bidirectional rules extended

Testing/objects_testing.py

@@ -254,7 +254,7 @@
 reversed_complexes_4 = [(0, 0), (1, 1), (2, 3)]
 pairs_4 = [(0, 2), (1, 3)]
 rate_4 = Rate("3.0*[K()::cyt]/2.0*v_1")
-reversed_rate4 = Rate("2.0*[K()::cyt]/3.0*v_1")
+reversed_rate_4 = Rate("2.0*[K()::cyt]/3.0*v_1")
 
 r4 = Rule(sequence_4, mid_4, compartments_4, complexes_4, pairs_4, rate_4)
 reversed_r4a = Rule(
@@ -266,8 +266,56 @@
     compartments_4,
     reversed_complexes_4,
     pairs_4,
-    reversed_rate4,
+    reversed_rate_4,
 )
+sequence_one_side_bidirectional = (s36, s37)
+mid_one_side_bidirectional_a = 2
+mid_one_side_bidirectional_b = 0
+compartments_one_side_bidirectional = ["cyt"] * 2
+complexes_one_side_bidirectional = [(0, 0), (1, 1)]
+pairs_one_side_bidirectional_a = [(0, None), (1, None)]
+pairs_one_side_bidirectional_b = [(None, 0), (None, 1)]
+one_side_bidirectional_a = Rule(
+    sequence_one_side_bidirectional,
+    mid_one_side_bidirectional_a,
+    compartments_one_side_bidirectional,
+    complexes_one_side_bidirectional,
+    pairs_one_side_bidirectional_a,
+    rate_4,
+)
+one_side_bidirectional_b = Rule(
+    sequence_one_side_bidirectional,
+    mid_one_side_bidirectional_b,
+    compartments_one_side_bidirectional,
+    complexes_one_side_bidirectional,
+    pairs_one_side_bidirectional_b,
+    rate_4,
+)
+one_side_bidirectional_b_reversed_rate = Rule(
+    sequence_one_side_bidirectional,
+    mid_one_side_bidirectional_b,
+    compartments_one_side_bidirectional,
+    complexes_one_side_bidirectional,
+    pairs_one_side_bidirectional_b,
+    reversed_rate_4,
+)
+one_side_bidirectional_a_no_rate = Rule(
+    sequence_one_side_bidirectional,
+    mid_one_side_bidirectional_a,
+    compartments_one_side_bidirectional,
+    complexes_one_side_bidirectional,
+    pairs_one_side_bidirectional_a,
+    None,
+)
+one_side_bidirectional_b_no_rate = Rule(
+    sequence_one_side_bidirectional,
+    mid_one_side_bidirectional_b,
+    compartments_one_side_bidirectional,
+    complexes_one_side_bidirectional,
+    pairs_one_side_bidirectional_b,
+    None,
+)
+
 
 sequence_5 = (s34, s35, s36, s37, s38)
 mid_5 = 2

Testing/parsing/test_rule.py

@@ -23,19 +23,47 @@ def test_parser():
 def test_bidirectional():
     rule_expr = "#! rules\nK(S{u}).B()::cyt <=> K(S{p})::cyt + B()::cyt"
     parsed = objects.rules_parser.parse(rule_expr)
+    assert parsed.success
     assert objects.rule_no_rate in parsed.data["rules"]
     assert objects.reversed_no_rate in parsed.data["rules"]
 
     rule_expr = (
         "#! rules\nK(S{u}).B()::cyt <=> K(S{p})::cyt + B()::cyt @ 3*[K()::cyt]/2*v_1"
     )
     parsed = objects.rules_parser.parse(rule_expr)
+    assert parsed.success
     assert objects.r4 in parsed.data["rules"]
     assert objects.reversed_r4a in parsed.data["rules"]
 
-    rule_expr = (
-        "#! rules\nK(S{u}).B()::cyt <=> K(S{p})::cyt + B()::cyt @ 3*[K()::cyt]/2*v_1 | 2*[K()::cyt]/3*v_1"
-    )
+    rule_expr = "#! rules\nK(S{u}).B()::cyt <=> K(S{p})::cyt + B()::cyt @ 3*[K()::cyt]/2*v_1 | 2*[K()::cyt]/3*v_1"
     parsed = objects.rules_parser.parse(rule_expr)
+    assert parsed.success
     assert objects.r4 in parsed.data["rules"]
     assert objects.reversed_r4b in parsed.data["rules"]
+
+    rule_expr = "#! rules\n <=> K(S{p})::cyt + B()::cyt @ 3*[K()::cyt]/2*v_1"
+    parsed = objects.rules_parser.parse(rule_expr)
+    assert parsed.success
+    assert objects.one_side_bidirectional_a in parsed.data["rules"]
+    assert objects.one_side_bidirectional_b in parsed.data["rules"]
+
+    rule_expr = "#! rules\n K(S{p})::cyt + B()::cyt <=> @ 3*[K()::cyt]/2*v_1"
+    parsed = objects.rules_parser.parse(rule_expr)
+    assert parsed.success
+    assert objects.one_side_bidirectional_a in parsed.data["rules"]
+    assert objects.one_side_bidirectional_b in parsed.data["rules"]
+
+    rule_expr = "#! rules\n K(S{p})::cyt + B()::cyt <=> @ 3*[K()::cyt]/2*v_1 | 2*[K()::cyt]/3*v_1"
+    parsed = objects.rules_parser.parse(rule_expr)
+    assert parsed.success
+    assert objects.one_side_bidirectional_a in parsed.data["rules"]
+    assert objects.one_side_bidirectional_b_reversed_rate in parsed.data["rules"]
+
+    rule_expr = "#! rules\n K(S{p})::cyt + B()::cyt <=>"
+    parsed = objects.rules_parser.parse(rule_expr)
+    assert parsed.success
+    assert objects.one_side_bidirectional_a_no_rate in parsed.data["rules"]
+    assert objects.one_side_bidirectional_b_no_rate in parsed.data["rules"]
+
+    rule_expr = "#! rules\nK(S{u}).B()::cyt => K(S{p})::cyt + B()::cyt @ 3*[K()::cyt]/2*v_1 | 2*[K()::cyt]/3*v_1"
+    assert not objects.rules_parser.parse(rule_expr).success