KarrLab/wc_rules

from wc_rules.modeling.rule import Rule
from wc_rules.modeling.model import RuleBasedModel

class BindingModel(RuleBasedModel):
    
    defaults = {'association_constant':1.0, 'dissociation_constant': 1.0}

    def __init__(self,name,reactants,targets):
        # assume reactants are provided in order
        n1, n2, n3 = reactants.keys()
        
        binding_rule = Rule(
            name = f'binding_rule',
            reactants = {n1:reactants[n1],n2:reactants[n2]},
            actions = [f'{n1}.{targets[n1]}.add_bond({n2}.{targets[n2]})'],
            rate_prefix = 'association_constant',
            parameters = ['association_constant']
            )

        unbinding_rule = Rule(
            name = f'unbinding_rule',
            reactants = {n3:reactants[n3]},
            actions = [f'{n3}.{targets[n3]}.remove_bond()'],
            rate_prefix = 'dissociation_constant',
            parameters = ['dissociation_constant']
            )

        super().__init__(name,rules=[binding_rule,unbinding_rule])
        self.verify(self.defaults)

class TransPhosphorylationModel(RuleBasedModel):

    defaults = {'phosphorylation_rate':1.0}

    def __init__(self,name,reactant,target):

        phosphorylation_rule = Rule(
            name = f'phosphorylation_rule',
            reactants = {'reactant':reactant},
            actions = [f'reactant.{target}.setTrue_ph()'],
            rate_prefix = 'phosphorylation_rate',
            parameters = ['phosphorylation_rate']
            )

        super().__init__(name,rules= [phosphorylation_rule])
        self.verify(self.defaults)


class DephosphorylationModel(RuleBasedModel):
    
    defaults = {'dephosphorylation_rate':1.0}

    def __init__(self,name,reactant,target):

        dephosphorylation_rule = Rule(
            name = f'dephosphorylation_rule',
            reactants = {'reactant':reactant},
            actions = [f'reactant.{target}.setFalse_ph()'],
            rate_prefix = 'dephosphorylation_rate',
            parameters = ['dephosphorylation_rate']
        )
        super().__init__(name,rules =[dephosphorylation_rule])
        self.verify(self.defaults)