Merge pull request #891 from padix-key/fix-missing-intra-bonds

Fix missing intra-residue bonds in PDBx files

Author: padix-key

src/biotite/database/rcsb/query.py

@@ -218,9 +218,9 @@ class FieldQuery(SingleQuery):
     Examples
     --------
 
-    >>> query = FieldQuery("reflns.d_resolution_high", less_or_equal=0.6)
+    >>> query = FieldQuery("reflns.d_resolution_high", less_or_equal=0.5)
     >>> print(sorted(search(query)))
-    ['1EJG', '1I0T', '3NIR', '3P4J', '4JLJ', '5D8V', '5NW3', '7ATG', '7R0H']
+    ['3NIR', '4JLJ', '5D8V', '7R0H']
     """
 
     def __init__(
@@ -731,12 +731,12 @@ def count(query, return_type="entry", group_by=None, content_types=("experimenta
     Examples
     --------
 
-    >>> query = FieldQuery("reflns.d_resolution_high", less_or_equal=0.6)
+    >>> query = FieldQuery("reflns.d_resolution_high", less_or_equal=0.5)
     >>> print(count(query))
-    9
+    4
     >>> ids = search(query)
     >>> print(sorted(ids))
-    ['1EJG', '1I0T', '3NIR', '3P4J', '4JLJ', '5D8V', '5NW3', '7ATG', '7R0H']
+    ['3NIR', '4JLJ', '5D8V', '7R0H']
     """
     query_dict = _initialize_query_dict(query, return_type, group_by, content_types)
 
@@ -853,22 +853,22 @@ def search(
     Examples
     --------
 
-    >>> query = FieldQuery("reflns.d_resolution_high", less_or_equal=0.6)
+    >>> query = FieldQuery("reflns.d_resolution_high", less_or_equal=0.5)
     >>> print(sorted(search(query)))
-    ['1EJG', '1I0T', '3NIR', '3P4J', '4JLJ', '5D8V', '5NW3', '7ATG', '7R0H']
+    ['3NIR', '4JLJ', '5D8V', '7R0H']
     >>> print(search(query, sort_by="rcsb_accession_info.initial_release_date"))
-    ['7R0H', '7ATG', '5NW3', '5D8V', '4JLJ', '3P4J', '3NIR', '1I0T', '1EJG']
+    ['7R0H', '5D8V', '4JLJ', '3NIR']
     >>> print(search(
     ...     query, range=(1,4), sort_by="rcsb_accession_info.initial_release_date"
     ... ))
-    ['7ATG', '5NW3', '5D8V']
+    ['5D8V', '4JLJ', '3NIR']
     >>> print(sorted(search(query, return_type="polymer_instance")))
-    ['1EJG.A', '1I0T.A', '1I0T.B', '3NIR.A', '3P4J.A', '3P4J.B', '4JLJ.A', '4JLJ.B', '5D8V.A', '5NW3.A', '7ATG.A', '7ATG.B', '7R0H.A']
+    ['3NIR.A', '4JLJ.A', '4JLJ.B', '5D8V.A', '7R0H.A']
     >>> print(search(
     ...     query, return_type="polymer_entity", return_groups=True,
     ...     group_by=UniprotGrouping(sort_by="rcsb_accession_info.initial_release_date"),
     ... ))
-    {'P24297': ['5NW3_1'], 'P27707': ['4JLJ_1'], 'P80176': ['5D8V_1'], 'O29777': ['7R0H_1'], 'P01542': ['3NIR_1', '1EJG_1']}
+    {'P27707': ['4JLJ_1'], 'P80176': ['5D8V_1'], 'O29777': ['7R0H_1'], 'P01542': ['3NIR_1']}
     """
     query_dict = _initialize_query_dict(query, return_type, group_by, content_types)
 

src/biotite/structure/io/pdbx/convert.py

@@ -47,6 +47,7 @@
     filter_highest_occupancy_altloc,
 )
 from biotite.structure.geometry import centroid
+from biotite.structure.info.bonds import bonds_in_residue
 from biotite.structure.io.pdbx.bcif import (
     BinaryCIFBlock,
     BinaryCIFColumn,
@@ -418,6 +419,11 @@ def get_structure(
         if "chem_comp_bond" in block:
             try:
                 custom_bond_dict = _parse_intra_residue_bonds(block["chem_comp_bond"])
+                # For some reason the PDB does not add `chem_comp_bond` entries for
+                # some residues
+                # Therefore add the most common missing residues manually
+                for res_name in ["UNK", "N"]:
+                    custom_bond_dict[res_name] = bonds_in_residue(res_name)
             except KeyError:
                 warnings.warn(
                     "The 'chem_comp_bond' category has missing columns, "