From a5356d58d247ac8eb29c74add16a922ceab56fa2 Mon Sep 17 00:00:00 2001 From: dcliebschner Date: Wed, 13 Nov 2024 15:44:26 -0800 Subject: [PATCH] Reduce2: bugfix for 3njw (links) --- mmtbx/monomer_library/linking_utils.py | 5 +++++ mmtbx/monomer_library/tst_linking.py | 4 ++-- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/mmtbx/monomer_library/linking_utils.py b/mmtbx/monomer_library/linking_utils.py index a0dbeaed78..d58302880b 100644 --- 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 index 8013506e64..c29e358dce 100644 --- 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],