feat: SCHWED-5783 don't rename/renumber ligands

modules/mol/alg/pymod/ligand_scoring.py

@@ -169,23 +169,25 @@ class LigandScorer:
             Return the new residue handle."""
             nonlocal next_chain_num, new_editor
 
+            # Does a residue with the same name already exist?
+            already_exists = new_entity.FindResidue(handle.chain.name,
+                                                    handle.number).IsValid()
+            if already_exists:
+                msg = "A residue number %s already exists in chain %s" %(
+                    handle.number, handle.chain.name)
+                raise RuntimeError(msg)
+
             # Instanciate the editor
             if new_editor is None:
                 new_editor = new_entity.EditXCS()
 
-            # Add a new chain
-            new_chain = None
-            while new_chain is None:
-                try:
-                    new_chain = new_editor.InsertChain(str(next_chain_num))
-                    next_chain_num += 1
-                    break
-                except Exception:
-                    next_chain_num += 1
-            # Add the residue with residue number 1
+            # Get or create the chain
+            new_chain = new_entity.FindChain(handle.chain.name)
+            if not new_chain.IsValid():
+                new_chain = new_editor.InsertChain(handle.chain.name)
+            # Add the residue with its original residue number
             new_res = new_editor.AppendResidue(new_chain, handle, deep=True)
             new_res.SetIsLigand(True)
-            new_editor.SetResidueNumber(new_res, mol.ResNum(1))
             return new_res
 
         def _process_ligand_residue(res):

modules/mol/alg/tests/test_ligand_scoring.py

@@ -56,7 +56,6 @@ class TestLigandScoring(unittest.TestCase):
         assert len(sc.target.Select("rname=G3D").residues) == 2
         assert len(sc.model.Select("rname=G3D").residues) == 1
 
-
     def test_init_sdf_ligands(self):
         """Test that we can instantiate the scorer with ligands from separate SDF files.
 
@@ -93,6 +92,29 @@ class TestLigandScoring(unittest.TestCase):
         assert len(sc.target_ligands) == 7
         assert len(sc.model_ligands) == 1
 
+    def test_init_reject_duplicate_ligands(self):
+        """Test that we reject input if multiple ligands with the same chain
+         name/residue number are given.
+        """
+        mdl = io.LoadPDB(os.path.join('testfiles', "P84080_model_02_nolig.pdb"))
+        mdl_ligs = [io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf"))]
+        trg = io.LoadPDB(os.path.join('testfiles', "1r8q_protein.pdb.gz"))
+        trg_ligs = [io.LoadEntity(os.path.join('testfiles', "1r8q_ligand_%d.sdf" % i)) for i in range(7)]
+
+        # Reject identical model ligands
+        with self.assertRaises(RuntimeError):
+            sc = LigandScorer(mdl, trg, [mdl_ligs[0], mdl_ligs[0]], trg_ligs)
+
+        # Reject identical target ligands
+        lig0 = trg_ligs[0]
+        lig1 = trg_ligs[1]
+        ed1 = lig1.EditXCS()
+        ed1.RenameChain(lig1.chains[0], lig0.chains[0].name)
+        ed1.SetResidueNumber(lig1.residues[0], lig0.residues[0].number)
+        with self.assertRaises(RuntimeError):
+            sc = LigandScorer(mdl, trg, mdl_ligs, [lig0, lig1])
+
+
 
 if __name__ == "__main__":
     from ost import testutils