Read chainID from PDBQT

package/CHANGELOG

@@ -35,7 +35,9 @@ Enhancements
     `DielectricConstant` (Issue #4262, PR #4263)
   * Add support for reading chainID info from prmtop amber topologies (PR #4007)
   * Add support for reading chainID info from GROMACS TPR topologies 
-    (Issue #3994, PR #4281)
+    (Issue #3994, PR #4281)  
+  * Add support for reading chainID info from Autodock PDBQT files (Issue #4207,
+    PR #4284)
 
 Changes
   * The `mda-xdrlib` module is now a core dependency of MDAnalysis

package/MDAnalysis/topology/PDBQTParser.py

@@ -75,6 +75,7 @@
     Resnums,
     Resnames,
     Segids,
+    ChainIDs,
     Tempfactors,
 )
 
@@ -88,7 +89,7 @@ class PDBQTParser(TopologyReaderBase):
      - atom names
      - altLocs
      - resnames
-     - chainIDs (becomes segid)
+     - chainIDs (assigned to segid as well)
      - resids
      - record_types (ATOM/HETATM)
      - icodes
@@ -166,6 +167,8 @@ def parse(self, **kwargs):
         resnames = np.array(resnames, dtype=object)
         chainids = np.array(chainids, dtype=object)
 
+        attrs.append(ChainIDs(chainids))
+
         residx, (resids, icodes, resnames, chainids) = change_squash(
             (resids, icodes), (resids, icodes, resnames, chainids))
         n_residues = len(resids)

testsuite/MDAnalysisTests/coordinates/test_pdbqt.py

@@ -39,11 +39,17 @@ def universe(self):
         return mda.Universe(PDBQT_input)
 
     def test_segid(self, universe):
-        sel = universe.select_atoms('segid A')
+        sel = universe.select_atoms("segid A")
         assert_equal(sel.n_atoms, 909, "failed to select segment A")
-        sel = universe.select_atoms('segid B')
+        sel = universe.select_atoms("segid B")
         assert_equal(sel.n_atoms, 896, "failed to select segment B")
 
+    def test_chainID(self, universe):
+        sel = universe.select_atoms("chainID A")
+        assert_equal(sel.n_atoms, 909, "failed to chainID segment A")
+        sel = universe.select_atoms("chainID B")
+        assert_equal(sel.n_atoms, 896, "failed to chainID segment B")
+
     def test_protein(self, universe):
         sel = universe.select_atoms('protein')
         assert_equal(sel.n_atoms, 1805, "failed to select protein")

testsuite/MDAnalysisTests/topology/test_pdbqt.py

@@ -32,8 +32,19 @@ class TestPDBQT(ParserBase):
     parser = mda.topology.PDBQTParser.PDBQTParser
     ref_filename = PDBQT_input
     expected_attrs = [
-        'ids', 'names', 'charges', 'types', 'altLocs', 'resids', 'resnames',
-        'segids', 'record_types', 'icodes', 'occupancies', 'tempfactors'
+        "ids",
+        "names",
+        "charges",
+        "types",
+        "altLocs",
+        "resids",
+        "resnames",
+        "segids",
+        "chainIDs",
+        "record_types",
+        "icodes",
+        "occupancies",
+        "tempfactors",
     ]
     guessed_attrs = ['masses']
     expected_n_atoms = 1805