Reduce2: bugfix for 3njw (links)

cctbx · Nov 13, 2024 · a5356d5 · a5356d5
1 parent aaef575
commit a5356d5
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/mmtbx/monomer_library/linking_utils.py b/mmtbx/monomer_library/linking_utils.py
@@ -495,6 +495,11 @@ def is_atom_pair_linked(atom1,
   if class1=="common_amino_acid" and class2=="common_amino_acid":
     if verbose:
       print("AMINO ACIDS",atom1.quote(), atom2.quote())
+    el1 = atom1.element.strip().upper()
+    el2 = atom2.element.strip().upper()
+    if ( (el1=='N' and el2=='C') or (el1=='C' and el2=='N')):
+      return True
+
   #
   # D-peptide special case...
   #

diff --git a/mmtbx/monomer_library/tst_linking.py b/mmtbx/monomer_library/tst_linking.py
@@ -2441,8 +2441,8 @@
   "linking_test_CD_GHE_A_B.pdb" : [0,0],             #4],
   "linking_test_XYP_XYP.pdb" : [18,19],
   "linking_test_ALY_MCM.pdb" : [11,12], # links AA with quasi-AA
-  # cross link not working
-  "linking_test_cyclic_side_chain.pdb" : [67,67], # side chain cross link
+  # cross link not working - DL: I think it works now
+  "linking_test_cyclic_side_chain.pdb" : [67,68], # side chain cross link
   "linking_test_cyclic_main_chain.pdb" : [34,35], # main chain cyclic
   "linking_test_over_valence.pdb" : [6,6],
   "linking_test_c2_c6.pdb" : [21,22],