Appendix A¶
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. Obsolete
clusterSurfacePlugin - 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
another
create_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 lattice
distance - convenience function calculating distance between two 3D
points
distance_between_cells - convenience function calculating distance between
COMs of two cells.
distance_vector - convenience function calculating distance vector beween
two 3D points
distance_vector_between_cells - convenience function calculating distance
vector beween COMs of two cells
elasticityTrackerPlugin - 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 links
get_cell_boundary_pixel_list - function returning list of boundary pixels
get_cell_neighbor_data_list - function returning Python-iterable list of
tuples (neighbor, common surface area) that allows iteration over cell
neighbors
get_cell_pixel_list - function returning Python-iterable list of pixels
belonging to a given cell
get_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 ElasticityPlugin
get_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 pixel
get_plasticity_data_list - function returning Python-iterable list of C++
tPlasticityData objects. Used in conjunction with PlasticityPlugin.
Deprecated
get_sbml_simulator - gets RoadRunner object for a given cell
get_sbml_state - gets Python-dictionary describing state of the SBML
model.
get_sbml_value - gets numerical value of the SBML model parameter
init - internal use only
invariant_distance - calculates invariant distance between two 3D points
invariant_distance_between_cells - calculates invariant distance between
COMs of two cells.
invariant_distance_vector - calculates invariant distance vector between
two 3D points
invariant_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 numbers
inventory - inventory of cells. C++ object
lengthConstraintPlugin - 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 vector
neighborTrackerPlugin - a reference to C++ NeighborTrackerPlugin object.
None if module not used.
new_cell - creates new cell of the user specified type
normalize_path - ensures that file path obeys rules of current operating
system
numpy_to_point_3d - converts numpy vector to Point3D object
pixelTrackerPlugin - 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 vector
polarization23Plugin - 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 object
reassign_cluster_id - reassignes cluster id. Notice: you cannot type
cell.clusterId=20. This will corrupt cell inventory. Use
reassignClusterId instead
remove_attribute - internal use
resize_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 variables
set_sbml_value - sets single SBML variable with a given name
set_step_size_for_cell - sets integration step for a given SBML Solver
object in a specified cell
set_step_size_for_cell_ids - sets integration step for a given SBML Solver
object in cells of specified ids
set_step_size_for_cell_types - sets integration step for a given SBML Solver
object in cells of specified types
set_step_size_for_free_floating_sbml - sets integration step for a given free
floating SBML Solver object
simulator - a reference to C++ Simulator object
start - core function of the steppable. Users provide implementation of
this function
step - core function of the steppable. Users provide implementation of
this function
stop_simulation - function used to stop simulation immediately
timestep_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 objects
timestep_sbml - function carrying out integration of all SBML models in
all SBML Solver objects
typeIdTypeNameDict - internal use only - translates type id to type name
vector_norm - function calculating norm of a vector
volumeTrackerPlugin - 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 mitosis
parent_cell - a reference to a cell object that underwent mitisos. After
mitosis this cell object will have smalle volume
set_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 axis
divide_cell_along_minor_axis - divides parent cell using cleavage plane
along minor axis
update_attributes - function called immediately after each mitosis
event.Users provide implementation of this function.