pycotools3.model.BuildAntimony

class pycotools3.model.BuildAntimony(copasi_file: str)

Build a copasi model using antimony

A context manager to create a copasi model copasi_file using the antimony language

Examples

working_directory = os.path.dirname(__file__)
copasi_filename = os.path.join(working_directory, 'NegativeFeedbackModel.cps')
with model.BuildAntimony(copasi_filename) as loader:
    negative_feedback = loader.load(
        '''
        model negative_feedback()
            // define compartments
            compartment cell = 1.0
            //define species
            var A in cell
            var B in cell
            //define some global parameter for use in reactions
            vAProd = 0.1
            kADeg = 0.2
            kBProd = 0.3
            kBDeg = 0.4
            //define initial conditions
            A = 0
            B = 0
            //define reactions
            AProd: => A; cell*vAProd
            ADeg: A =>; cell*kADeg*A*B
            BProd: => B; cell*kBProd*A
            BDeg: B => ; cell*kBDeg*B
        end
        '''
    )
print(negative_feedback)

__init__(copasi_file: str)

Parameters:copasi_file (str) – Path to a valid location on disk to store the copasi file

Methods

__init__(copasi_file)	param copasi_file:  Path to a valid location on disk to store the copasi file
load(antimony_str)	Load the antimony string antimony_str into a copasi_file and Model.

load(antimony_str)

Load the antimony string antimony_str into a copasi_file and Model.

Args

antimony_str (str): A valid antimony string encoding a model

return

model (Model)

A PyCoTools model containing the model defined in the :parameter:`antiomny_str`.

Parameters:antimony_str –

Returns: