stop reading many frames to get times for shifted_correlation

Reviewed-on: #5

src/mdevaluate/autosave.py

@@ -166,8 +166,10 @@ def autosave_data(
         @functools.wraps(function)
         def autosave(*args, **kwargs):
             description = kwargs.pop("description", "")
+            autosave_dir_overwrite = kwargs.pop("autosave_dir_overwrite", None)
+            autosave_dir = autosave_dir_overwrite if autosave_dir_overwrite is not None else autosave_directory
             autoload = kwargs.pop("autoload", True) and load_autosave_data
-            if autosave_directory is not None:
+            if autosave_dir is not None:
                 relevant_args = list(args[:nargs])
                 if kwargs_keys is not None:
                     for key in [*posargs_keys, *kwargs_keys]:

src/mdevaluate/coordinates.py

@@ -434,6 +434,34 @@ def center_of_masses(
         ]
     ).T[mask]
     return np.array(positions)
+    
+    
+@map_coordinates
+def center_of_atoms(
+    frame: CoordinateFrame, atom_indices=None, shear: bool = False
+) -> NDArray:
+    if atom_indices is None:
+        atom_indices = list(range(len(frame)))
+    res_ids = frame.residue_ids[atom_indices]
+    if shear:
+        coords = frame[atom_indices]
+        box = frame.box
+        sort_ind = res_ids.argsort(kind="stable")
+        i = np.concatenate([[0], np.where(np.diff(res_ids[sort_ind]) > 0)[0] + 1])
+        coms = coords[sort_ind[i]][res_ids - min(res_ids)]
+        cor = pbc_diff(coords, coms, box)
+        coords = coms + cor
+    else:
+        coords = frame.whole[atom_indices]
+    mask = np.bincount(res_ids)[1:] != 0
+    positions = np.array(
+        [
+            np.bincount(res_ids, weights=c)[1:]
+            / np.bincount(res_ids)[1:]
+            for c in coords.T
+        ]
+    ).T[mask]
+    return np.array(positions)
 
 
 @map_coordinates

src/mdevaluate/correlation.py

@@ -147,7 +147,8 @@ def shifted_correlation(
     num_frames = int(len(frames) * window)
     ls = np.logspace(0, np.log10(num_frames + 1), num=points)
     idx = np.unique(np.int_(ls) - 1)
-    t = np.array([frames[i].time for i in idx]) - frames[0].time
+    dt = round(frames[1].time - frames[0].time, 6) # round to avoid bad floats
+    t = idx * dt
 
     result = np.array(
         [

src/mdevaluate/pbc.py

@@ -149,32 +149,21 @@ def nojump(frame: CoordinateFrame, usecache: bool = True) -> CoordinateFrame:
             i0 = 0
             delta = 0
 
-        delta = (
-            delta
-            + np.array(
-                np.vstack(
-                    [m[i0 : abstep + 1].sum(axis=0) for m in reader.nojump_matrices]
-                ).T
-            )
-            @ frame.box
-        )
+        delta = (delta
+            + np.vstack(
+                [m[i0 : abstep + 1].sum(axis=0) for m in reader.nojump_matrices]
+            ).T)
 
         reader._nojump_cache[abstep] = delta
         while len(reader._nojump_cache) > NOJUMP_CACHESIZE:
             reader._nojump_cache.popitem(last=False)
-        delta = delta[selection, :]
     else:
-        delta = (
-            np.array(
-                np.vstack(
-                    [
-                        m[: frame.step + 1, selection].sum(axis=0)
-                        for m in reader.nojump_matrices
-                    ]
+        delta = np.vstack(
+                [m[: frame.step + 1, selection].sum(axis=0) for m in reader.nojump_matrices]
                 ).T
-            )
-            @ frame.box
-        )
+    
+    delta = delta[selection, :]
+    delta = np.array(delta @ frame.box)
     return frame - delta
 
 

src/mdevaluate/reader.py

@@ -275,7 +275,7 @@ def load_nojump_matrices(reader: BaseReader):
                 "Loaded Nojump matrices: {}".format(nojump_load_filename(reader))
             )
         else:
-            logger.info("Invlaid Nojump Data: {}".format(nojump_load_filename(reader)))
+            logger.info("Invalid Nojump Data: {}".format(nojump_load_filename(reader)))
     except KeyError:
         logger.info("Removing zip-File: %s", zipname)
         os.remove(nojump_load_filename(reader))