FIX: metabolite thermo data was not recovered upon serialization

pytfa/io/dict.py

@@ -18,6 +18,8 @@
 from ..optim.constraints import ReactionConstraint, MetaboliteConstraint, ModelConstraint
 from ..optim.utils import symbol_sum
 
+from ..thermo.metabolite import MetaboliteThermo
+
 from optlang.util import expr_to_json, parse_expr
 
 from copy import copy
@@ -215,7 +217,7 @@ def model_to_dict(model):
 
         if is_thermo and not is_peptide: # peptides have no thermo
             the_met = model.metabolites.get_by_id(the_met_id)
-            _add_thermo_metabolite_info(the_met, rxn_dict)
+            _add_thermo_metabolite_info(the_met, met_dict)
             met_dict['kind'] = 'Metabolite'
 
     # Relaxation info
@@ -425,6 +427,9 @@ def init_thermo_model_from_dict(new, obj):
 
         if 'thermo' in met_dict:
             new._prepare_metabolite(met)
+            met.thermo = MetaboliteThermo(metData=None, pH=7,ionicStr=0)
+            for k,v in met_dict['thermo'].items():
+                setattr(met.thermo,k,v)
     return new
 
 def rebuild_compositions(new, compositions_dict):

pytfa/io/json.py

@@ -54,3 +54,27 @@ def load_json_model(filepath):
 
     model = model_from_dict(obj)
     return model
+
+
+def json_dumps_model(model):
+    """
+    Returns a JSON dump as a string
+
+    :param model:
+    :return:
+    """
+
+    obj = model_to_dict(model)
+
+    return json.dumps(obj,cls=MyEncoder)
+
+
+def json_loads_model(s):
+    """
+    Loads a model from a string JSON dump
+
+    :param s: JSON string
+    :return:
+    """
+    obj = json.loads(s)
+    return model_from_dict(obj)