:py:mod:`neurorosettes.clocks`
==============================

.. py:module:: neurorosettes.clocks

.. autoapi-nested-parse::

   This module deals with the proliferation, differentiation and death cycles



Module Contents
---------------

Classes
~~~~~~~

.. autoapisummary::

   neurorosettes.clocks.Clock
   neurorosettes.clocks.CellClocks
   neurorosettes.clocks.ClocksFactory




.. py:class:: Clock(rate = None)

   Class to represent a cell's internal clock.

   Cells start in an inactive status and can be flagged for an event based
   on a rate. Alternatively, this status can be manually induced.
   Active states can also be blocked. When a rate is not defined, cells remain
   in an inactive state.

   :param rate: The rate of the clock's event

   .. py:method:: set_rate(rate)

      Sets the clock's event rate.

      :param rate: The clock's event rate


   .. py:method:: advance_clock(timestep)

      Updates the cell cycle status based on the proliferation rate (may happen or not).

      :param timestep: The simulation time step (time passed between status updates).


   .. py:method:: flag()

      Updates the cell cycle to proliferation (will always happen)


   .. py:method:: remove_flag()

      Updates the cell cycle to arrest (will always happen)


   .. py:method:: trigger_block()

      Activates the cycle block to avoid proliferation



.. py:class:: CellClocks(proliferation_rate, death_rate, differentiation_rate)

   Class to represent all of the internal biological clocks of a cell.

   :param proliferation_rate: A cell's proliferation rate.
   :param death_rate: A cell's death rate.
   :param differentiation_rate: A cell's differentiation rate.

   .. py:method:: set_proliferation_clock(proliferation_rate)

      Sets the proliferation rate.

      :param proliferation_rate: A cell's proliferation rate


   .. py:method:: set_death_clock(death_rate)

      Sets the death rate.

      :param death_rate: A cell's proliferation rate


   .. py:method:: set_differentiation_clock(differentiation_rate)

      Sets the differentiation rate.

      :param differentiation_rate: A cell's differentiation rate


   .. py:method:: set_clocks(proliferation_rate, death_rate, differentiation_rate)

      Sets the rates for all biological events (proliferation, death and differentiation).

      :param proliferation_rate: A cell's proliferation rate
      :param death_rate: A cell's proliferation rate
      :param differentiation_rate: A cell's differentiation rate


   .. py:method:: get_clock_rates()

      Returns all the clock rates for biological events.


   .. py:method:: advance_clocks(timestep)

      Advance all biological clocks and flag cells for biological events.

      :param timestep: The simulation time step (time passed between status updates)


   .. py:method:: block_all_clocks()

      Blocks the cycling, death and differentiation clocks.



.. py:class:: ClocksFactory

   Helper class to create instances of cell internal clocks based on the same rates.

   .. py:attribute:: proliferation_rate
      :annotation: :float

      The rate of proliferation of the cells.

   .. py:attribute:: death_rate
      :annotation: :float

      The rate of death of the cells.

   .. py:attribute:: differentiation_rate
      :annotation: :float

      The rate of differntiation of the cells.

   .. py:method:: get_clocks()

      Returns an instance of a CellClocks object with the chosen biology rates.