VirtualMicrobes.cython_gsl_interface package

Submodules

VirtualMicrobes.cython_gsl_interface.integrate module

Created on Nov 4, 2013

@author: thocu

class VirtualMicrobes.cython_gsl_interface.integrate.Integrator

Bases: object

This will wrap the integrator from (cython)gsl, by initializing a stepper with the ‘master’-equation

run_system()
sys_c
class VirtualMicrobes.cython_gsl_interface.integrate.SpatialIntegrator

Bases: object

diffusion_step()
gp_to_integrators_c_dict
grid
print_spatial_sys_vars()

print out all variable values

run_spatial_system()
store_nr_time_points_py()
update_diffusion_stepping()
update_drivers()
update_integrators()

VirtualMicrobes.cython_gsl_interface.odes module

class VirtualMicrobes.cython_gsl_interface.odes.CELL

Bases: object

CELL is a parallel structure to the python class Cell that is tasked with generating the set of equations to be solved by integration procedure

enzymes_c
pumps_c
py_cell
small_mols_c
tfs_c
class VirtualMicrobes.cython_gsl_interface.odes.ENVIRONMENT

Bases: object

py_env
small_mols_c
class VirtualMicrobes.cython_gsl_interface.odes.ENZYME

Bases: object

py_enzyme
class VirtualMicrobes.cython_gsl_interface.odes.POPULATION

Bases: object

cells_c
class VirtualMicrobes.cython_gsl_interface.odes.PUMP

Bases: object

py_pump
class VirtualMicrobes.cython_gsl_interface.odes.REG_SEQ

Bases: object

class VirtualMicrobes.cython_gsl_interface.odes.SMALL_MOL

Bases: object

py_mol
class VirtualMicrobes.cython_gsl_interface.odes.SYSTEM

Bases: object

env_c
pop_c
py_loc
class VirtualMicrobes.cython_gsl_interface.odes.TF

Bases: object

py_tf

Module contents