Merge pull request #219 from jonls/sbml-ignore-boundary-comp

sbml: Ignore boundary compartments
zhanglab · Mar 6, 2017 · 38722c5 · 38722c5
2 parents 36aa737 + b5c00cb
commit 38722c5
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Showing 2 changed files with 160 additions and 77 deletions.
diff --git a/psamm/datasource/sbml.py b/psamm/datasource/sbml.py
@@ -521,7 +521,7 @@ class SBMLReader(object):
 
     If ``ignore_boundary`` is ``True``, the species that are marked as
     boundary conditions will simply be dropped from the species list and from
-    the reaction equations.
+    the reaction equations, and any boundary compartment will be dropped too.
     """
 
     def __init__(self, file, strict=False, ignore_boundary=False,
@@ -632,6 +632,23 @@ def __init__(self, file, strict=False, ignore_boundary=False,
             entry = ReactionEntry(self, reaction, filemark=filemark)
             self._model_reactions[entry.id] = entry
 
+        if self._ignore_boundary:
+            # Remove compartments that only contain boundary compounds
+            empty_compartments = set(self._model_compartments)
+            valid_compartments = set()
+            for species in itervalues(self._model_species):
+                empty_compartments.discard(species.compartment)
+                if not species.boundary:
+                    valid_compartments.add(species.compartment)
+
+            boundary_compartments = (
+                set(self._model_compartments) - empty_compartments -
+                valid_compartments)
+            for compartment in boundary_compartments:
+                logger.info('Ignoring boundary compartment: {}'.format(
+                    compartment))
+                del self._model_compartments[compartment]
+
         # Objectives
         self._model_objectives = {}
         self._active_objective = None