MemoryReader.

.travis.yml

@@ -63,7 +63,7 @@ install:
 
 # command to run tests
 script:
-  - ./testsuite/MDAnalysisTests/mda_nosetests --with-coverage --cover-package MDAnalysis --processes=2 --process-timeout=300 --with-memleak
+  - ./testsuite/MDAnalysisTests/mda_nosetests --with-coverage --cover-package MDAnalysis --processes=2 --process-timeout=400 --with-memleak
   - |
      test ${TRAVIS_PULL_REQUEST} == "false" && \
      test ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} && \

package/MDAnalysis/analysis/align.py

@@ -183,6 +183,7 @@
 import MDAnalysis.lib.qcprot as qcp
 from MDAnalysis.exceptions import SelectionError, SelectionWarning
 import MDAnalysis.analysis.rms as rms
+from MDAnalysis.coordinates.memory import MemoryReader
 # remove after rms_fit_trj deprecation over
 from MDAnalysis.lib.log import ProgressMeter
 
@@ -600,6 +601,7 @@ def rms_fit_trj(
         strict=False,
         force=True,
         quiet=False,
+        in_memory=False,
         **kwargs):
     """RMS-fit trajectory to a reference structure using a selection.
 
@@ -652,15 +654,19 @@ def rms_fit_trj(
          - ``True``: suppress progress and logging for levels INFO and below.
          - ``False``: show all status messages and do not change the the logging
            level (default)
-
+      *in_memory*
+         Default: ``False``
+         - ``True``: Switch to an in-memory trajectory so that alignment can
+           be done in-place, which can improve performance substantially in
+           some cases.
 
       *kwargs*
          All other keyword arguments are passed on the trajectory
          :class:`~MDAnalysis.coordinates.base.Writer`; this allows manipulating/fixing
          trajectories on the fly (e.g. change the output format by changing the extension of *filename*
          and setting different parameters as described for the corresponding writer).
 
-    :Returns: *filename* (either provided or auto-generated)
+    :Returns: *filename* (either provided or auto-generated), or None if in_memory=True
 
     .. _ClustalW: http://www.clustal.org/
     .. _STAMP: http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/
@@ -682,19 +688,24 @@ def rms_fit_trj(
         logging.disable(logging.WARN)
 
     kwargs.setdefault('remarks', 'RMS fitted trajectory to reference')
-    if filename is None:
-        path, fn = os.path.split(frames.filename)
-        filename = os.path.join(path, prefix + fn)
-        _Writer = frames.Writer
+    writer = None
+    if in_memory or isinstance(traj.trajectory, MemoryReader):
+        traj.transfer_to_memory()
+        frames = traj.trajectory
+        filename = None
+        logger.info("Moved trajectory to in-memory representation")
     else:
-        _Writer = frames.OtherWriter
-    if os.path.exists(filename) and not force:
-        logger.warn(
-            "{0} already exists and will NOT be overwritten; use force=True if you want this".format(filename))
-        return filename
-    writer = _Writer(filename, **kwargs)
-    del _Writer
-
+        if filename is None:
+            path, fn = os.path.split(frames.filename)
+            filename = os.path.join(path, prefix + fn)
+            _Writer = frames.Writer
+        else:
+            _Writer = frames.OtherWriter
+        if os.path.exists(filename) and not force:
+            logger.warn("{0} already exists and will NOT be overwritten; use force=True if you want this".format(filename))
+            return filename
+        writer = _Writer(filename, **kwargs)
+        del _Writer
     select = rms.process_selection(select)
     ref_atoms = reference.select_atoms(*select['reference'])
     traj_atoms = traj.select_atoms(*select['mobile'])
@@ -756,10 +767,11 @@ def rms_fit_trj(
         ts.positions[:] = ts.positions * R
         ts.positions += ref_com
 
-        writer.write(traj.atoms)  # write whole input trajectory system
-        percentage.echo(ts.frame)
+        if writer is not None:
+            writer.write(traj.atoms)  # write whole input trajectory system
+            percentage.echo(ts.frame)
     logger.info("Wrote %d RMS-fitted coordinate frames to file %r",
-                frames.n_frames, filename)
+            frames.n_frames, filename)
 
     if rmsdfile is not None:
         np.savetxt(rmsdfile, rmsd)

package/MDAnalysis/coordinates/DCD.py

@@ -500,13 +500,15 @@ def _read_frame(self, frame):
         ts.frame = frame
         return ts
 
-    def timeseries(self, asel, start=None, stop=None, step=None, skip=None,
+    def timeseries(self, asel=None, start=None, stop=None, step=None, skip=None,
                    format='afc'):
         """Return a subset of coordinate data for an AtomGroup
 
         :Arguments:
             *asel*
                :class:`~MDAnalysis.core.AtomGroup.AtomGroup` object
+               Defaults to None, in which case the full set of coordinate data
+               is returned.
             *start, stop, step*
                A range of the trajectory to access, with start being inclusive
                and stop being exclusive.
@@ -527,12 +529,17 @@ def timeseries(self, asel, start=None, stop=None, step=None, skip=None,
                           category=DeprecationWarning)
 
         start, stop, step = self.check_slice_indices(start, stop, step)
-        if len(asel) == 0:
-            raise NoDataError("Timeseries requires at least one atom to analyze")
+
+        if asel is not None:
+            if len(asel) == 0:
+                raise NoDataError("Timeseries requires at least one atom to analyze")
+            atom_numbers = list(asel.indices)
+        else:
+            atom_numbers = range(self.n_atoms)
+
         if len(format) != 3 and format not in ['afc', 'acf', 'caf', 'cfa', 'fac', 'fca']:
             raise ValueError("Invalid timeseries format")
-        atom_numbers = list(asel.indices)
-        # Check if the atom numbers can be grouped for efficiency, then we can read partial buffers
+       # Check if the atom numbers can be grouped for efficiency, then we can read partial buffers
         # from trajectory file instead of an entire timestep
         # XXX needs to be implemented
         return self._read_timeseries(atom_numbers, start, stop, step, format)

package/MDAnalysis/coordinates/__init__.py

@@ -709,6 +709,7 @@
 from . import TRZ
 from . import XTC
 from . import XYZ
+from . import memory
 
 try:
     from . import DCD

package/MDAnalysis/coordinates/base.py

@@ -1401,6 +1401,7 @@ def next_as_aux(self, auxname):
         --------
         :meth:`iter_as_aux`
         """
+
         aux = self._check_for_aux(auxname)
         ts = self.ts
         # catch up auxiliary if it starts earlier than trajectory
@@ -1416,7 +1417,7 @@ def next_as_aux(self, auxname):
         while self.frame != next_frame or getattr(self, '_frame', 0) == -1:
             # iterate trajectory until frame is reached
             ts = self.next()       
-        return ts 
+        return ts
 
     def iter_as_aux(self, auxname):
         """Iterate through timesteps for which there is at least one assigned