Revert "[_bmutils] new methods for jast joining/copying of geoms"

This reverts commit 9d88f9e.

molpx/_bmutils.py

@@ -586,8 +586,7 @@ def data_from_input(projected_data):
 
     return idata
 
-def save_traj_wrapper(traj_inp, indexes, outfile, top=None, stride=1, chunksize=1000, image_molecules=False, verbose=True,
-                      copy_not_join=False):
+def save_traj_wrapper(traj_inp, indexes, outfile, top=None, stride=1, chunksize=1000, image_molecules=False, verbose=True):
     r"""wrapper for :pyemma:`save_traj` so that it works seamlessly with lists of :mdtraj:`Trajectories`
 
     Parameters
@@ -606,90 +605,15 @@ def save_traj_wrapper(traj_inp, indexes, outfile, top=None, stride=1, chunksize=
         geom_smpl = _save_traj(traj_inp, indexes, None, top=top, stride=stride,
                                chunksize=chunksize, image_molecules=image_molecules, verbose=verbose)
     elif isinstance(traj_inp[0], _md.Trajectory):
-        geom_smpl = fast_join_geom_list_from_indexes(traj_inp, indexes)
+        file_idx, frame_idx = indexes[0]
+        geom_smpl = traj_inp[file_idx][frame_idx]
+        for file_idx, frame_idx in indexes[1:]:
+            geom_smpl = geom_smpl.join(traj_inp[file_idx][frame_idx])
     else:
         raise TypeError("Cant handle input of type %s now"%(type(traj_inp[0])))
 
     return geom_smpl
 
-def join_geom_list(geom_list, fast=False):
-    r"""
-
-    :param geom_list: list of :mdtraj:`Trajectory` objects
-    :param fast boolean, default is True. Opt for a quick-n-dirty way of joining the geometries.
-    Currently only works with lists of one-framed-geometries
-    :return: one single :mdtraj:`Trajectory` object with all the above geometries joined into one
-
-
-    """
-    if fast:
-        if not _np.allclose(1, _np.unique([len(igeom) for igeom in geom_list])):
-            raise NotImplementedError("At the moment, when fast=True, the list can only be composed of " \
-                                      "one-framed mdTrajectories ")
-
-        xyz = []
-        unitcell_lengths = []
-        unitcell_angles = []
-        time = []
-
-        for ii, igeom in enumerate(geom_list):
-            xyz.append(igeom.xyz[0])
-            unitcell_lengths.append(igeom.unitcell_lengths[0])
-            unitcell_angles.append(igeom.unitcell_angles[0])
-            time.append(igeom.time[0])
-
-        return  _md.Trajectory(xyz, geom_list[0].top,
-                               time=time,
-                               unitcell_lengths=unitcell_lengths,
-                               unitcell_angles=unitcell_angles)
-
-    else:
-        igeom = geom_list[0]
-        # TODO: avoid joining via copy_not_join
-        for jgeom in geom_list[1:]:
-            igeom = igeom.join(jgeom)
-
-        return igeom
-
-def fast_join_geom_list_from_indexes(mdTrajectory_list, indexes):
-    r"""
-    Provided a list of trajectories and a list of file-and-frame indexes, return a single trajectory
-    composed of these file-and-frame indexes joined together
-
-    The join method of mdtraj is rather slow for this purpose, because it is not thought of as a sth
-    to be iterated over many times, whereas methods like save_traj of PyEMMA heavily rely on this
-
-    :param mdTrajectory_list: list of :mdtraj:`Trajectory` objects
-    :param indexes: iterable of file-and-frame pairs
-
-    :return: :mdtraj:`Trajectory` object
-    """
-
-    xyz = []
-    unitcell_lengths = []
-    unitcell_angles = []
-    time = []
-
-    #TODO although wrapping around "join_geom_list" with fast=True would result in less code repetition
-    # the following code allows for extracting attributes like geom.time, geom.xyz without
-    # instantiating a new geometry, resulting in significant speedup
-    for ii, (file_idx, frame_idx) in enumerate(indexes):
-        try:
-            xyz.append(mdTrajectory_list[file_idx].xyz[frame_idx])
-        except IndexError:
-            print(ii, file_idx, frame_idx, len(mdTrajectory_list), len(mdTrajectory_list[file_idx]))
-            raise
-        unitcell_lengths.append(mdTrajectory_list[file_idx].unitcell_lengths[frame_idx])
-        unitcell_angles.append(mdTrajectory_list[file_idx].unitcell_angles[frame_idx])
-        time.append(mdTrajectory_list[file_idx].time[frame_idx])
-
-    return  _md.Trajectory(xyz, mdTrajectory_list[0].top,
-                           time=time,
-                           unitcell_lengths=unitcell_lengths,
-                           unitcell_angles=unitcell_angles)
-
-
-
 def slice_list_of_geoms_to_closest_to_ref(geom_list, ref):
     r"""
     For a list of md.Trajectory objects, reduce md.Trajectory in the list
@@ -1107,7 +1031,7 @@ def add_atom_idxs_widget(atom_idxs, ngl_wdg, color_list=None, radius=1):
 
     return ngl_wdg
 
-def transpose_geom_list(geom_list, fast=False):
+def transpose_geom_list(geom_list):
     r"""
     Transpose a list of md.Trajectory objects, so that an input having the frames input
     geom_list[0] = md.Trajectory with frames f00, f01, f02,..., f0M
@@ -1142,11 +1066,14 @@ def transpose_geom_list(geom_list, fast=False):
         "All geometries in the list have to have the same length"
 
 
-    # Expand all geometires to a list of lists
     list_out = [[igeom[ii] for igeom in geom_list] for ii in range(n_frames_per_element)]
-    print(list_out)
-    # Join them in the column order
-    geom_list_T = [join_geom_list(ilist, fast=fast) for ilist in list_out]
+    geom_list_T = []
+    for ilist in list_out:
+        igeom = ilist[0]
+        #TODO: avoid joining via copy_not_join
+        for jgeom in ilist[1:]:
+            igeom = igeom.join(jgeom)
+        geom_list_T.append(igeom)
 
     return(geom_list_T)