adding mechanism to add specific link

cctbx/geometry_restraints/standard_cif_links.py

@@ -1,4 +1,7 @@
 from __future__ import absolute_import, division, print_function
+#
+# regenerate using python <PHENIX>/modules/cctbx_project/mmtbx/monomer_library/populate_auto_linking_origin_ids.py
+#
 standard_cif_links = [
   ['link_ACE_C-N', 'ACE_C-N from Monomer Library or GeoStd'],
   ['link_AHT-ALA', 'AHT-ALA from Monomer Library or GeoStd'],
@@ -8,6 +11,7 @@
   ['link_ALPHA1-6', 'ALPHA1-6 from Monomer Library or GeoStd'],
   ['link_ALPHA2-3', 'ALPHA2-3 from Monomer Library or GeoStd'],
   ['link_ALPHA2-6', 'ALPHA2-6 from Monomer Library or GeoStd'],
+  ['link_ASP_CG-ANY_N', 'ASP_CG-ANY_N from Monomer Library or GeoStd'],
   ['link_BETA1-2', 'BETA1-2 from Monomer Library or GeoStd'],
   ['link_BETA1-3', 'BETA1-3 from Monomer Library or GeoStd'],
   ['link_BETA1-4', 'BETA1-4 from Monomer Library or GeoStd'],

mmtbx/monomer_library/linking_mixins.py

@@ -261,6 +261,9 @@ def check_for_peptide_links(atom1,
       other = atom_group2
     else:
       other = atom_group1
+    #
+    # only for AA to other
+    #
     if linking_utils.get_class(other.resname) not in ["other"]:
       return None
     # sulfur bridge
@@ -758,6 +761,7 @@ def _nonbonded_pair_objects(max_bonded_cutoff=3., i_seqs=None):
                                                                   atom2,
                                                                   classes1.important_only,
                                                                   classes2.important_only,
+                                                                  self.mon_lib_srv,
                                                                   )
         if link=='TRANS':
           key=link
@@ -783,6 +787,7 @@ def _nonbonded_pair_objects(max_bonded_cutoff=3., i_seqs=None):
                                              return_none_if_absent=True,
                                              )
         if verbose: print('apply standard link', key, origin_id)
+        assert origin_id
         if origin_id is None:
           # user defined links should not be applied here
           continue

mmtbx/monomer_library/linking_utils.py

@@ -319,18 +319,13 @@ def is_atom_group_pair_linked(atom_group1,
   #
   # look in link list for atom group links
   #
-  simple_key = "%s-%s" % (
-    atom_group1.resname,
-    atom_group2.resname,
-    )
-  if simple_key in mon_lib_srv.link_link_id_dict:
-    return mon_lib_srv.link_link_id_dict[simple_key], False, simple_key
-  simple_key = "%s-%s" % (
-    atom_group2.resname,
-    atom_group1.resname,
-    )
-  if simple_key in mon_lib_srv.link_link_id_dict:
-    return mon_lib_srv.link_link_id_dict[simple_key], True, simple_key
+  key_data = [
+    ["%s-%s" % (atom_group1.resname, atom_group2.resname), False],
+    ["%s-%s" % (atom_group2.resname, atom_group1.resname), True],
+    ]
+  for i, (simple_key, swap) in enumerate(key_data):
+    if simple_key in mon_lib_srv.link_link_id_dict:
+      return mon_lib_srv.link_link_id_dict[simple_key], swap, simple_key
   return None, None, None
 
 def is_atom_metal_coordinated(lookup,
@@ -363,15 +358,32 @@ def allow_cis_trans(classes1, classes2):
 def is_atom_pair_linked_tuple(atom1,
                               atom2,
                               class_important_1,
-                              class_important_2):
-  # if class_important_1=='common_amino_acid' and class_important_2==class_important_1:
+                              class_important_2,
+                              mon_lib_srv,
+                              ):
+  #
+  # atom name specific links
+  #
   if allow_cis_trans_important(class_important_1, class_important_2):
     if atom1.name==' N  ' and atom2.name==' C  ':
       return _get_cis_trans(), False, '?'
     elif atom1.name==' C  ' and atom2.name==' N  ':
       return _get_cis_trans(), True, '?'
-    # else:
-    #   print('amino acid link not found',atom1.quote(),atom2.quote())
+  atom_group1 = atom1.parent()
+  atom_group2 = atom2.parent()
+  key_data = [
+    # ['%s_%s-%s_%s' % (atom_group1.resname, atom1.name.strip(),
+    #                   atom_group2.resname, atom2.name.strip()), False],
+    # ['%s_%s-%s_%s' % (atom_group2.resname, atom2.name.strip(),
+    #                   atom_group1.resname, atom1.name.strip()), True],
+    ['%s_%s-%s_%s' % (atom_group1.resname, atom1.name.strip(),
+                      'ANY', atom2.name.strip()), False],
+    ['%s_%s-%s_%s' % (atom_group2.resname, atom2.name.strip(),
+                      'ANY', atom1.name.strip()), True],
+    ]
+  for i, (simple_key, swap) in enumerate(key_data):
+    if simple_key in mon_lib_srv.link_link_id_dict:
+      return mon_lib_srv.link_link_id_dict[simple_key], swap, simple_key
   return None, None, None
 
 def is_atom_pair_linked(atom1,