver object with a given name from individual cell.delete_sbml_from_cell_ids- function deleting SBML Solver object with a given name from individual cells with specified ids.delete_sbml_from_cell_types- function deleting SBML Solver object with a given name from individual cells of specified types.destroy_wall- function destroying wall of frozen cells around the lattice (if the wall exists)dim- dimension of the latticedistance- convenience function calculating distance between two 3D pointsdistance_between_cells- convenience function calculating distance between COMs of two cells.distance_vector- convenience function calculating distance vector beween two 3D pointsdistance_vector_between_cells- convenience function calculating distance vector beween COMs of two cellselasticityTrackerPlugin- a reference to C++ ElasticityTrackerPlugin object. None if module not used.every_pixel- Python-iterable object returning tuples (x,y,z) for every pixel in the simulation. Allows iteration with user-defined steps between pixels.every_pixel_with_steps- internal function used by everyPixel.fetch_cell_by_id- fetches cell from cell inventory with specified id. Returns None if cell cannot be found.finish- core function of each CC3D steppable. Called at the end of the simulation. User provide implementation of this function.focalPointPlasticityPlugin- a reference to C++ FocalPointPlasticityPlugin object. None if module not used.frequency- steppable call frequency.get_anchor_focal_point_plasticity_data_list- returns a list anchored linksget_cell_boundary_pixel_list- function returning list of boundary pixelsget_cell_neighbor_data_list- function returning Python-iterable list of tuples (neighbor, common surface area) that allows iteration over cell neighborsget_cell_pixel_list- function returning Python-iterable list of pixels belonging to a given cellget_cluster_cells- function returning Python iterable list of cells in a cluster with a given cluster id.get_copy_of_cell_boundary_pixels- function creating and returning new Python-iterable list of cell pixels of all pixels belonging to a boundary of a given cell.get_copy_of_cell_pixels- function creating and returning new Python-iterable list of cell pixels of all pixels belonging to a given cell.get_elasticity_data_list- function returning Python-iterable list of C++ ElasticityData objects. Used in conjunction with ElasticityPluginget_field_secretor- function returning Secretor object that allows implementation of secretion in a cell-by-cell fashion.get_focal_point_plasticity_data_list- function returning Python-iterable list of C++ FocalPointPlasticityData objects. Used in conjunction with FocalPointPlasticityPlugin.get_internal_focal_point_plasticity_data_list- function returning Python-iterable list of C++ InternalFocalPointPlasticityData objects. Used in conjunction with FocalPointPlasticityPlugin.get_pixel_neighbors_based_on_neighbor_order- function returning Python-iterable list of pixels which are withing given neighbor order of the specified pixelget_plasticity_data_list- function returning Python-iterable list of C++ tPlasticityData objects. Used in conjunction with PlasticityPlugin. Deprecatedget_sbml_simulator- gets RoadRunner object for a given cellget_sbml_state- gets Python-dictionary describing state of the SBML model.get_sbml_value- gets numerical value of the SBML model parameterinit- internal use onlyinvariant_distance- calculates invariant distance between two 3D pointsinvariant_distance_between_cells- calculates invariant distance between COMs of two cells.invariant_distance_vector- calculates invariant distance vector between two 3D pointsinvariant_distance_vector_between_cells- calculates invariant distance vector between COMs of two cells.invariant_distance_vector_integer- calculates invariant distance vector between two 3D points. Keeps vector components as integer numbersinventory- inventory of cells. C++ objectlengthConstraintPlugin- a reference to C++ LengthConstraintPlugin object. None if module not used.momentOfInertiaPlugin- a reference to C++ MomentOfInertiaPlugin object. None if module not used.move_cell- moves cell by a specified shift vectorneighborTrackerPlugin- a reference to C++ NeighborTrackerPlugin object. None if module not used.new_cell- creates new cell of the user specified typenormalize_path- ensures that file path obeys rules of current operating systemnumpy_to_point_3d- converts numpy vector to Point3D objectpixelTrackerPlugin- a reference to C++ PixelTrackerPlugin object. None if module not used.plasticityTrackerPlugin- a reference to C++ PlasticityTrackerPlugin object. None if module not used.point_3d_to_numpy- converts Point3D to numpy vectorpolarization23Plugin- a reference to C++ Polarization23Plugin object. None if module not used.polarizationVectorPlugin- a reference to C++ PolarizationVectorPlugin object. None if module not used.potts- reference to C++ Potts objectreassign_cluster_id- reassignes cluster id. **Notice:** you cannot type cell.clusterId=20. This will corrupt cell inventory. Use reassignClusterId insteadremove_attribute- internal useresize_and_shift_lattice- resizes lattice and shifts its content by a specified vector. Throws an exception if operation cannot be safely performed.runBeforeMCS- flag determining if steppable gets called before (runBeforeMCS=1) Monte Carlo Step of after (runBeforeMCS=1). Default value is 0.secretionPlugin- a reference to C++ SecretionPlugin object. None if module not used.set_max_mcs- sets maximum MCS. Used to increase or decrease number of MCS that simulation shuold complete.set_sbml_state- used to pass dictionary of values of SBML variablesset_sbml_value- sets single SBML variable with a given nameset_step_size_for_cell- sets integration step for a given SBML Solver object in a specified cellset_step_size_for_cell_ids- sets integration step for a given SBML Solver object in cells of specified idsset_step_size_for_cell_types- sets integration step for a given SBML Solver object in cells of specified typesset_step_size_for_free_floating_sbml- sets integration step for a given free floating SBML Solver objectsimulator- a reference to C++ Simulator objectstart- core function of the steppable. Users provide implementation of this functionstep- core function of the steppable. Users provide implementation of this functionstop_simulation- function used to stop simulation immediatelytimestep_cell_sbml- function carrying out integration of all SBML models in the SBML Solver objects belonging to cells.timestep_free_floating_sbml- function carrying out integration of all SBML models in the free floating SBML Solver objectstimestep_sbml- function carrying out integration of all SBML models in all SBML Solver objectstypeIdTypeNameDict- internal use only - translates type id to type namevector_norm- function calculating norm of a vectorvolumeTrackerPlugin- a reference to C++ VolumeTrackerPlugin object. None if module not used. Additionally MitosisPlugin base has these functions:child_Cell- a reference to a cell object that has jus been created as a result of mitosisparent_cell- a reference to a cell object that underwent mitisos. After mitosis this cell object will have smalle volumeset_parent_child_position_flag- function which sets flag determining relative positions of child and parent cells after mitosis. Value 0 means that parent child position will be randomized between mitosis event. Negative integer value means parent appears on the 'left' of the child and positive integer values mean that parent appears on the 'right' of the child.get_parent_child_position_flag- returns current value of parentChildPositionFlag.divide_cell_random_orientation- divides parent cell using randomly chosen cleavage plane.divide_cell_orientation_vector_based- divides parent cell using cleavage plane perpendicular to a given vector.divide_cell_along_major_axis- divides parent cell using cleavage plane along major axisdivide_cell_along_minor_axis- divides parent cell using cleavage plane along minor axisupdate_attributes`` - function called immediately after each mitosis event.Users provide implementation of this function.