nojump.py raises a valueerror when applied not at 0

Author: spyke7

package/CHANGELOG

@@ -20,6 +20,8 @@ The rules for this file:
  * 2.11.0
 
 Fixes
+ * NoJump shows a more informative message and fails  when applied
+   outside of the first frame (Issue #4915, PR #5199)
  * DSSP now explicitly checks for a minimum of 6 residues and raises a clear
    error message, unlike the previous behavior where it would fail with an
    incomprehensible broadcasting error at execution time (Issue #5046, PR #5163)

package/MDAnalysis/transformations/nojump.py

@@ -118,6 +118,14 @@ def _transform(self, ts):
         except np.linalg.LinAlgError:
             msg = f"Periodic box dimensions are not invertible at step {ts.frame}"
             raise NoDataError(msg)
+
+        if self.prev is None and ts.frame != 0:
+            raise ValueError(
+                "NoJump transformation must be applied starting from frame 0. "
+                f"Currently at frame {ts.frame}. Please reset trajectory to frame 0 "
+                "before adding this transformation."
+            )
+
         if ts.frame == 0:
             # We don't need to apply the transformation here. However, we need to
             # ensure we have the 0th frame coordinates in reduced form. We also need to

testsuite/MDAnalysisTests/transformations/test_nojump.py

@@ -379,3 +379,32 @@ def test_notinvertible(nojump_universe):
         ]
         u.trajectory.add_transformations(*workflow)
         transformed_coordinates = u.trajectory.timeseries()[0]
+
+
+def test_nojump_fails_when_not_at_frame_0():
+    """
+    Test that NoJump raises a clear error when applied to a trajectory
+    that is not at frame 0.
+    """
+    u = mda.Universe(data.PSF_TRICLINIC, data.DCD_TRICLINIC)
+    u.trajectory[-1]
+
+    with pytest.raises(
+        ValueError, match="must be applied starting from frame 0"
+    ):
+        u.trajectory.add_transformations(NoJump())
+        _ = u.trajectory[0]
+
+
+def test_nojump_fails_midtrajectory():
+    """
+    Test that NoJump raises a clear error when applied in the middle of a trajectory.
+    """
+    u = mda.Universe(data.PSF_TRICLINIC, data.DCD_TRICLINIC)
+    u.trajectory[5]
+
+    with pytest.raises(
+        ValueError, match="must be applied starting from frame 0"
+    ):
+        u.trajectory.add_transformations(NoJump())
+        _ = u.trajectory.timeseries()