Improve grammar syntax

Testing/objects_testing.py

@@ -178,7 +178,7 @@
 
 cx1 = Complex([a20], "cyt")
 cx2 = Complex([s46], "cyt")
-cx3 = Complex([s47], "cyt") # K(S{u},T{i})::cyt
+cx3 = Complex([s47], "cyt")  # K(S{u},T{i})::cyt
 cx4 = Complex([s46, a20], "cyt")
 cx5 = Complex([s47, a20], "cyt")
 
@@ -261,7 +261,7 @@
 pairs_5 = [(0, 2), (1, 3), (None, 4)]
 rate_5 = Rate("3.0*[K()::cyt]/2.0*v_1")
 
-r5 = Rule(sequence_5, mid_5, compartments_5, complexes_5, pairs_2, rate_5)
+r5 = Rule(sequence_5, mid_5, compartments_5, complexes_5, pairs_5, rate_5)
 
 sequence_6 = (s39, s35, s38, s40, s37)
 mid_6 = 3

Testing/parsing/test_complex.py

@@ -2,57 +2,59 @@
 
 
 def test_parser():
-    ret = objects.complex_parser.parse("B(T{s})::cell")
+    ret = objects.rate_complex_parser.parse("B(T{s})::cell")
     assert ret.success
     assert ret.data.children[0] == objects.c1
 
-    ret = objects.complex_parser.parse("B(T{s}).D().K(T{s},S{s},S{_})::cell")
+    ret = objects.rate_complex_parser.parse("B(T{s}).D().K(T{s},S{s},S{_})::cell")
     assert ret.success
     assert ret.data.children[0] == objects.c2
 
-    ret = objects.complex_parser.parse("B(T{s}).K(T{s}, S{s}, S{_}).D(S{_},T{p})::cyt")
+    ret = objects.rate_complex_parser.parse(
+        "B(T{s}).K(T{s}, S{s}, S{_}).D(S{_},T{p})::cyt"
+    )
     assert ret.success
     assert ret.data.children[0] == objects.c3
 
-    ret = objects.complex_parser.parse("B(T{s}).T{s}::cyt")
+    ret = objects.rate_complex_parser.parse("B(T{s}).T{s}::cyt")
     assert ret.success
     assert ret.data.children[0] == objects.c4
 
-    ret = objects.complex_parser.parse("D().D().D().B(T{_}).B(T{_}).B(T{_})::cell")
+    ret = objects.rate_complex_parser.parse("D().D().D().B(T{_}).B(T{_}).B(T{_})::cell")
     assert ret.success
     assert ret.data.children[0] == objects.c5
 
-    ret = objects.complex_parser.parse("K().K().T{p}::cyt")
+    ret = objects.rate_complex_parser.parse("K().K().T{p}::cyt")
     assert ret.success
     assert ret.data.children[0] == objects.c6
 
-    ret = objects.complex_parser.parse("T{u}.T{_}::cell")
+    ret = objects.rate_complex_parser.parse("T{u}.T{_}::cell")
     assert ret.success
     assert ret.data.children[0] == objects.c7
 
-    ret = objects.complex_parser.parse("(T{s})::cell")
+    ret = objects.rate_complex_parser.parse("(T{s})::cell")
     assert not ret.success
 
-    ret = objects.complex_parser.parse("()::cell")
+    ret = objects.rate_complex_parser.parse("()::cell")
     assert not ret.success
 
-    ret = objects.complex_parser.parse("x::cell")
+    ret = objects.rate_complex_parser.parse("x::cell")
     assert not ret.success
 
-    ret = objects.complex_parser.parse("BT{s})::cell")
+    ret = objects.rate_complex_parser.parse("BT{s})::cell")
     assert not ret.success
 
-    ret = objects.complex_parser.parse("B(T{s}::cell")
+    ret = objects.rate_complex_parser.parse("B(T{s}::cell")
     assert not ret.success
 
-    ret = objects.complex_parser.parse("B(T{s}::cell)")
+    ret = objects.rate_complex_parser.parse("B(T{s}::cell)")
     assert not ret.success
 
-    ret = objects.complex_parser.parse("B(T{})::cell")
+    ret = objects.rate_complex_parser.parse("B(T{})::cell")
     assert not ret.success
 
-    ret = objects.complex_parser.parse("B(T{s}))::cell")
+    ret = objects.rate_complex_parser.parse("B(T{s}))::cell")
     assert not ret.success
 
-    ret = objects.complex_parser.parse("B(T{s})::")
+    ret = objects.rate_complex_parser.parse("B(T{s})::")
     assert not ret.success

Testing/test_complex.py

@@ -55,6 +55,7 @@ def test_create_all_compatible(self):
         results = set()
         with open("Testing/complexes_1.txt") as file:
             for complex in file.readlines():
+                complex = complex.strip()
                 results.add(objects.rate_complex_parser.parse(complex).data.children[0])
 
         complex = objects.rate_complex_parser.parse(
@@ -71,6 +72,7 @@ def test_create_all_compatible(self):
         results = set()
         with open("Testing/complexes_2.txt") as file:
             for complex in file.readlines():
+                complex = complex.strip()
                 results.add(objects.rate_complex_parser.parse(complex).data.children[0])
 
         complex = objects.rate_complex_parser.parse(

Testing/test_rule.py

@@ -37,6 +37,7 @@ def test_create_reactions(self):
         reactions = set()
         with open("Testing/reactions.txt") as file:
             for complex in file.readlines():
+                complex = complex.strip()
                 rule = objects.rule_parser.parse(complex).data[1]
                 reactions.add(rule.to_reaction())
 

Testing/test_side.py

@@ -36,10 +36,12 @@ def test_create_all_compatible(self):
         results = set()
         with open("Testing/complexes_1.txt") as file:
             for complex in file.readlines():
+                complex = complex.strip()
                 results.add(objects.rate_complex_parser.parse(complex).data.children[0])
 
         with open("Testing/complexes_2.txt") as file:
             for complex in file.readlines():
+                complex = complex.strip()
                 results.add(objects.rate_complex_parser.parse(complex).data.children[0])
 
         side = "KaiC().KaiC().KaiC().KaiC().KaiC().KaiC()::cyt + 2 KaiB().KaiB().KaiB()::cyt"