fix: catch zero volume PDB box and warn

pycgtool/frame.py

@@ -34,6 +34,29 @@ def __init__(self, msg=None):
         super(NonMatchingSystemError, self).__init__(msg)
 
 
+def try_load_traj(filepath: PathLike, **kwargs) -> mdtraj.Trajectory:
+    """Load a trajectory, if a PDB fails with zero box volume disable volume check and try again."""
+    filepath = pathlib.Path(filepath)
+
+    try:
+        return mdtraj.load(str(filepath), **kwargs)
+
+    except FloatingPointError:
+        # PDB file loading checks density using the simulation box
+        # This can fail if the box volume is zero
+        if filepath.suffix.lower() == '.pdb':
+            kwargs.pop('top', None)  # Can't specify a topology for `load_pdb`
+            trajectory = mdtraj.load_pdb(str(filepath), no_boxchk=True, **kwargs)
+            logger.warning(
+                'Unitcell has zero volume - periodic boundaries will not be accounted for. '
+                'If the molecule is split by a periodic boundary, results will be incorrect.'
+            )
+
+            return trajectory
+
+        raise
+
+
 class Frame:
     """Load and store data from a simulation trajectory."""
     def __init__(self,
@@ -51,15 +74,14 @@ def __init__(self,
         if topology_file is not None:
             try:
                 logging.info('Loading topology file')
-                self._trajectory = mdtraj.load(str(topology_file))
+                self._trajectory = try_load_traj(topology_file)
                 self._topology = self._trajectory.topology
                 logging.info('Finished loading topology file')
 
                 if trajectory_file is not None:
                     try:
                         logging.info('Loading trajectory file - this may take a while')
-                        self._trajectory = mdtraj.load(str(trajectory_file),
-                                                       top=self._topology)
+                        self._trajectory = try_load_traj(trajectory_file, top=self._topology)
                         self._trajectory = self._slice_trajectory(frame_start, frame_end)
                         logging.info(
                             'Finished loading trajectory file - loaded %d frames',