API Reference

The API Reference aims to convey an exhaustive and detailed description of the package functions, classes, methods etc.

Useful info

Here are some things you might find interesting.

• Arrays and numbers

Core features

Core features are those essential for reaction-diffusion system building and simulation.

Directly imported

This is the part of the interface that is (mostly) directly accessible using “import strengths”:

• Reaction-diffusion networks
  • Species
    • Species.D
    • Species.chstt
    • Species.copy()
    • Species.density
    • Species.label
    • Species.units_system
  • Reaction
    • Reaction.K
    • Reaction.copy()
    • Reaction.dsto()
    • Reaction.environments
    • Reaction.equilibrium_constant()
    • Reaction.get_product_stoechiometry()
    • Reaction.get_substrate_stoechiometry()
    • Reaction.kf
    • Reaction.kf_units_dimensions()
    • Reaction.kr
    • Reaction.kr_units_dimensions()
    • Reaction.label
    • Reaction.order()
    • Reaction.products
    • Reaction.psto()
    • Reaction.rorder()
    • Reaction.set_k()
    • Reaction.split()
    • Reaction.ssto()
    • Reaction.substrates
    • Reaction.to_string()
    • Reaction.units_system
  • RDNetwork
    • RDNetwork.copy()
    • RDNetwork.environments
    • RDNetwork.get_environment_index()
    • RDNetwork.get_reaction()
    • RDNetwork.get_reaction_index()
    • RDNetwork.get_species()
    • RDNetwork.get_species_index()
    • RDNetwork.nenvironments()
    • RDNetwork.nreactions()
    • RDNetwork.nspecies()
    • RDNetwork.reactions
    • RDNetwork.species
    • RDNetwork.species_labels()
    • RDNetwork.units_system
  • load_rdnetwork()
  • save_rdnetwork()
  • rdnetwork_to_dict()
  • rdnetwork_from_dict()
• Reaction-diffusion spaces
  • RDGridSpace
    • RDGridSpace.are_neighbors()
    • RDGridSpace.cell_env
    • RDGridSpace.cell_vol
    • RDGridSpace.copy()
    • RDGridSpace.d
    • RDGridSpace.get_boundary_conditions()
    • RDGridSpace.get_cell_coordinates()
    • RDGridSpace.get_cell_env_array()
    • RDGridSpace.get_cell_index()
    • RDGridSpace.get_cell_vol_array()
    • RDGridSpace.h
    • RDGridSpace.is_within_bounds()
    • RDGridSpace.set_boundary_conditions()
    • RDGridSpace.size()
    • RDGridSpace.units_system
    • RDGridSpace.w
  • RDGraphSpace
    • RDGraphSpace.check()
    • RDGraphSpace.copy()
    • RDGraphSpace.edges
    • RDGraphSpace.get_cell_env_array()
    • RDGraphSpace.get_cell_index()
    • RDGraphSpace.get_cell_vol_array()
    • RDGraphSpace.get_edge()
    • RDGraphSpace.nodes
    • RDGraphSpace.size()
    • RDGraphSpace.units_system
  • load_rdspace()
  • save_rdspace()
  • rdspace_to_dict()
  • rdspace_from_dict()
• Reaction-diffusion systems
  • RDSystem
    • RDSystem.apply_reaction()
    • RDSystem.chemostats
    • RDSystem.copy()
    • RDSystem.get_cell_index()
    • RDSystem.get_chemostat()
    • RDSystem.get_error()
    • RDSystem.get_state()
    • RDSystem.get_state_index()
    • RDSystem.is_valid()
    • RDSystem.make_dxdtf()
    • RDSystem.network
    • RDSystem.reset_chemostats()
    • RDSystem.reset_state()
    • RDSystem.set_chemostat()
    • RDSystem.set_default_chemostats()
    • RDSystem.set_default_state()
    • RDSystem.set_state()
    • RDSystem.space
    • RDSystem.state
    • RDSystem.state_size()
    • RDSystem.units_system
  • generate_species_state()
  • generate_system_state()
  • generate_species_chemostats()
  • generate_system_chemostats()
  • load_rdsystem()
  • save_rdsystem()
  • rdsystem_to_dict()
  • rdsystem_from_dict()
• Reaction-diffusion simulation script
  • RDScript
    • RDScript.copy()
    • RDScript.rng_seed
    • RDScript.sampling_interval
    • RDScript.sampling_policy
    • RDScript.system
    • RDScript.t_max
    • RDScript.t_sample
    • RDScript.time_step
    • RDScript.units_system
  • rdscript_from_dict()
  • rdscript_to_dict()
  • load_rdscript()
  • save_rdscript()
• Reaction-diffusion system trajectory
  • RDTrajectory
    • RDTrajectory.cgmap
    • RDTrajectory.data
    • RDTrajectory.engine_description
    • RDTrajectory.engine_option
    • RDTrajectory.get_sample_index()
    • RDTrajectory.get_state()
    • RDTrajectory.get_trajectory()
    • RDTrajectory.get_trajectory_point()
    • RDTrajectory.ncells()
    • RDTrajectory.nsamples()
    • RDTrajectory.nspecies()
    • RDTrajectory.script
    • RDTrajectory.system
    • RDTrajectory.t
  • save_rdtrajectory()
  • load_rdtrajectory()
  • References
• Reaction-diffusion simulations
  • simulate()
  • simulate_script()
• Units
  • UnitsSystem
  • UnitsDimensions
  • Units
    • Units.copy()
    • Units.dim
    • Units.invert()
    • Units.multiply()
    • Units.raiseto()
    • Units.sys
  • UnitValue
    • UnitValue.__abs__()
    • UnitValue.__add__()
    • UnitValue.__eq__()
    • UnitValue.__ge__()
    • UnitValue.__gt__()
    • UnitValue.__le__()
    • UnitValue.__lt__()
    • UnitValue.__mod__()
    • UnitValue.__mul__()
    • UnitValue.__neg__()
    • UnitValue.__neq__()
    • UnitValue.__pos__()
    • UnitValue.__pow__()
    • UnitValue.__radd__()
    • UnitValue.__rmod__()
    • UnitValue.__rmul__()
    • UnitValue.__rpow__()
    • UnitValue.__rsub__()
    • UnitValue.__rtruediv__()
    • UnitValue.__sub__()
    • UnitValue.__truediv__()
    • UnitValue.convert()
    • UnitValue.copy()
    • UnitValue.invert()
    • UnitValue.units
    • UnitValue.value
  • UnitArray
    • UnitArray.convert()
    • UnitArray.copy()
    • UnitArray.get_at()
    • UnitArray.invert()
    • UnitArray.set_at()
    • UnitArray.set_value()
    • UnitArray.units
    • UnitArray.value
  • density_units_dimensions()
  • volume_units_dimensions()
  • quantity_units_dimensions()
  • space_units_dimensions()
  • time_units_dimensions()
  • parse_units()
  • parse_unitvalue()
  • convert_value()
  • unitssystem_from_dict()
  • unitsdimensions_from_dict()
  • convert_unitvalue()
  • unitarray_from_dict()
  • unitarray_to_dict()
  • References
• Engine Collection
  • euler_engine()
  • gillespie_engine()
  • tauleap_engine()
• References

Not directly imported

This is the interface that is not directly accessible from “import strengths”. You will need to import those specific modules to access their features:

• Simulation engines
  • RDEngineBase
    • RDEngineBase.description
    • RDEngineBase.finalize()
    • RDEngineBase.get_output()
    • RDEngineBase.get_progress()
    • RDEngineBase.is_complete()
    • RDEngineBase.iterate()
    • RDEngineBase.iterate_n()
    • RDEngineBase.option
    • RDEngineBase.run()
    • RDEngineBase.sample()
    • RDEngineBase.setup()
• Constants
  • avogadro_number()
• Kinetics
  • compute_reaction_rates()
  • compute_diffusion_rates()
  • compute_dspeciesdt()
  • compute_dstatedt()

Side features

Side features cover other aspects such as plots, and their corresponding submodules must be imported to access them:

• Plot
  • plot_trajectory()
  • plot_sample_state_2D()
  • plot_state_2D()
  • plot_environments_2D()
  • plot_chemostats_2D()