KarrLab/wc_rules

######## "No templated rules" version #########

from ..templates.graphs import gLigand, gReceptorAlpha
from wc_rules.modeling.pattern import Pattern
from wc_rules.modeling.rule import Rule
from wc_rules.modeling.model import RuleBasedModel, AggregateModel

free_ligand = Pattern(
    parent = gLigand,
    constraints = ['len(fc1.bond)==0', 'len(fc2.bond)==0']
    )

singly_bound_ligand = Pattern(
    parent = gLigand,
    constraints = ['len(fc1.bond)==1', 'len(fc2.bond)==0']
    )

doubly_bound_ligand = Pattern(
    parent = gLigand,
    constraints = ['len(fc1.bond)==1', 'len(fc2.bond)==1']
    )

free_receptor = Pattern(
    parent = gReceptorAlpha,
    constraints = ['len(alpha.bond)==0']
    )

# Monomer model
monomer_binding_rule = Rule(
    name = 'monomer_binding_rule',
    reactants = {'ligand_reactant': free_ligand, 'free_receptor': free_receptor},
    actions = ['ligand_reactant.fc1.add_bond(free_receptor.alpha)'],
    rate_prefix = 'association_constant',
    params = ['association_constant']
    )

monomer_unbinding_rule = Rule(
    name = 'monomer_unbinding_rule',
    reactants = {'ligand_reactant': singly_bound_ligand},
    actions = ['ligand_reactant.fc1.remove_bond()'],
    rate_prefix = 'dissociation_constant',
    params = ['dissociation_constant']
    )

monomer_ligand_model = RuleBasedModel(
    name = 'monomer_ligand',
    rules = [monomer_binding_rule, monomer_unbinding_rule]
    )

# Dimer model
dimer_binding_rule = Rule(
    name = 'dimer_binding_rule',
    reactants = {'ligand_reactant': singly_bound_ligand, 'free_receptor': free_receptor},
    actions = ['ligand_reactant.fc2.add_bond(free_receptor.alpha)'],
    rate_prefix = 'association_constant',
    params = ['association_constant']
    )

dimer_unbinding_rule = Rule(
    name = 'dimer_unbinding_rule',
    reactants = {'ligand_reactant':doubly_bound_ligand},
    actions = ['ligand_reactant.fc1.remove_bond()'],
    rate_prefix = 'dissociation_constant',
    params = ['dissociation_constant']
    )

monomer_ligand_model = RuleBasedModel(
    name = 'monomer_ligand',
    rules = [monomer_binding_rule, monomer_unbinding_rule]
    )

dimer_ligand_model = RuleBasedModel(
    name = 'dimer_ligand',
    rules = [dimer_binding_rule, dimer_unbinding_rule]
    )

model = AggregateModel(
    name = 'ligand_receptor_binding',
    models = [monomer_ligand_model, dimer_ligand_model]
    )

data = {
    'monomer_ligand': {
        'association_constant' : 1.3e-7,
        'dissociation_constant': 0.0,
    },
    'dimer_ligand': {
        'association_constant' : 2.5e-1,
        'dissociation_constant': 0.0,
    }
}

model.verify(data)
model.defaults = data