Merge pull request #96 from mopichalova/30-bidirectional-rules

Bidirectional rules

Testing/objects_testing.py

@@ -20,6 +20,7 @@
 side_parser = Parser("side")
 rate_complex_parser = Parser("rate_complex")
 rule_parser = Parser("rule")
+rules_parser = Parser("rules")
 model_parser = Parser("model")
 
 # atomic
@@ -246,13 +247,75 @@
 r3 = Rule(sequence_3, mid_3, compartments_3, complexes_3, pairs_3, rate_3)
 
 sequence_4 = (s34, s35, s36, s37)
+reversed_sequence_4 = (s36, s37, s34, s35)
 mid_4 = 2
 compartments_4 = ["cyt"] * 4
 complexes_4 = [(0, 1), (2, 2), (3, 3)]
+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_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(
+    reversed_sequence_4, mid_4, compartments_4, reversed_complexes_4, pairs_4, rate_4
+)
+reversed_r4b = Rule(
+    reversed_sequence_4,
+    mid_4,
+    compartments_4,
+    reversed_complexes_4,
+    pairs_4,
+    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
@@ -272,6 +335,9 @@
 
 r6 = Rule(sequence_6, mid_6, compartments_6, complexes_6, pairs_6, rate_6)
 rule_no_rate = Rule(sequence_4, mid_4, compartments_4, complexes_4, pairs_4, None)
+reversed_no_rate = Rule(
+    reversed_sequence_4, mid_4, compartments_4, reversed_complexes_4, pairs_4, None
+)
 
 sequence_c1 = (s34, s35, s36, s37, s2)
 mid_c1 = 2

Testing/parsing/test_rule.py

@@ -1,10 +1,8 @@
 import pytest
 
-from eBCSgen.Core.Rule import Rule
-from eBCSgen.Core.Rate import Rate
-
 import Testing.objects_testing as objects
 
+
 def test_parser():
     rule_expr = "K(S{u}).B()::cyt => K(S{p})::cyt + B()::cyt + D(B{_})::cell @ 3*[K()::cyt]/2*v_1"
     assert objects.rule_parser.parse(rule_expr).data[1] == objects.r5
@@ -20,3 +18,55 @@ def test_parser():
 
     rule_expr = "K(S{u}).B()::cyt => K(S{p})::cyt + B()::cyt"
     assert objects.rule_parser.parse(rule_expr).data[1] == objects.rule_no_rate
+
+
+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 | 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"
+    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 | 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 | 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"
+    )
+    assert not objects.rules_parser.parse(rule_expr).success
+
+    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