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