Merge pull request #153 from andthum/fix/trajectory-unwrapping-fix

Fix some errors introduced by PR #151
andthum · Mar 10, 2023 · 6738d00 · 6738d00
2 parents 53d7780 + 229f6d5
commit 6738d00
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Showing 5 changed files with 115 additions and 72 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -6,12 +6,14 @@
     "cSpell.ignoreWords": [
         "Andreas",
         "Autoregressive",
+        "BLANKLINE",
         "CBAR",
         "CODEQL",
         "Correlogram",
         "Corrensstraße",
         "Cython",
         "EDRFILE",
+        "GROMACS",
         "GitHub",
         "GitLab",
         "Gromacs",
@@ -35,6 +37,7 @@
         "amin",
         "andthum",
         "arange",
+        "arccos",
         "argmax",
         "argparse",
         "asarray",
@@ -49,6 +52,8 @@
         "autoupdate",
         "basex",
         "basey",
+        "biggl",
+        "biggr",
         "bincount",
         "binwidth",
         "biomolecular",
@@ -65,6 +70,7 @@
         "columnspacing",
         "commited",
         "confint",
+        "copyto",
         "cumav",
         "cumsum",
         "currentmodule",
@@ -75,6 +81,7 @@
         "dtrj",
         "dtype",
         "edgecolor",
+        "einsum",
         "errorbar",
         "ezavod",
         "facecolor",
@@ -117,7 +124,9 @@
         "mdabackend",
         "mdacli",
         "mdadist",
+        "mdamath",
         "mdanalysis",
+        "mdtools",
         "mdtplt",
         "mksh",
         "modindex",

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -52,7 +52,7 @@ graft src
 prune .github
 prune .vscode
 prune docs/buid
-prune **/_sphinx_autosummary
+prune **/_sphinx_autosummary*
 prune misc
 prune **__pycache__
 

diff --git a/scripts/structure/rmsd_trj_trj.py b/scripts/structure/rmsd_trj_trj.py
@@ -270,7 +270,6 @@
         "--weights",
         dest="WEIGHTS",
         type=str,
-        nargs=2,
         required=False,
         choices=("masses", "charges"),
         default=None,
@@ -331,13 +330,6 @@
                 n_frames_tot=u[i].trajectory.n_frames,
             )
         )
-    if any(fr[-1] != frames[0][-1] for fr in frames):
-        print("\n")
-        for i, fr in enumerate(frames):
-            print("Trajectory {}: {} frames".format(i + 1, fr[-1]))
-        raise ValueError(
-            "You must read the same number of frames from all trajectories."
-        )
 
     if args.WEIGHTS is None:
         weights = None
@@ -354,6 +346,10 @@
         print("First frame to read:    {:>8d}".format(fr[0]))
         print("Last frame to read:     {:>8d}".format(fr[1]))
         print("Read every n-th frame:  {:>8d}".format(fr[2]))
+    if any(fr[-1] != frames[0][-1] for fr in frames):
+        raise ValueError(
+            "You must read the same number of frames from all trajectories."
+        )
     timer = datetime.now()
     times = np.full(frames[0][-1], np.nan, dtype=np.float64)
     rmsd = np.full((frames[0][-1], 3), np.nan, dtype=np.float64)
@@ -402,13 +398,13 @@
     timer = datetime.now()
     rmsd_tot = np.sqrt(np.sum(rmsd, axis=-1))
     header = (
-        "Root Mean Square Deviation (RMSD) between two trajectories for each"
+        "Root Mean Square Deviation (RMSD) between two trajectories for each\n"
         "frame.  The first trajectory is the reference trajectory.\n"
         "\n"
-        "\n"
     )
     for i, sl in enumerate(SEL):
         header += (
+            "\n"
             "Trajectory {}:"
             "Selection: '{}'\n"
             "Compound:  {}\n".format(i + 1, " ".join(sl), args.CMP[i])

diff --git a/scripts/trajectory/unwrap_trj.py b/scripts/trajectory/unwrap_trj.py
@@ -325,9 +325,9 @@
         )
         sel.positions = pos_w_prev
     else:
-        pos_w_prev = sel.positions
-    pos_u_prev = pos_w_prev
-    box_prev = ts.dimensions
+        pos_w_prev = np.copy(sel.positions)
+    pos_u_prev = np.copy(pos_w_prev)
+    box_prev = np.copy(ts.dimensions)
 
     if args.TOPFILE_OUT is not None:
         mdt.fh.backup(args.TOPFILE_OUT)
@@ -349,11 +349,12 @@
                 method=args.METHOD,
                 out=out,
                 out_tmp=out_tmp,
+                dtype=np.float64,
             )
-            pos_w_prev[:] = sel.positions
+            np.copyto(pos_w_prev, sel.positions)
             sel.positions = pos_u
-            pos_u_prev[:] = pos_u
-            box_prev[:] = ts.dimensions
+            np.copyto(pos_u_prev, pos_u)
+            np.copyto(box_prev, ts.dimensions)
             w.write(sel)
             # ProgressBar update.
             trj.set_postfix_str(