docs: update docstring and test description to reflect implementation (…

…#620) * docs: update docstring and test description to reflect the implementation
opencobra · Mar 11, 2019 · fec22ee · fec22ee
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -3,6 +3,7 @@ History
 
 Next Release
 ------------
+* Update docstring of test_find_duplicate_reactions.
 
 0.9.6 (2019-03-06)
 ------------------

diff --git a/memote/suite/tests/test_basic.py b/memote/suite/tests/test_basic.py
@@ -640,15 +640,14 @@ def test_find_duplicate_reactions(model):
     Implementation:
 
     Compare reactions in a pairwise manner.
-    First, if there are duplicate metabolites in the set of
-    metabolites of each reaction, add them to the set belonging to each
-    reaction respectively. Then, if the sets for each reaction are
-    identical, check the reversibility of each reaction:
-    - If both reactions differ in reversibility they are assumed to be
-      different.
-    - If both are reversible they are assumed to be identical.
-    - If both are irreversible, the upper bound and product metabolites
-      have to be identical for the reactions to be assumed to be identical.
+    For each reaction, the metabolite annotations are checked for a description
+    of the structure (via InChI and InChIKey).If they exist, substrates and
+    products as well as the stoichiometries of any reaction pair are compared.
+    Only reactions where the substrates, products, stoichiometry and
+    reversibility are identical are considered to be duplicates.
+    This test will not be able to identify duplicate reactions if there are no
+    structure annotations. Further, it will report reactions with
+    differing bounds as equal if they otherwise match the above conditions.
 
     """
     ann = test_find_duplicate_reactions.annotation

diff --git a/memote/support/basic.py b/memote/support/basic.py
@@ -417,15 +417,14 @@ def find_duplicate_reactions(model):
 
     This can be useful to curate merged models or to clean-up bulk model
     modifications. The heuristic compares reactions in a pairwise manner.
-    First, if there are duplicate metabolites in the set of
-    metabolites of each reaction, they are added to the set of each reaction
-    respectively. Then, if the sets for each reaction are
-    identical the reversibility of each reaction is checked:
-    - If both reactions differ in reversibility they are assumed to be
-    different.
-    - If both are reversible they are assumed to be identical.
-    - If both are irreversible, the upper bound and product metabolites
-     have to be identical for the reactions to be assumed to be identical.
+    For each reaction, the metabolite annotations are checked for a description
+    of the structure (via InChI and InChIKey).If they exist, substrates and
+    products as well as the stoichiometries of any reaction pair are compared.
+    Only reactions where the substrates, products, stoichiometry and
+    reversibility are identical are considered to be duplicates.
+    This test will not be able to identify duplicate reactions if there are no
+    structure annotations. Further, it will report reactions with
+    differing bounds as equal if they otherwise match the above conditions.
 
     Parameters
     ----------