test: SCHWED-6117 tests for reserved and obsolete skips

modules/conop/tests/test_complib.py

@@ -6,19 +6,25 @@ import tempfile
 import warnings
 
 
+def CreateComplib(compound_dict_path, chemlib_out_path, extra_args=None):
+    prefix_path = ost.GetPrefixPath()
+    chemdict_tool_path = os.path.join(prefix_path, "bin", "chemdict_tool")
+    if not os.path.exists(chemdict_tool_path):
+        raise RuntimeError("Expect chemdict_tool:", chemdict_tool_path)
+    cmd = [chemdict_tool_path, "create", compound_dict_path, chemlib_out_path]
+    if extra_args:
+        cmd += extra_args
+    subprocess.run(cmd, stdout=subprocess.PIPE)
+
+
 class TestCompLib(unittest.TestCase):
 
     @classmethod
     def setUpClass(cls):
-        prefix_path = ost.GetPrefixPath()
-        chemdict_tool_path = os.path.join(prefix_path, "bin", "chemdict_tool")
-        if not os.path.exists(chemdict_tool_path):
-            raise RuntimeError("Expect chemdict_tool:", chemdict_tool_path)
         cls.tmp_dir = tempfile.TemporaryDirectory()
-        compounds_path = os.path.join("testfiles", "test_compounds.cif")
+        compound_dict_path = os.path.join("testfiles", "test_compounds.cif")
         complib_path = os.path.join(cls.tmp_dir.name, "test_complib.dat")
-        cmd = [chemdict_tool_path, "create", compounds_path, complib_path]
-        subprocess.run(cmd)
+        CreateComplib(compound_dict_path, complib_path)
         cls.complib = conop.CompoundLib.Load(complib_path)
 
     @classmethod
@@ -29,11 +35,11 @@ class TestCompLib(unittest.TestCase):
         complib = self.complib
 
         comp_001 = complib.FindCompound("001")
-        comp_hello = complib.FindCompound("hello")
+        comp_A1LU6 = complib.FindCompound("A1LU6")
         comp_yolo = complib.FindCompound("yolo")
 
         self.assertFalse(comp_001 is None)
-        self.assertFalse(comp_hello is None)
+        self.assertFalse(comp_A1LU6 is None)
         self.assertTrue(comp_yolo is None)
 
     def test_smiles(self):
@@ -68,6 +74,50 @@ class TestCompLib(unittest.TestCase):
             if lib_version < ost.__version__:
                 warnings.warn("Using old version of the compound library: %s" % lib_version)
 
+    def test_ignore_reserved(self):
+        compound_dict_path = os.path.join("testfiles", "test_compounds.cif")
+        complib_no_reserved_path = os.path.join(self.tmp_dir.name, "test_complib_no_reserved.dat")
+        CreateComplib(compound_dict_path, complib_no_reserved_path, ["-i"])
+        complib_no_reserved = conop.CompoundLib.Load(complib_no_reserved_path)
+
+        # 01-98 are reserved
+        assert self.complib.FindCompound("98") is not None
+        assert complib_no_reserved.FindCompound("98") is None
+
+        # DRG, INH and LIG are reserved
+        assert self.complib.FindCompound("DRG") is not None
+        assert complib_no_reserved.FindCompound("DRG") is None
+        assert self.complib.FindCompound("INH") is not None
+        assert complib_no_reserved.FindCompound("INH") is None
+        assert self.complib.FindCompound("LIG") is not None
+        assert complib_no_reserved.FindCompound("LIG") is None
+
+        # OX is obsolete but not reserved
+        assert complib_no_reserved.FindCompound("OX") is not None
+
+        # 00, 000, 001, 010, 986, 98B are not reserved
+        assert complib_no_reserved.FindCompound("00") is not None
+        assert complib_no_reserved.FindCompound("000") is not None
+        assert complib_no_reserved.FindCompound("001") is not None
+        assert complib_no_reserved.FindCompound("010") is not None
+        assert complib_no_reserved.FindCompound("986") is not None
+        assert complib_no_reserved.FindCompound("98B") is not None
+
+    def test_ignore_obsolete(self):
+        compound_dict_path = os.path.join("testfiles", "test_compounds.cif")
+        complib_no_obsolete_path = os.path.join(self.tmp_dir.name, "test_complib_no_obsolete.dat")
+        CreateComplib(compound_dict_path, complib_no_obsolete_path, ["-o"])
+        complib_no_obsolete = conop.CompoundLib.Load(complib_no_obsolete_path)
+
+        # 01-98, DRG, INH and LIG are reserved but not obsolete
+        assert complib_no_obsolete.FindCompound("98") is not None
+        assert complib_no_obsolete.FindCompound("DRG") is not None
+        assert complib_no_obsolete.FindCompound("INH") is not None
+        assert complib_no_obsolete.FindCompound("LIG") is not None
+
+        # OX is obsolete
+        assert complib_no_obsolete.FindCompound("OX") is None
+
 
 if __name__ == "__main__":
     from ost import testutils