Update of test structure and bug fixes

glyles/glycans/mono/monomer.py

@@ -81,12 +81,12 @@ def get_name(self, mode: Literal["name", "full", "slim"] = "name"):
         if mode in {"slim", "full"}:
             core, mods = [], []
             for v, t in self.recipe:
-                if t in {IUPACLexer.MOD, IUPACLexer.COUNT}:
-                    core.append(v)
+                if t in {IUPACLexer.MOD}:  # , IUPACLexer.COUNT}:
+                    mods.append(v)
                 else:
                     if mode == "slim" and t == IUPACLexer.RING:
                         continue
-                    mods.append(v)
+                    core.append(v)
             name = "".join(core) + "".join(mods)
             if mode == "slim":
                 name = name.replace("L-", "").replace("D-", "")

glyles/glycans/poly/glycan.py

@@ -408,3 +408,7 @@ def parse(self):
                           f"Error message: {msg}")
             self.glycan_smiles = ""
             raise e
+
+
+if __name__ == "__main__":
+    print(Glycan("Fuc(a1-2)[GalNAc(a1-3)]Gal(b1-4)GlcNAc(b1-3)[Fuc(a1-2)[GalNAc(a1-3)]Gal(b1-4)GlcNAc(b1-6)]Gal(b1-3)[GlcNAc(a1-4)Gal(b1-4)GlcNAc6S(b1-6)]GalNAc", tree_only=True).summary())

glyles/glycans/poly/gwb_glycan.py

@@ -7,7 +7,6 @@
 from glyles.glycans.poly.merger import Merger
 from glyles.glycans.utils import ParseError
 from glyles.gwb.GWBLexer import GWBLexer
-print(GWBLexer.QMARK)
 from glyles.gwb.GWBParser import GWBParser
 from glyles.glycans.poly.glycan import Glycan
 

glyles/glycans/poly/gwb_walker.py

@@ -105,7 +105,7 @@ def add_node(self, node, parent, config=""):
         # add the node to the network and store the enum of the glycan as attribute
         recipe = self.build_recipe(node)
         if len(set.intersection({IUPACLexer.SAC, IUPACLexer.COUNT}, set(x for _, x in recipe))) == 0:
-            self.update_node(parent, recipe)
+            self.update_recipe(parent, recipe)
             return parent
         elif len(recipe) > 2 and recipe[-2][0] == ",":
             recipe = recipe[:-2] + [recipe[-1]]

tests/test_convert.py

@@ -38,122 +38,120 @@ def compare_smiles(computed, solution):
     assert c_rdkit == s_rdkit
 
 
-class TestConverter:
-
-    @pytest.mark.parametrize("iupac", [
-        "Man",
-        "Man(a1-4)Man",
-        "Man(a1-4)[Man(a1-3)]Man",
-        "Man(a1-4)[Man(a1-3)][Man(a1-2)]Man",
-    ])
-    def test_demo(self, iupac):
-        output = convert(iupac)
-
-        assert len(output) == 1
-        assert len(output[0]) == 2
-        assert output[0][0] == iupac
-        assert all(c in output[0][1] for c in {"C", "O", "[", "]", "@"})
-
-    @pytest.mark.parametrize("iupac", [
-        "Man(?1-4)Man",
-        "Man(a1-?)Man",
-        "Man(?1-?)Man",
-        "{Man(a1-4)}Man(a1-2)Man",
-        "{Man(?1-4)}Man(a1-?)Man",
-        "{Man(?1-?)}Man(?1-?)Man",
-    ])
-    def test_demo_no_resolution(self, iupac):
-        output = convert(iupac)
-
-        assert len(output) == 1
-        assert len(output[0]) == 2
-        assert output[0][0] == iupac
-        assert output[0][1] == ""
-
-    def test_file_output(self):
-        args = setup_test()
-
-        convert(args["glycan"], args["glycan_list"], args["glycan_file"], args["glycan_generator"],
-                output_file="./output.txt")
-        output = [line.split(",") for line in open("./output.txt", "r").readlines()]
-        check_results(output)
-
-    def test_return_output(self):
-        args = setup_test()
-
-        output = convert(args["glycan"], args["glycan_list"], args["glycan_file"], args["glycan_generator"],
-                         returning=True)
-        check_results(output)
-
-    def test_generator(self):
-        args = setup_test()
-
-        output = convert_generator(args["glycan"], args["glycan_list"], args["glycan_file"], args["glycan_generator"])
-        check_results(output)
-
-    def test_orientation_1(self):
-        output = convert("Glc a", returning=True)
-
-        assert len(output) == 1
-        assert output[0][0] == "Glc a"
-        compare_smiles(output[0][1], "OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O")
-
-    def test_orientation_2(self):
-        output = convert("Glc b", returning=True)
-
-        assert len(output) == 1
-        assert output[0][0] == "Glc b"
-        compare_smiles(output[0][1], "OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O")
-
-    @pytest.mark.slow
-    def test_parallel_list_input(self):
-        with open("data/runtime.tsv", "r") as runtime:
-            glycans = [line.strip().split("\t")[0] for line in runtime.readlines()]
-        start = time.time()
-        smiles1 = convert(glycan_list=glycans)
-        mid = time.time()
-        smiles2 = convert(glycan_list=glycans, cpu_count=14)
-        end = time.time()
-
-        assert len(smiles1) == len(smiles2) == len(glycans)
-        assert (end - mid) < (mid - start)
-
-    @pytest.mark.slow
-    def test_parallel_gen_input(self):
-        with open("data/runtime.tsv", "r") as runtime:
-            glycans = [line.strip().split("\t")[0] for line in runtime.readlines()]
-        start = time.time()
-        smiles1 = convert(glycan_generator=iter(glycans))
-        mid = time.time()
-        smiles2 = convert(glycan_generator=iter(glycans), cpu_count=14)
-        end = time.time()
-
-        assert len(smiles1) == len(smiles2) == len(glycans)
-        assert (end - mid) < (mid - start)
-
-    def test_smiles_clean(self):
-        assert sanitize_smiles("SDJCBPIOUCODJCOBC") == "SDJCBPIOUCODJCOBC"
-        assert sanitize_smiles("DIC(DONC)WOUC") == "DIC(DONC)WOUC"
-        assert sanitize_smiles("DPIUCDBPSIDU((CPIDBC)PID)") == "DPIUCDBPSIDU(CPIDBCPID)"
-        assert sanitize_smiles("SDJC((PSODUCBN))SOD:C") == "SDJC(PSODUCBN)SOD:C"
-        assert sanitize_smiles("A:DO(C(OPDIC))PODUC") == "A:DO(COPDIC)PODUC"
-
-    def test_summary(self):
-        output = Glycan("Fuc(a1-2)[GalNAc(a1-3)]Gal(b1-4)GlcNAc(b1-3)[Fuc(a1-2)[GalNAc(a1-3)]Gal(b1-4)GlcNAc(b1-6)]"
-                        "Gal(b1-3)[GlcNAc(a1-4)Gal(b1-4)GlcNAc6S(b1-6)]GalNAc", tree_only=True).summary()
-        assert output["formula"] == "C92H153N7O67S"
-        assert 2459 < output["weight"] < 2460
-        assert output["atoms"] == 167
-        assert output["bonds"] == 179
-        assert output["rings"] == 13
-        assert output["monomers"] == 13
-        assert output["types"]["GalNAc"] == 3
-        assert output["types"]["GlcNAc6S"] == 1
-        assert output["types"]["Gal"] == 4
-        assert output["types"]["GlcNAc"] == 3
-        assert output["types"]["Fuc"] == 2
-        assert output["root"] == "GalNAc"
-        assert output["leaves"].count("GlcNAc") == 1
-        assert output["leaves"].count("GalNAc") == 2
-        assert output["leaves"].count("Fuc") == 2
-        assert output["depth"] == 4
+@pytest.mark.parametrize("iupac", [
+    "Man",
+    "Man(a1-4)Man",
+    "Man(a1-4)[Man(a1-3)]Man",
+    "Man(a1-4)[Man(a1-3)][Man(a1-2)]Man",
+])
+def test_demo(iupac):
+    output = convert(iupac)
+
+    assert len(output) == 1
+    assert len(output[0]) == 2
+    assert output[0][0] == iupac
+    assert all(c in output[0][1] for c in {"C", "O", "[", "]", "@"})
+
+@pytest.mark.parametrize("iupac", [
+    "Man(?1-4)Man",
+    "Man(a1-?)Man",
+    "Man(?1-?)Man",
+    "{Man(a1-4)}Man(a1-2)Man",
+    "{Man(?1-4)}Man(a1-?)Man",
+    "{Man(?1-?)}Man(?1-?)Man",
+])
+def test_demo_no_resolution(iupac):
+    output = convert(iupac)
+
+    assert len(output) == 1
+    assert len(output[0]) == 2
+    assert output[0][0] == iupac
+    assert output[0][1] == ""
+
+def test_file_output():
+    args = setup_test()
+
+    convert(args["glycan"], args["glycan_list"], args["glycan_file"], args["glycan_generator"],
+            output_file="./output.txt")
+    output = [line.split(",") for line in open("./output.txt", "r").readlines()]
+    check_results(output)
+
+def test_return_output():
+    args = setup_test()
+
+    output = convert(args["glycan"], args["glycan_list"], args["glycan_file"], args["glycan_generator"],
+                        returning=True)
+    check_results(output)
+
+def test_generator():
+    args = setup_test()
+
+    output = convert_generator(args["glycan"], args["glycan_list"], args["glycan_file"], args["glycan_generator"])
+    check_results(output)
+
+def test_orientation_1():
+    output = convert("Glc a", returning=True)
+
+    assert len(output) == 1
+    assert output[0][0] == "Glc a"
+    compare_smiles(output[0][1], "OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O")
+
+def test_orientation_2():
+    output = convert("Glc b", returning=True)
+
+    assert len(output) == 1
+    assert output[0][0] == "Glc b"
+    compare_smiles(output[0][1], "OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O")
+
+@pytest.mark.slow
+def test_parallel_list_input():
+    with open("data/runtime.tsv", "r") as runtime:
+        glycans = [line.strip().split("\t")[0] for line in runtime.readlines()]
+    start = time.time()
+    smiles1 = convert(glycan_list=glycans)
+    mid = time.time()
+    smiles2 = convert(glycan_list=glycans, cpu_count=14)
+    end = time.time()
+
+    assert len(smiles1) == len(smiles2) == len(glycans)
+    assert (end - mid) < (mid - start)
+
+@pytest.mark.slow
+def test_parallel_gen_input():
+    with open("data/runtime.tsv", "r") as runtime:
+        glycans = [line.strip().split("\t")[0] for line in runtime.readlines()]
+    start = time.time()
+    smiles1 = convert(glycan_generator=iter(glycans))
+    mid = time.time()
+    smiles2 = convert(glycan_generator=iter(glycans), cpu_count=14)
+    end = time.time()
+
+    assert len(smiles1) == len(smiles2) == len(glycans)
+    assert (end - mid) < (mid - start)
+
+def test_smiles_clean():
+    assert sanitize_smiles("SDJCBPIOUCODJCOBC") == "SDJCBPIOUCODJCOBC"
+    assert sanitize_smiles("DIC(DONC)WOUC") == "DIC(DONC)WOUC"
+    assert sanitize_smiles("DPIUCDBPSIDU((CPIDBC)PID)") == "DPIUCDBPSIDU(CPIDBCPID)"
+    assert sanitize_smiles("SDJC((PSODUCBN))SOD:C") == "SDJC(PSODUCBN)SOD:C"
+    assert sanitize_smiles("A:DO(C(OPDIC))PODUC") == "A:DO(COPDIC)PODUC"
+
+def test_summary():
+    output = Glycan("Fuc(a1-2)[GalNAc(a1-3)]Gal(b1-4)GlcNAc(b1-3)[Fuc(a1-2)[GalNAc(a1-3)]Gal(b1-4)GlcNAc(b1-6)]"
+                    "Gal(b1-3)[GlcNAc(a1-4)Gal(b1-4)GlcNAc6S(b1-6)]GalNAc", tree_only=True).summary()
+    assert output["formula"] == "C92H153N7O67S"
+    assert 2459 < output["weight"] < 2460
+    assert output["atoms"] == 167
+    assert output["bonds"] == 179
+    assert output["rings"] == 13
+    assert output["monomers"] == 13
+    assert output["types"]["GalNAc"] == 3
+    assert output["types"]["GlcNAc6S"] == 1
+    assert output["types"]["Gal"] == 4
+    assert output["types"]["GlcNAc"] == 3
+    assert output["types"]["Fuc"] == 2
+    assert output["root"] == "GalNAc"
+    assert output["leaves"].count("GlcNAc") == 1
+    assert output["leaves"].count("GalNAc") == 2
+    assert output["leaves"].count("Fuc") == 2
+    assert output["depth"] == 4