14.8. API_1 References

Namespaces:

Currently STEPS has 6 major namespaces, divided by functionality. The steps.API_1.model namespace defines classes of chemical species in the model, as well as the reaction and diffusion objects. The steps.API_1.geom namespace contains classes that define the geometry of the model (i.e. tetrahedral meshes, compartments and patches). The steps.API_1.rng namespace contains the random number generators (currently only one generator is available). The steps.API_1.solver and steps.API_1.mpi.solver namespaces implement the simulation solvers. The steps.API_1.utilities namespace provides useful tools related to the model and geometry description, currently providing 3D tetrahedral mesh loading and saving support.

../_images/steps.jpg — STEPS main class diagram.

Methods and attributes

For most of the set and get methods, STEPS provides corresponding attributes which can be accessed and modified directly. For example (spec is a reference to an object of type steps.API_1.model.Spec):

>>> spec.setID('Ca')

is equivalent to:

>>> spec.id = 'Ca'

and,

>>> spec_id = spec.getID()

is equivalent to:

>>> spec_id = spec.id

Available methods and attributes of an object can be found by the built-in dir command in Python. A convention maintained in STEPS is that all attributes are completely lower-case:

>>> dir(spec)
['__class__', '__del__', '__delattr__', '__dict__', '__doc__', '__getattr__',
'__getattribute__', '__hash__', '__init__', '__module__', '__new__',
'__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__str__',
'__swig_destroy__', '__swig_getmethods__', '__swig_setmethods__',
'__weakref__', 'getID', 'getModel', 'id', 'model', 'setID', 'this']

All attributes beginning with double underscore are built-in attributes related to the implementation of the type and can be ignored. So, for our steps.API_1.model.Spec() object (one of the most basic objects in STEPS) we have functions getID, setID and getModel available with attributes id and model related to those functions.