support unit definitions

xbanalysis/model/__init__.py

 """Subpackage with XBA model classes """
 
 from .xba_model import XbaModel
+from .xba_unit_def import XbaUnitDef, XbaUnit
 from .xba_compartment import XbaCompartment
 from .xba_function import XbaFunction
 from .xba_parameter import XbaParameter
@@ -8,5 +9,5 @@ from .xba_reaction import XbaReaction
 from .xba_species import XbaSpecies
 from .sbo_term import SboTerm
 
-__all__ = ['XbaModel', 'XbaCompartment', 'XbaFunction', 'XbaParameter',
-           'XbaReaction', 'XbaSpecies', 'SboTerm']
+__all__ = ['XbaModel', 'XbaUnitDef', 'XbaUnit', 'XbaCompartment',
+           'XbaFunction', 'XbaParameter', 'XbaReaction', 'XbaSpecies', 'SboTerm']

xbanalysis/model/xba_model.py

@@ -9,6 +9,7 @@ import numpy as np
 import sbmlxdf
 from scipy.sparse import coo_array
 
+from .xba_unit_def import XbaUnitDef
 from .xba_compartment import XbaCompartment
 from .xba_function import XbaFunction
 from .xba_parameter import XbaParameter
@@ -32,6 +33,8 @@ class XbaModel:
             print(f'{sbml_file} seems not to be a valid SBML model')
             return
         model_dict = sbml_model.to_df()
+        self.unit_defs = {udid: XbaUnitDef(row)
+                          for udid, row in model_dict['unitDefs'].iterrows()}
         self.compartments = {cid: XbaCompartment(row)
                              for cid, row in model_dict['compartments'].iterrows()}
         self.parameters = {pid: XbaParameter(row)

xbanalysis/model/xba_unit_def.py

+"""Implementation of XbaUnitDef class.
+
+Peter Schubert, HHU Duesseldorf, May 2022
+"""
+
+import numpy as np
+import sbmlxdf
+
+
+class XbaUnitDef:
+
+    def __init__(self, s_unit_def):
+        self.id = s_unit_def.name
+        self.name = s_unit_def.get('name', self.id)
+        self.units = [XbaUnit(sbmlxdf.extract_params(u))
+                      for u in sbmlxdf.record_generator(s_unit_def['units'])]
+
+    def is_equivalent(self, qry_units):
+        if len(qry_units) != len(self.units):
+            return False
+        else:
+            equivalent_u = np.zeros(len(qry_units))
+            for i, qry_unit in enumerate(qry_units):
+                for unit in self.units:
+                    if unit == qry_unit:
+                        equivalent_u[i] = 1
+                        break
+            return np.all(equivalent_u)
+
+
+class XbaUnit:
+
+    def __init__(self, params):
+        self.kind = params.get('kind')
+        self.exp = float(params.get('exp', '1.0'))
+        self.scale = int(params.get('scale', '0'))
+        self.mult = float(params.get('mult', '1.0'))
+
+    def __eq__(self, other):
+        if (self.kind == other.kind and
+                self.exp == other.exp and
+                self.scale == other.scale and
+                self.mult == other.mult):
+            return True
+        else:
+            return False
+
+    def __str__(self):
+        factor = self.mult * 10**self.scale
+        factor_str = f'{factor} ' if factor != 1.0 else ''
+        if self.exp != 1.0:
+            unit_str = f'({factor_str}{self.kind})^{self.exp}'
+        else:
+            unit_str = f'{factor_str}{self.kind}'
+        return unit_str