Add edge case checking for Universe._resolve_formats (#5148)

* Fixes #5147
* Changes made in this Pull Request: add edge case checking for _resolve_formats
    * Don't set topology_format = format when format is a coordinate reader
    * Don't set format = topology_format when topology_format is a topology reader
* update CHANGELOG
* add tests

Author: ljwoods2

package/CHANGELOG

@@ -14,11 +14,13 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
-??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy
+??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2
 
  * 2.11.0
 
 Fixes
+ * Fix incorrect assignment of topology_format to format (and vice versa)
+   when a parsing class is provided to either (Issue #5147, PR #5148)
  * Fix incorrect TPR file parsing for GROMACS topologies produced prior
    to version 5.1.0 (Issue #5145, PR #5146)
  * Fixes incorrect assignment of secondary structure to proline residues in

package/MDAnalysis/core/universe.py

@@ -60,6 +60,7 @@
 import warnings
 import contextlib
 import collections
+import inspect
 
 import MDAnalysis
 import sys
@@ -255,10 +256,33 @@ def _topology_from_file_like(topology_file, topology_format=None, **kwargs):
 
 def _resolve_formats(*coordinates, format=None, topology_format=None):
     if not coordinates:
+        # ensure that a TopologyReader is not used to attempt to parse a trajectory
+        # Issue #5147
+        # fully qualified absolute names prevents circular import
         if format is None:
-            format = topology_format
+            format = (
+                None
+                if (inspect.isclass(topology_format))
+                and (
+                    issubclass(
+                        topology_format,
+                        MDAnalysis.topology.base.TopologyReaderBase,
+                    )
+                )
+                else topology_format
+            )
         elif topology_format is None:
-            topology_format = format
+            topology_format = (
+                None
+                if (inspect.isclass(format))
+                and (
+                    issubclass(
+                        format,
+                        MDAnalysis.Analysis.coordinates.base.ProtoReader,
+                    )
+                )
+                else format
+            )
     return format, topology_format
 
 

testsuite/MDAnalysisTests/core/test_universe.py

@@ -255,6 +255,28 @@ def test_universe_empty_ROMol(self):
         u = mda.Universe(mol, format="RDKIT")
         assert len(u.atoms) == 0
 
+    def test_Universe_top_format_no_coords(self):
+        # Issue #5147- ensure traj format is not set to topology format
+        u = mda.Universe(
+            PDB,
+            topology_format=MDAnalysis.topology.PDBParser.PDBParser,
+            format=None,
+        )
+        assert not isinstance(
+            u.trajectory, MDAnalysis.topology.PDBParser.PDBParser
+        )
+
+    def test_Universe_traj_format_no_coords(self):
+        # Issue #5147- ensure top format is not set to traj format
+        # no way to get inferred top format from Universe- use internal method call
+        format, topology_format = MDAnalysis.core.universe._resolve_formats(
+            None,
+            format=MDAnalysis.coordinates.PDB.PDBReader,
+            topology_format=None,
+        )
+
+        assert topology_format is None
+
 
 class TestUniverseFromSmiles(object):
     def setup_class(self):