remove TimeseriesCollection

Author: kain88-de

package/MDAnalysis/__init__.py

@@ -143,7 +143,7 @@
 """
 from __future__ import absolute_import
 
-__all__ = ['Timeseries', 'Universe', 'as_Universe', 'Writer', 'collection',
+__all__ = ['Timeseries', 'Universe', 'as_Universe', 'Writer',
            'fetch_mmtf']
 
 import logging
@@ -192,15 +192,12 @@
 from . import units
 
 # Bring some often used objects into the current namespace
-from .core import Timeseries
 from .core.universe import Universe, as_Universe, Merge
 from .coordinates.core import writer as Writer
 
 # After Universe import
 from .coordinates.MMTF import fetch_mmtf
 
-collection = Timeseries.TimeseriesCollection()
-
 from .migration.ten2eleven import ten2eleven
 
 import six

package/MDAnalysis/coordinates/DCD.py

@@ -92,9 +92,6 @@
 from . import core
 # Add the c functions to their respective classes so they act as class methods
 from . import _dcdmodule
-# dcdtimeseries is implemented with Pyrex - hopefully all dcd reading functionality can move to pyrex
-from . import dcdtimeseries
-
 
 
 class Timestep(base.Timestep):
@@ -399,8 +396,6 @@ class DCDReader(base.ReaderBase):
            random access into the trajectory (i corresponds to frame number)
         ``data = dcd.timeseries(...)``
            retrieve a subset of coordinate information for a group of atoms
-        ``data = dcd.correl(...)``
-           populate a :class:`MDAnalysis.core.Timeseries.Collection` object with computed timeseries
 
     Note
     ----
@@ -578,55 +573,6 @@ def timeseries(self, asel=None, start=None, stop=None, step=None, skip=None,
         # XXX needs to be implemented
         return self._read_timeseries(atom_numbers, start, stop, step, format)
 
-    def correl(self, timeseries, start=None, stop=None, step=None, skip=None):
-        """Populate a :class:`~MDAnalysis.core.Timeseries.TimeseriesCollection` object
-        with time series computed from the trajectory.
-
-        Calling this method will iterate through the whole trajectory and
-        perform the calculations prescribed in `timeseries`.
-
-        Parameters
-        ----------
-        timeseries : :class:`MDAnalysis.core.Timeseries.TimeseriesCollection`
-             The :class:`MDAnalysis.core.Timeseries.TimeseriesCollection` that defines what kind
-             of computations should be performed on the data in this trajectory.
-        start :  int (optional)
-             Begin reading the trajectory at frame index `start` (where 0 is the index
-             of the first frame in the trajectory); the default ``None`` starts
-             at the beginning.
-        stop : int (optional)
-             End reading the trajectory at frame index `stop`-1, i.e, `stop` is excluded.
-             The trajectory is read to the end with the default ``None``.
-        step : int (optional)
-             Step size for reading; the default ``None`` is equivalent to 1 and means to
-             read every frame.
-
-        Note
-        ----
-        The `correl` functionality is only implemented for DCD trajectories and
-        the :class:`DCDReader`.
-
-
-        .. deprecated:: 0.16.0
-           `skip` has been deprecated in favor of the standard keyword `step`.
-
-        """
-        if skip is not None:
-            step = skip
-            warnings.warn("Skip is deprecated and will be removed in"
-                          "in 1.0. Use step instead.",
-                          category=DeprecationWarning)
-
-        start, stop, step = self.check_slice_indices(start, stop, step)
-        atomlist = timeseries._getAtomList()
-        format = timeseries._getFormat()
-        lowerb, upperb = timeseries._getBounds()
-        sizedata = timeseries._getDataSize()
-        atomcounts = timeseries._getAtomCounts()
-        auxdata = timeseries._getAuxData()
-        return self._read_timecorrel(atomlist, atomcounts, format, auxdata,
-                                     sizedata, lowerb, upperb, start, stop, step)
-
     def close(self):
         if self.dcdfile is not None:
             self._finish_dcd_read()
@@ -706,6 +652,3 @@ def dt(self):
 DCDWriter._write_dcd_header = types.MethodType(_dcdmodule.__write_dcd_header, None, DCDWriter)
 DCDWriter._write_next_frame = types.MethodType(_dcdmodule.__write_next_frame, None, DCDWriter)
 DCDWriter._finish_dcd_write = types.MethodType(_dcdmodule.__finish_dcd_write, None, DCDWriter)
-
-#DCDReader._read_timeseries = types.MethodType(dcdtimeseries.__read_timeseries, None, DCDReader)
-DCDReader._read_timecorrel = types.MethodType(dcdtimeseries.__read_timecorrel, None, DCDReader)

package/MDAnalysis/coordinates/__init__.py

@@ -538,11 +538,6 @@ class can choose an appropriate reader automatically.
  ``timeseries(atomGroup, [start[,stop[,skip[,format]]]])``
      returns a subset of coordinate data
 
- ``correl(timeseriesCollection[,start[,stop[,skip]]])``
-     populate a :class:`MDAnalysis.core.Timeseries.TimeseriesCollection` object
-     with observable timeseries computed from the trajectory
-
-
 Attributes
 ..........