Add tests comparing output to foldseek gold standard

tests/__init__.py

@@ -0,0 +1,61 @@
+import unittest
+import importlib.resources
+
+import Bio.PDB
+from mini3di import Encoder
+
+
+class TestEncoder(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        cls.encoder = Encoder()
+        cls.parser = Bio.PDB.PDBParser(QUIET=True)
+
+    @classmethod
+    def get_structure(cls, name):
+        path = importlib.resources.files(__package__).joinpath("data", name).with_suffix(".pdb")
+        return cls.parser.get_structure(name, path)
+
+    def test_encode_3bww(self):
+        structure = self.get_structure("3bww")
+        states = self.encoder.encode_chain(structure[0]["A"])
+        sequence = self.encoder.build_sequence(states)
+        self.assertEqual(
+            sequence,
+            "DKDFFEAAEDDLVCLVVLLPPPACPQRQAYEDALVVQVPDDPVSVVSVVNSLVHHAYAYEYEAQQL"
+            "LDDPQGDVVSLVSVLVCCVVSVPQEYEYENDPPDADALDVVSLVSSLVSQLVSCVSSVGAYAYEDA"
+            "ADQDHDPRHPDDVLVSRQSNCVSNVHAHAYELVRLVRCCVRPVPDDSLVSLVRHPLQRHQHYEYQV"
+            "VSVVSVLVNLVDHQAHHYYYHDYPDDVVVNSVVRVVSRVSNVVSCVVVVHYIDMD",
+        )
+
+    def test_encode_8crb(self):
+        structure = self.get_structure("8crb")
+
+        states = self.encoder.encode_chain(structure[0]["A"])
+        sequence = self.encoder.build_sequence(states)
+        self.assertEqual(
+            sequence,
+            "DWAKDKDWADEDAAQAKTKIKMATPPDLLQDFFKFKWFDAPPDDIDGQAPGACPSPPLADDVHHHH"
+            "GKGWHDDSVRRMIMIMGGNDDQVVFGKMKMFTADDADPQVVVPDGDDTDDMHDIDTYGHPPDDFFA"
+            "WDKDKDQDDPVPCPVQKPKIKMKTDDGDDDDKDKAWLVNPGDPQKDDFDWDADPVRGIIDMIIGMD"
+            "GNVCFQVGFTKIWMAGVVVRDIDIDGGHD",
+        )
+
+        states = self.encoder.encode_chain(structure[0]["B"])
+        sequence = self.encoder.build_sequence(states)
+        self.assertEqual(
+            sequence,
+            "DAAKDFDQQEEEAAQAKDKGWIFAADVPPVPDAFWKWWDAPPDDIDTAADPNQAGDPVDHSQKGWD"
+            "ADHGITIIMGGRDDNSRQGFIWRAQPDDPDHNGHTDDTHGYYHCPDDQDDKDKDWDDAAVVVLVVL"
+            "FGKTKIKIDDGDDPPKDKFKDLQNHTDDAQWDWDDWDLDPVRTIMTMIIRRDGVVSCVVSQKMKMW"
+            "IDDDVHTDIDMDGNVVHD",
+        )
+
+        states = self.encoder.encode_chain(structure[0]["C"])
+        sequence = self.encoder.build_sequence(states)
+        self.assertEqual(
+            sequence,
+            "DPCVLVVLVLQLVLVVLLLVVVVVVLVVCVVVLFKDWQDPVHDWQLACVSPDHDCPDCCSVPGSNN"
+            "VQQCPKPLDDVTATNQSVQQIDDGDLDHDDDDDTIQGCPPPVRCSVVVVVVSVVSVVVSVVSCVVS"
+            "VVVVVVD",
+        )