Update ResidueGroup/SegmentGroup with ids (PDBParser: force chainid to segid / Universe: set groups)

package/AUTHORS

@@ -248,6 +248,7 @@ Chronological list of authors
   - Tanish Yelgoe
  2025
   - Joshua Raphael Uy
+  - Yu-Yuan (Stuart) Yang
 
 External code
 -------------

package/MDAnalysis/coordinates/PDB.py

@@ -214,7 +214,8 @@ class PDBReader(base.ReaderBase):
     47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
     55 - 60        Real(6.2)     occupancy    Occupancy.
     61 - 66        Real(6.2)     tempFactor   Temperature  factor.
-    67 - 76        String        segID        (unofficial CHARMM extension ?)
+    67 - 72        -             -            (not in the official PDB format)
+    73 - 76        String        segID        (unofficial CHARMM extension ?)
     77 - 78        LString(2)    element      Element symbol, right-justified.
     79 - 80        LString(2)    charge       Charge  on the atom.
     =============  ============  ===========  =============================================

package/MDAnalysis/topology/PDBParser.py

@@ -212,7 +212,7 @@
         -------
         MDAnalysis Topology object
         """
-        top = self._parseatoms()
+        top = self._parseatoms(**kwargs)
 
         try:
             bonds = self._parsebonds(top.ids.values)
@@ -229,7 +229,7 @@
 
         return top
 
-    def _parseatoms(self):
+    def _parseatoms(self, **kwargs):
         """Create the initial Topology object"""
         resid_prev = 0  # resid looping hack
 
@@ -302,7 +302,7 @@
                 occupancies.append(float_or_default(line[54:60], 0.0))
                 tempfactors.append(float_or_default(line[60:66], 1.0))  # AKA bfactor
 
-                segids.append(line[66:76].strip())
+                segids.append(line[72:76].strip())
 
         # Warn about wrapped serials
         if self._wrapped_serials:
@@ -313,6 +313,10 @@
         if not any(segids):
             segids = chainids
 
+        # If force_chainids_to_segids is set, use chainids as segids
+        if "force_chainids_to_segids" in kwargs.keys() and kwargs["force_chainids_to_segids"]:
+            segids = chainids
+
         n_atoms = len(serials)
 
         attrs = []