get_kinlawid_by_rxn in query sabiork odl

KarrLab · Oct 21, 2019 · d4c22bf · d4c22bf
1 parent 11518bb
commit d4c22bf
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Showing 2 changed files with 34 additions and 7 deletions.
diff --git a/datanator_query_python/query/query_sabiork_old.py b/datanator_query_python/query/query_sabiork_old.py
@@ -59,11 +59,6 @@ def get_kinlaw_by_environment(self, taxon=None, taxon_wildtype=None, ph_range=No
 
         return docs, count
 
-    def get_kinlaw_by_rxn(self):
-        '''Place holder 
-        '''
-        pass
-
     def get_reaction_doc(self, kinlaw_id, projection={'_id': 0}):
         '''Find a document on reaction with the kinlaw_id
         Args:
@@ -78,4 +73,28 @@ def get_reaction_doc(self, kinlaw_id, projection={'_id': 0}):
         query = {'kinlaw_id': {'$in': kinlaw_id}}
         docs = self.collection.find(filter=query, projection=projection)
         count = self.collection.count_documents(query)
-        return docs, count
+        return docs, count
+
+    def get_kinlawid_by_rxn(self, substrates, products):
+        ''' Find the kinlaw_id defined in sabio_rk using 
+            rxn participants' inchi string
+
+            Args:
+                substrates: list of substrates' inchi
+                products: list of products' inchi
+
+            Return:
+                rxns: list of kinlaw_ids that satisfy the condition
+                [id0, id1, id2,...,  ]
+        '''
+        result = []
+        substrate = 'reaction_participant.substrate.substrate_structure.inchi_structure'
+        product = 'reaction_participant.product.product_structure.inchi_structure'
+        projection = {'kinlaw_id': 1, '_id': 0}
+        constraint_0 = {substrate: {'$in': substrates}}
+        constraint_1 = {product: {'$in': products}}
+        query = {'$and': [constraint_0, constraint_1]}
+        docs = self.collection.find(filter=query, projection=projection)
+        for doc in docs:
+            result.append(doc['kinlaw_id'])
+        return result
diff --git a/tests/query/test_query_sabiork_old.py b/tests/query/test_query_sabiork_old.py
@@ -55,4 +55,12 @@ def test_get_reaction_doc(self):
         _id = [31, 32]
         result, count = self.src.get_reaction_doc(_id)
         self.assertEqual(count, 2)
-        self.assertTrue('kinlaw_id' in result[0])
+        self.assertTrue('kinlaw_id' in result[0])
+
+    def test_get_kinlawid_by_rxn(self):
+        substrate_0 = 'InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1'
+        substrate_1 = 'InChI=1S/C6H8O7/c7-3(8)1-2(5(10)11)4(9)6(12)13/h2,4,9H,1H2,(H,7,8)(H,10,11)(H,12,13)'
+        product_0 = 'InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)'
+        product_1 = 'InChI=1S/CO2/c2-1-3'
+        result = self.src.get_kinlawid_by_rxn([substrate_0, substrate_1], [product_0, product_1])
+        self.assertTrue(7923 in result)