KarrLab/wc_lang

""" Create the implicit zero concentrations in a model

:Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
:Author: Jonathan Karr <jonrkarr@gmail.com>
:Date: 2018-11-28
:Copyright: 2017-2018, Karr Lab
:License: MIT
"""

from .core import Transform
from wc_lang.core import DistributionInitConcentration
from wc_utils.util.units import unit_registry


class CreateImplicitDistributionZeroInitConcentrationsTransform(Transform):
    """ Create the implicit zero concentrations in a model
    """

    class Meta(object):
        id = 'CreateImplicitDistributionZeroInitConcentrations'
        label = 'Create the implicit zero concentrations in a model'

    def run(self, model):
        """ Create the implicit zero concentrations in a model

        Args:
            model (:obj:`Model`): model

        Returns:
            :obj:`Model`: same model, but transformed
        """
        for species in model.get_species():
            if species.distribution_init_concentration is None:
                species.distribution_init_concentration = DistributionInitConcentration(
                    model=model,
                    species=species,
                    mean=0.0, std=0.0, units=unit_registry.parse_units('M'))
                species.distribution_init_concentration.id = species.distribution_init_concentration.gen_id()

        return model