From 93b52b00a65d6acb24caf105ffa1881ea5c5afab Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Fri, 29 Jul 2016 10:53:31 -0700
Subject: [PATCH 01/28] Reformatting commit

---
 package/MDAnalysis/coordinates/src/dcd.c | 490 +++++++++++------------
 1 file changed, 235 insertions(+), 255 deletions(-)

diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 4b8b761a4af..dea24b6884a 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -63,12 +63,12 @@ __write_dcd_header(PyObject *self, PyObject *args)
     charmm |= DCD_HAS_EXTRA_BLOCK;
 
   if (! self) {
-    /* we were in fact called as a module function, try to retrieve 
+    /* we were in fact called as a module function, try to retrieve
        a matching object from args */
     if( !PyArg_ParseTuple(args, "Oi|iids", &self, &natoms, &istart, &nsavc, &delta, &remarks) )
       return NULL;
   } else {
-    /* we were obviously called as an object method so args should 
+    /* we were obviously called as an object method so args should
        only have the int value. */
     if( !PyArg_ParseTuple(args, "i|iids", &natoms, &istart, &nsavc, &delta, &remarks) )
       return NULL;
@@ -80,23 +80,23 @@ __write_dcd_header(PyObject *self, PyObject *args)
     PyErr_SetString(PyExc_AttributeError, "dcdfile is not an attribute");
     return NULL;
   }
-  
+
   if ((temp = PyObject_GetAttrString(self, "dcdfile")) == NULL) { // This gives me a New Reference
     // Raise exception
     PyErr_SetString(PyExc_AttributeError, "dcdfile is not an attribute");
     return NULL;
   }
-  
+
   if (!PyFile_CheckExact(temp)) {
     // Raise exception
     PyErr_SetString(PyExc_TypeError, "dcdfile does not refer to a file object");
     Py_DECREF(temp);
     return NULL;
   }
-  fd = fileno(PyFile_AsFile(temp)); 
+  fd = fileno(PyFile_AsFile(temp));
   // No longer need the reference to temp
   Py_DECREF(temp);
-  
+
   dcd = (dcdhandle *)malloc(sizeof(dcdhandle));
   memset(dcd, 0, sizeof(dcdhandle));
   dcd->fd = fd;
@@ -122,7 +122,7 @@ __write_dcd_header(PyObject *self, PyObject *args)
     return NULL;
   }
   Py_DECREF(temp);
-  
+
   // For debugging purposes
   temp = PyBuffer_FromMemory(dcd, sizeof(dcdhandle)); // Creates a New Reference
   if (PyObject_SetAttrString(self, "_dcd_C_str", temp) == -1) {
@@ -132,7 +132,7 @@ __write_dcd_header(PyObject *self, PyObject *args)
     return NULL;
   }
   Py_DECREF(temp);
-  
+
   Py_INCREF(Py_None);
   return Py_None;
 }
@@ -146,14 +146,14 @@ __write_next_frame(PyObject *self, PyObject *args)
   int rc, curstep;
   float* uc_array;
   double unitcell[6];
-	
+
   if (!self) {
-    /* we were in fact called as a module function, try to retrieve 
+    /* we were in fact called as a module function, try to retrieve
        a matching object from args */
     if( !PyArg_ParseTuple(args, "OO!O!O!O!", &self, &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc) )
       return NULL;
   } else {
-    /* we were obviously called as an object method so args should 
+    /* we were obviously called as an object method so args should
        only have the int value. */
     if( !PyArg_ParseTuple(args, "O!O!O!O!", &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc) )
       return NULL;
@@ -198,29 +198,29 @@ __finish_dcd_write(PyObject *self, PyObject *args)
   //PyObject* temp;
   //dcdhandle *dcd;
 
-  if (! self) { 
-    /* we were in fact called as a module function, try to retrieve 
+  if (! self) {
+    /* we were in fact called as a module function, try to retrieve
        a matching object from args */
     if( !PyArg_ParseTuple(args, "O", &self) )
       return NULL;
-  } else { 
-    /* we were obviously called as an object method so args should 
+  } else {
+    /* we were obviously called as an object method so args should
        only have the int value. */
     if( !PyArg_ParseTuple(args, "") )
-      return NULL; 
-  } 
+      return NULL;
+  }
 
   /*if ( !PyObject_HasAttrString(self, "_dcd_C_ptr") ) {
   // Raise exception
   PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
   return NULL;
   }
-  
+
   if ((temp = PyObject_GetAttrString(self, "_dcd_C_ptr")) == NULL) { // This gives me a New Reference
   // Raise exception
   PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
   return NULL;
-  } 
+  }
   dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
   free(dcd);
   Py_DECREF(temp);*/
@@ -250,16 +250,16 @@ __read_dcd_header(PyObject *self, PyObject *args)
   dcdhandle *dcd = NULL;
 
   if (! self) {
-    /* we were in fact called as a module function, try to retrieve 
-       a matching object from args */ 
-    if( !PyArg_ParseTuple(args, "O", &self) ) 
-      return NULL; 
-  } else { 
-    /* we were obviously called as an object method so args should 
-       only have the int value. */ 
-    if( !PyArg_ParseTuple(args, "") ) 
-      return NULL; 
-  } 
+    /* we were in fact called as a module function, try to retrieve
+       a matching object from args */
+    if( !PyArg_ParseTuple(args, "O", &self) )
+      return NULL;
+  } else {
+    /* we were obviously called as an object method so args should
+       only have the int value. */
+    if( !PyArg_ParseTuple(args, "") )
+      return NULL;
+  }
 
   // Get the file object from the class
   if (!PyObject_HasAttrString(self, "dcdfile")) {
@@ -273,7 +273,7 @@ __read_dcd_header(PyObject *self, PyObject *args)
     PyErr_SetString(PyExc_AttributeError, "dcdfile is not an attribute");
     return NULL;
   }
-	
+
   if (!PyFile_CheckExact(temp)) {
     // Raise exception
     PyErr_SetString(PyExc_TypeError, "dcdfile does not refer to a file object");
@@ -282,7 +282,7 @@ __read_dcd_header(PyObject *self, PyObject *args)
   fd = fileno(PyFile_AsFile(temp));
   // No longer need the reference to temp
   Py_DECREF(temp);
-	
+
   dcd = (dcdhandle *)malloc(sizeof(dcdhandle));
   memset(dcd, 0, sizeof(dcdhandle));
   dcd->fd = fd;
@@ -295,7 +295,7 @@ __read_dcd_header(PyObject *self, PyObject *args)
     goto error;
   }
 
-  /* 
+  /*
    * Check that the file is big enough to really hold all the frames it claims to have
    */
   {
@@ -319,8 +319,8 @@ __read_dcd_header(PyObject *self, PyObject *args)
     // Size of header
     dcd->header_size = fio_ftell(dcd->fd);
 
-    /* 
-     * It's safe to use ftell, even though ftell returns a long, because the 
+    /*
+     * It's safe to use ftell, even though ftell returns a long, because the
      * header size is < 4GB.
      */
     filesize = stbuf.st_size - fio_ftell(dcd->fd) - firstframesize;
@@ -384,7 +384,7 @@ __read_dcd_header(PyObject *self, PyObject *args)
     goto error;
   }
   Py_DECREF(temp);
-	
+
   temp = PyCObject_FromVoidPtr(dcd, NULL);
   if (temp == NULL) goto error;
   if (PyObject_SetAttrString(self, "_dcd_C_ptr", temp) == -1) {
@@ -404,7 +404,7 @@ __read_dcd_header(PyObject *self, PyObject *args)
     goto error;
   }
   Py_DECREF(temp);
-	
+
   // For debugging purposes
   temp = PyBuffer_FromMemory(dcd, sizeof(dcdhandle));
   if (temp == NULL) goto error;
@@ -427,212 +427,193 @@ __read_dcd_header(PyObject *self, PyObject *args)
 static PyObject *
 __read_timeseries(PyObject *self, PyObject *args)
 {
-  PyObject *temp = NULL;
-  PyArrayObject *coord = NULL;
-  PyListObject *atoms = NULL;
-  int lowerb = 0, upperb = 0, range=0;
-  float *tempX = NULL, *tempY = NULL, *tempZ = NULL;
-  int rc;
-  int i, j, index;
-  int n_atoms = 0, n_frames = 0;
-  int start = 0, stop = -1, skip = 1, numskip = 0;
-  dcdhandle *dcd = NULL;
-  int *atomlist = NULL;
-  npy_intp dimensions[3];
-  float unitcell[6];
-  const char* format = "afc";
-	
-  if (!self) {
-    /* we were in fact called as a module function, try to retrieve 
-       a matching object from args */
-    if( !PyArg_ParseTuple(args, "OO!|iiis", &self, &PyList_Type, &atoms, &start, &stop, &skip, &format) )
-      return NULL; 
-  } else {
-    /* we were obviously called as an object method so args should 
-       only have the int value. */
-    if( !PyArg_ParseTuple(args, "O!|iiis", &PyList_Type, &atoms, &start, &stop, &skip, &format) )
+   PyObject *temp = NULL;
+   PyArrayObject *coord = NULL;
+   PyListObject *atoms = NULL;
+   int lowerb = 0, upperb = 0, range=0;
+   float *tempX = NULL, *tempY = NULL, *tempZ = NULL;
+   int rc;
+   int i, j, index;
+   int n_atoms = 0, n_frames = 0;
+   int start = 0, stop = -1, skip = 1, numskip = 0;
+   dcdhandle *dcd = NULL;
+   int *atomlist = NULL;
+   npy_intp dimensions[3];
+   float unitcell[6];
+   const char* format = "afc";
+
+   if (!self) {
+      /* we were in fact called as a module function, try to retrieve
+      a matching object from args */
+      if( !PyArg_ParseTuple(args, "OO!|iiis", &self, &PyList_Type, &atoms, &start, &stop, &skip, &format) )
       return NULL;
-  }
-
-  if ((temp = PyObject_GetAttrString(self, "_dcd_C_ptr")) == NULL) { // This gives me a New Reference
-    // Raise exception
-    PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
-    return NULL;
-  }
+   } else {
+      /* we were obviously called as an object method so args should
+      only have the int value. */
+      if( !PyArg_ParseTuple(args, "O!|iiis", &PyList_Type, &atoms, &start, &stop, &skip, &format) )
+      return NULL;
+   }
 
-  dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
-  Py_DECREF(temp);
+   if ((temp = PyObject_GetAttrString(self, "_dcd_C_ptr")) == NULL) { // This gives me a New Reference
+      // Raise exception
+      PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
+      return NULL;
+   }
+
+   dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
+   Py_DECREF(temp);
+
+   // Assume that start and stop are valid
+   if (stop == -1) { stop = dcd->nsets; }
+   n_frames = (stop-start+1) / skip;
+   //n_frames = dcd->nsets / skip;
+   n_atoms = PyList_Size((PyObject*)atoms);
+   if (n_atoms == 0) {
+      PyErr_SetString(PyExc_Exception, "No atoms passed into _read_timeseries function");
+      return NULL;
+   }
+   atomlist = (int*)malloc(sizeof(int)*n_atoms);
+   memset(atomlist, 0, sizeof(int)*n_atoms);
+
+   // Get the atom indexes
+   for (i=0;i<n_atoms;i++) {
+      temp = PyList_GetItem((PyObject*)atoms, i); // Borrowed Reference
+      if (temp==NULL) goto error;
+      // Make sure temp is an integer
+      /* TODO: this is not the proper check but [OB] cannot figure out how
+      to check if this is a numpy.int64 or similar; PyInt_Check would fail
+      on those (Issue 18)
+      */
+      if (!PyArray_IsAnyScalar((PyObject*)temp)) {
+         PyErr_SetString(PyExc_ValueError, "Atom number is not an integer");
+         goto error;
+      }
+      atomlist[i] = PyInt_AsLong(temp);
+   }
 
-  // Assume that start and stop are valid
-  if (stop == -1) { stop = dcd->nsets; }
-  n_frames = (stop-start+1) / skip;
-  //n_frames = dcd->nsets / skip;
-  n_atoms = PyList_Size((PyObject*)atoms);
-  if (n_atoms == 0) {
-    PyErr_SetString(PyExc_Exception, "No atoms passed into _read_timeseries function");
-    return NULL;
-  }
-  atomlist = (int*)malloc(sizeof(int)*n_atoms);
-  memset(atomlist, 0, sizeof(int)*n_atoms);
-
-  // Get the atom indexes
-  for (i=0;i<n_atoms;i++) {
-    temp = PyList_GetItem((PyObject*)atoms, i); // Borrowed Reference
-    if (temp==NULL) goto error;
-    // Make sure temp is an integer
-    /* TODO: this is not the proper check but [OB] cannot figure out how
-       to check if this is a numpy.int64 or similar; PyInt_Check would fail
-       on those (Issue 18)
-    */
-    if (!PyArray_IsAnyScalar((PyObject*)temp)) {
-      PyErr_SetString(PyExc_ValueError, "Atom number is not an integer");
-      goto error;
-    }
-    atomlist[i] = PyInt_AsLong(temp);
-  }
+   lowerb = atomlist[0]; upperb = atomlist[n_atoms-1];
+   range = upperb-lowerb+1;
 
-  lowerb = atomlist[0]; upperb = atomlist[n_atoms-1];
-  range = upperb-lowerb+1;
-	
-  // Figure out the format string
-  if (strncasecmp(format, "afc", 3) == 0) {
-    dimensions[0] = n_atoms; dimensions[1] = n_frames; dimensions[2] = 3;
-  } else
-    if (strncasecmp(format, "acf", 3) == 0) {
+   // Figure out the format string
+   if (strncasecmp(format, "afc", 3) == 0) {
+      dimensions[0] = n_atoms; dimensions[1] = n_frames; dimensions[2] = 3;
+   } else
+   if (strncasecmp(format, "acf", 3) == 0) {
       dimensions[0] = n_atoms; dimensions[1] = 3; dimensions[2] = n_frames;
-    } else
-      if (strncasecmp(format, "fac", 3) == 0) {
-	dimensions[0] = n_frames; dimensions[1] = n_atoms; dimensions[2] = 3;
-      } else
-	if (strncasecmp(format, "fca", 3) == 0) {
-	  dimensions[0] = n_frames; dimensions[1] = 3; dimensions[2] = n_atoms;
-	} else
-	  if (strncasecmp(format, "caf", 3) == 0) {
-	    dimensions[0] = 3; dimensions[1] = n_atoms; dimensions[2] = n_frames;
-	  } else
-	    if (strncasecmp(format, "cfa", 3) == 0) {
-	      dimensions[0] = 3; dimensions[1] = n_frames; dimensions[2] = n_atoms;
-	    }
-	
-  coord = (PyArrayObject*) PyArray_SimpleNew(3, dimensions, NPY_DOUBLE);
-  if (coord == NULL) goto error;
-
-  // Reset trajectory
-  rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
-  dcd->setsread = 0;
-  dcd->first = 1;
+   } else
+   if (strncasecmp(format, "fac", 3) == 0) {
+      dimensions[0] = n_frames; dimensions[1] = n_atoms; dimensions[2] = 3;
+   } else
+   if (strncasecmp(format, "fca", 3) == 0) {
+      dimensions[0] = n_frames; dimensions[1] = 3; dimensions[2] = n_atoms;
+   } else
+   if (strncasecmp(format, "caf", 3) == 0) {
+      dimensions[0] = 3; dimensions[1] = n_atoms; dimensions[2] = n_frames;
+   } else
+   if (strncasecmp(format, "cfa", 3) == 0) {
+      dimensions[0] = 3; dimensions[1] = n_frames; dimensions[2] = n_atoms;
+   }
+
+   coord = (PyArrayObject*) PyArray_SimpleNew(3, dimensions, NPY_DOUBLE);
+   if (coord == NULL) goto error;
+
+   // Reset trajectory
+   rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
+   dcd->setsread = 0;
+   dcd->first = 1;
+
+   // Jump to starting frame
+   jump_to_frame(dcd, start);
+
+   // Now read through trajectory and get the atom pos
+   tempX = (float*)malloc(sizeof(float)*range);
+   tempY = (float*)malloc(sizeof(float)*range);
+   tempZ = (float*)malloc(sizeof(float)*range);
+   if ((tempX == NULL) | (tempY == NULL) || (tempZ == NULL)) {
+      PyErr_SetString(PyExc_MemoryError, "Can't allocate temporary space for coordinate arrays");
+      goto error;
+   }
 
-  // Jump to starting frame
-  jump_to_frame(dcd, start);
-	
-  // Now read through trajectory and get the atom pos
-  tempX = (float*)malloc(sizeof(float)*range);
-  tempY = (float*)malloc(sizeof(float)*range);
-  tempZ = (float*)malloc(sizeof(float)*range);
-  if ((tempX == NULL) | (tempY == NULL) || (tempZ == NULL)) {
-    PyErr_SetString(PyExc_MemoryError, "Can't allocate temporary space for coordinate arrays");
-    goto error;
-  }
-	
-  for (i=0;i<n_frames;i++)
-    {
+   for (i=0;i<n_frames;i++)
+   {
       if (skip > 1) {
-	/*if (dcd->first && dcd->nfixed) {
-	  rc = read_dcdsubset(dcd->fd, dcd->natoms, lowerb, upperb, tempX, tempY, tempZ,
-	  unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
-	  dcd->reverse, dcd->charmm);
-	  dcd->first=0;
-	  if (rc < 0) {
-          // return an exception
-          PyErr_SetString(PyExc_IOError, "Error reading first frame from DCD file");
-          //fprintf(stderr, "read_dcdstep returned %d\n", rc);
-          return NULL;
-          //return MOLFILE_ERROR;
-	  }
-	  dcd->setsread++;
-	  }*/
-	// Figure out how many steps to skip
-	numskip = skip - (dcd->setsread % skip) - 1;
-	rc = skip_dcdstep(dcd->fd, dcd->natoms, dcd->nfixed, dcd->charmm, numskip);
-    	if (rc < 0) {
-	  // return an exception
-	  PyErr_SetString(PyExc_IOError, "Error skipping frame from DCD file");
-	  goto error;
-    	}
-    	dcd->setsread+=numskip;                                                                              
+         // Figure out how many steps to skip
+         numskip = skip - (dcd->setsread % skip) - 1;
+         rc = skip_dcdstep(dcd->fd, dcd->natoms, dcd->nfixed, dcd->charmm, numskip);
+         if (rc < 0) {
+            // return an exception
+            PyErr_SetString(PyExc_IOError, "Error skipping frame from DCD file");
+            goto error;
+         }
+         dcd->setsread+=numskip;
       }
       rc = read_dcdsubset(dcd->fd, dcd->natoms, lowerb, upperb, tempX, tempY, tempZ,
-			  unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
-			  dcd->reverse, dcd->charmm);
+         unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
+         dcd->reverse, dcd->charmm);
       dcd->first = 0;
       dcd->setsread++;
       if (rc < 0) {
-    	// return an exception
-    	PyErr_SetString(PyExc_IOError, "Error reading frame from DCD file");
-    	goto error;
+         // return an exception
+         PyErr_SetString(PyExc_IOError, "Error reading frame from DCD file");
+         goto error;
       }
       // Copy into Numeric array only those atoms we are interested in
       for (j=0;j<n_atoms;j++) {
-	index = atomlist[j]-lowerb;
-	/* 
-	 * coord[a][b][c] = *(float*)(coord->data + a*coord->strides[0] + b*coord->strides[1] + c*coord->strides[2])
-	 */
-	if (strncasecmp(format, "afc", 3) == 0) {
-	  *(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 0*coord->strides[2]) = tempX[index];
-	  *(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 1*coord->strides[2]) = tempY[index];
-	  *(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 2*coord->strides[2]) = tempZ[index];
-	} else
-	  if (strncasecmp(format, "acf", 3) == 0) {
-	    *(double*)(coord->data + j*coord->strides[0] + 0*coord->strides[1] + i*coord->strides[2]) = tempX[index];
-	    *(double*)(coord->data + j*coord->strides[0] + 1*coord->strides[1] + i*coord->strides[2]) = tempY[index];
-	    *(double*)(coord->data + j*coord->strides[0] + 2*coord->strides[1] + i*coord->strides[2]) = tempZ[index];
-	  } else
-	    if (strncasecmp(format, "fac", 3) == 0) {
-	      *(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 0*coord->strides[2]) = tempX[index];
-	      *(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 1*coord->strides[2]) = tempY[index];
-	      *(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 2*coord->strides[2]) = tempZ[index];
-	    } else
-	      if (strncasecmp(format, "fca", 3) == 0) {
-		*(double*)(coord->data + i*coord->strides[0] + 0*coord->strides[1] + j*coord->strides[2]) = tempX[index];
-		*(double*)(coord->data + i*coord->strides[0] + 1*coord->strides[1] + j*coord->strides[2]) = tempY[index];
-		*(double*)(coord->data + i*coord->strides[0] + 2*coord->strides[1] + j*coord->strides[2]) = tempZ[index];
-	      } else
-  		if (strncasecmp(format, "caf", 3) == 0) {
-		  *(double*)(coord->data + 0*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempX[index];
-		  *(double*)(coord->data + 1*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempY[index];
-		  *(double*)(coord->data + 2*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempZ[index];
-  		} else
-		  if (strncasecmp(format, "cfa", 3) == 0) {
-		    *(double*)(coord->data + 0*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempX[index];
-		    *(double*)(coord->data + 1*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempY[index];
-		    *(double*)(coord->data + 2*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempZ[index];
-		  }
+         index = atomlist[j]-lowerb;
+         /*
+         * coord[a][b][c] = *(float*)(coord->data + a*coord->strides[0] + b*coord->strides[1] + c*coord->strides[2])
+         */
+         if (strncasecmp(format, "afc", 3) == 0) {
+            *(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 0*coord->strides[2]) = tempX[index];
+            *(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 1*coord->strides[2]) = tempY[index];
+            *(double*)(coord->data + j*coord->strides[0] + i*coord->strides[1] + 2*coord->strides[2]) = tempZ[index];
+         } else if (strncasecmp(format, "acf", 3) == 0) {
+            *(double*)(coord->data + j*coord->strides[0] + 0*coord->strides[1] + i*coord->strides[2]) = tempX[index];
+            *(double*)(coord->data + j*coord->strides[0] + 1*coord->strides[1] + i*coord->strides[2]) = tempY[index];
+            *(double*)(coord->data + j*coord->strides[0] + 2*coord->strides[1] + i*coord->strides[2]) = tempZ[index];
+         } else if (strncasecmp(format, "fac", 3) == 0) {
+            *(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 0*coord->strides[2]) = tempX[index];
+            *(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 1*coord->strides[2]) = tempY[index];
+            *(double*)(coord->data + i*coord->strides[0] + j*coord->strides[1] + 2*coord->strides[2]) = tempZ[index];
+         } else if (strncasecmp(format, "fca", 3) == 0) {
+            *(double*)(coord->data + i*coord->strides[0] + 0*coord->strides[1] + j*coord->strides[2]) = tempX[index];
+            *(double*)(coord->data + i*coord->strides[0] + 1*coord->strides[1] + j*coord->strides[2]) = tempY[index];
+            *(double*)(coord->data + i*coord->strides[0] + 2*coord->strides[1] + j*coord->strides[2]) = tempZ[index];
+         } else if (strncasecmp(format, "caf", 3) == 0) {
+            *(double*)(coord->data + 0*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempX[index];
+            *(double*)(coord->data + 1*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempY[index];
+            *(double*)(coord->data + 2*coord->strides[0] + j*coord->strides[1] + i*coord->strides[2]) = tempZ[index];
+         } else if (strncasecmp(format, "cfa", 3) == 0) {
+            *(double*)(coord->data + 0*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempX[index];
+            *(double*)(coord->data + 1*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempY[index];
+            *(double*)(coord->data + 2*coord->strides[0] + i*coord->strides[1] + j*coord->strides[2]) = tempZ[index];
+         }
       }
       // Check if we've been interupted by the user
       if (PyErr_CheckSignals() == 1) goto error;
-    }
-
-  // Reset trajectory
-  rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
-  dcd->setsread = 0;
-  dcd->first = 1;	
-  free(atomlist);
-  free(tempX);
-  free(tempY);
-  free(tempZ);
-  return PyArray_Return(coord);
-
- error:
-  // Reset trajectory
-  rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
-  dcd->setsread = 0;
-  dcd->first = 1;	
-  Py_XDECREF(coord);
-  if (atomlist != NULL) free(atomlist);
-  if (tempX != NULL) free(tempX);
-  if (tempY != NULL) free(tempY);
-  if (tempZ != NULL) free(tempZ);
-  return NULL;
+   }
+
+   // Reset trajectory
+   rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
+   dcd->setsread = 0;
+   dcd->first = 1;
+   free(atomlist);
+   free(tempX);
+   free(tempY);
+   free(tempZ);
+   return PyArray_Return(coord);
+
+   error:
+   // Reset trajectory
+   rc = fio_fseek(dcd->fd, dcd->header_size, FIO_SEEK_SET);
+   dcd->setsread = 0;
+   dcd->first = 1;
+   Py_XDECREF(coord);
+   if (atomlist != NULL) free(atomlist);
+   if (tempX != NULL) free(tempX);
+   if (tempY != NULL) free(tempY);
+   if (tempZ != NULL) free(tempZ);
+   return NULL;
 }
 
 static PyObject *
@@ -645,16 +626,16 @@ __read_next_frame(PyObject *self, PyObject *args)
   int rc,numskip;
   float* unitcell;
   float alpha, beta, gamma;
-	
+
   if (!self) {
-    /* we were in fact called as a module function, try to retrieve 
+    /* we were in fact called as a module function, try to retrieve
        a matching object from args */
     if( !PyArg_ParseTuple(args, "OO!O!O!O!|i", &self, &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc, &skip) )
-      return NULL; 
+      return NULL;
   } else {
-    /* we were obviously called as an object method so args should 
+    /* we were obviously called as an object method so args should
        only have the int value. */
-    if( !PyArg_ParseTuple(args, "O!O!O!O!|i", &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc, &skip) ) 
+    if( !PyArg_ParseTuple(args, "O!O!O!O!|i", &PyArray_Type, &x, &PyArray_Type, &y, &PyArray_Type, &z, &PyArray_Type, &uc, &skip) )
       return NULL;
   }
 
@@ -669,7 +650,7 @@ __read_next_frame(PyObject *self, PyObject *args)
 
   unitcell = (float*) uc->data;
   unitcell[0] = unitcell[2] = unitcell[5] = 0.0f;
-  unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;                                                                     
+  unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;
 
   /* Check for EOF here; that way all EOF's encountered later must be errors */
   if (dcd->setsread == dcd->nsets) {
@@ -722,7 +703,7 @@ __read_next_frame(PyObject *self, PyObject *args)
     //fprintf(stderr, "read_dcdstep returned %d\n", rc);
     return NULL;
     //return MOLFILE_ERROR;
-  }                                                                                            
+  }
 
   if (unitcell[1] >= -1.0 && unitcell[1] <= 1.0 &&
       unitcell[3] >= -1.0 && unitcell[3] <= 1.0 &&
@@ -746,7 +727,7 @@ __read_next_frame(PyObject *self, PyObject *args)
   unitcell[4] = alpha;
   unitcell[3] = beta;
   unitcell[1] = gamma;
-	
+
   // Return the frame read
   temp = Py_BuildValue("i", dcd->setsread);
   return temp;
@@ -759,17 +740,17 @@ __finish_dcd_read(PyObject *self, PyObject *args)
   dcdhandle *dcd;
 
   if (! self) {
-    /* we were in fact called as a module function, try to retrieve 
-       a matching object from args */ 
+    /* we were in fact called as a module function, try to retrieve
+       a matching object from args */
     if( !PyArg_ParseTuple(args, "O", &self) )
-      return NULL; 
-  } else { 
-    /* we were obviously called as an object method so args should 
-       only have the int value. */ 
+      return NULL;
+  } else {
+    /* we were obviously called as an object method so args should
+       only have the int value. */
     if( !PyArg_ParseTuple(args, "") )
-      return NULL; 
+      return NULL;
   }
- 
+
   if ( !PyObject_HasAttrString(self, "_dcd_C_ptr") ) {
     // Raise exception
     PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
@@ -783,13 +764,13 @@ __finish_dcd_read(PyObject *self, PyObject *args)
   }
 
   dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
-	
+
   close_dcd_read(dcd->freeind, dcd->fixedcoords);
   free(dcd);
   Py_DECREF(temp);
   Py_INCREF(Py_None);
   return Py_None;
-}                                                                                                                      
+}
 int jump_to_frame(dcdhandle *dcd, int frame)
 {
   int rc;
@@ -828,23 +809,23 @@ __jump_to_frame(PyObject *self, PyObject *args)
   int frame;
 
   if (! self) {
-    /* we were in fact called as a module function, try to retrieve 
+    /* we were in fact called as a module function, try to retrieve
        a matching object from args */
     if( !PyArg_ParseTuple(args, "Oi", &self, &frame) )
       return NULL;
   } else {
-    /* we were obviously called as an object method so args should 
+    /* we were obviously called as an object method so args should
        only have the int value. */
     if( !PyArg_ParseTuple(args, "i", &frame) )
       return NULL;
-  }             
-  
+  }
+
   if ( !PyObject_HasAttrString(self, "_dcd_C_ptr") ) {
     // Raise exception
     PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
     return NULL;
-  } 
-  
+  }
+
   if ((temp = PyObject_GetAttrString(self, "_dcd_C_ptr")) == NULL) { // This gives me a New Reference
     // Raise exception
     PyErr_SetString(PyExc_AttributeError, "_dcd_C_ptr is not an attribute");
@@ -852,7 +833,7 @@ __jump_to_frame(PyObject *self, PyObject *args)
   }
   dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
   Py_DECREF(temp);
-	
+
   /*if (frame > dcd->nsets) {
     PyErr_SetString(PyExc_IndexError, "Invalid frame");
     return NULL;
@@ -865,7 +846,7 @@ __jump_to_frame(PyObject *self, PyObject *args)
     extrablocksize = dcd->charmm & DCD_HAS_EXTRA_BLOCK ? 48 + 8 : 0;
     ndims = dcd->charmm & DCD_HAS_4DIMS ? 4 : 3;
     firstframesize = (dcd->natoms+2) * ndims * sizeof(float) + extrablocksize;
-    framesize = (dcd->natoms-dcd->nfixed+2) * ndims * sizeof(float) 
+    framesize = (dcd->natoms-dcd->nfixed+2) * ndims * sizeof(float)
     + extrablocksize;
     // Use zero indexing
     if (frame == 0) {
@@ -890,18 +871,18 @@ __reset_dcd_read(PyObject *self, PyObject *args)
   PyObject* temp;
   dcdhandle *dcd;
   int rc;
-	
+
   if (! self) {
-    /* we were in fact called as a module function, try to retrieve 
+    /* we were in fact called as a module function, try to retrieve
        a matching object from args */
     if( !PyArg_ParseTuple(args, "O", &self) )
       return NULL;
   } else {
-    /* we were obviously called as an object method so args should 
+    /* we were obviously called as an object method so args should
        only have the int value. */
     if( !PyArg_ParseTuple(args, "") )
       return NULL;
-  }                                                                                                                    
+  }
 
   if ( !PyObject_HasAttrString(self, "_dcd_C_ptr") ) {
     // Raise exception
@@ -943,4 +924,3 @@ init_dcdmodule(void)
   (void) Py_InitModule("_dcdmodule", DCDMethods);
   import_array();
 }
-

From 9a58b1b802e7411618370c31158cd185ef7bb0e7 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Tue, 26 Jul 2016 17:13:27 -0700
Subject: [PATCH 02/28] RMSF fix

---
 package/MDAnalysis/analysis/rms.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/analysis/rms.py b/package/MDAnalysis/analysis/rms.py
index f644bf63a6e..c6170938d1e 100644
--- a/package/MDAnalysis/analysis/rms.py
+++ b/package/MDAnalysis/analysis/rms.py
@@ -556,7 +556,7 @@ def __init__(self, atomgroup):
         self.atomgroup = atomgroup
         self._rmsf = None
 
-    def run(self, start=0, stop=-1, step=1, progout=10, quiet=False):
+    def run(self, start=None, stop=None, step=None, progout=10, quiet=False):
         """Calculate RMSF of given atoms across a trajectory.
 
         This method implements an algorithm for computing sums of squares while
@@ -565,11 +565,11 @@ def run(self, start=0, stop=-1, step=1, progout=10, quiet=False):
         Parameters
         ----------
         start : int (optional)
-            starting frame [0]
+            starting frame, default None becomes 0.
         stop : int (optional)
-            stopping frame [-1]
+            stopping frame, default None becomes n_frames.
         step : int (optional)
-            step between frames [1]
+            step between frames, default None becomes 1.
         progout : int (optional)
             number of frames to iterate through between updates to progress
             output; ``None`` for no updates [10]
@@ -583,6 +583,9 @@ def run(self, start=0, stop=-1, step=1, progout=10, quiet=False):
            Calculating Corrected Sums of Squares and Products." Technometrics
            4(3):419-420.
         """
+        start, stop, step = self.atomgroup.universe.check_slice_indices(start,
+                                                                        stop,
+                                                                        step)
         sumsquares = np.zeros((self.atomgroup.n_atoms, 3))
         means = np.array(sumsquares)
 

From 814542109f200125d3055f775103b84e203ee9a4 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Tue, 26 Jul 2016 17:24:12 -0700
Subject: [PATCH 03/28] Fixed DCD defaults and documentation.

---
 package/MDAnalysis/coordinates/DCD.py  | 18 ++++++++++--------
 package/MDAnalysis/coordinates/base.py |  2 +-
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py
index a61c2db42e8..47acfd1a740 100644
--- a/package/MDAnalysis/coordinates/DCD.py
+++ b/package/MDAnalysis/coordinates/DCD.py
@@ -498,14 +498,15 @@ def _read_frame(self, frame):
         ts.frame = frame
         return ts
 
-    def timeseries(self, asel, start=0, stop=-1, skip=1, format='afc'):
+    def timeseries(self, asel, start=None, stop=None, step=None, format='afc'):
         """Return a subset of coordinate data for an AtomGroup
 
         :Arguments:
             *asel*
                :class:`~MDAnalysis.core.AtomGroup.AtomGroup` object
-            *start, stop, skip*
-               range of trajectory to access, start and stop are inclusive
+            *start, stop, step*
+               A range of the trajectory to access, with start being inclusive
+               and stop being exclusive.
             *format*
                the order/shape of the return data array, corresponding
                to (a)tom, (f)rame, (c)oordinates all six combinations
@@ -513,7 +514,7 @@ def timeseries(self, asel, start=0, stop=-1, skip=1, format='afc'):
                where the shape is (frame, number of atoms,
                coordinates)
         """
-        start, stop, skip = self.check_slice_indices(start, stop, skip)
+        start, stop, skip = self.check_slice_indices(start, stop, step)
         if len(asel) == 0:
             raise NoDataError("Timeseries requires at least one atom to analyze")
         if len(format) != 3 and format not in ['afc', 'acf', 'caf', 'cfa', 'fac', 'fca']:
@@ -524,16 +525,17 @@ def timeseries(self, asel, start=0, stop=-1, skip=1, format='afc'):
         # XXX needs to be implemented
         return self._read_timeseries(atom_numbers, start, stop, skip, format)
 
-    def correl(self, timeseries, start=0, stop=-1, skip=1):
+    def correl(self, timeseries, start=None, stop=None, skip=None):
         """Populate a TimeseriesCollection object with timeseries computed from the trajectory
 
         :Arguments:
             *timeseries*
                :class:`MDAnalysis.core.Timeseries.TimeseriesCollection`
-            *start, stop, skip*
-               subset of trajectory to use, with start and stop being inclusive
+            *start, stop, step*
+               A subset of the trajectory to use, with start being inclusive
+               and stop being exclusive.
         """
-        start, stop, skip = self.check_slice_indices(start, stop, skip)
+        start, stop, step = self.check_slice_indices(start, stop, step)
         atomlist = timeseries._getAtomList()
         format = timeseries._getFormat()
         lowerb, upperb = timeseries._getBounds()
diff --git a/package/MDAnalysis/coordinates/base.py b/package/MDAnalysis/coordinates/base.py
index 6723237098d..16eb08bfba8 100644
--- a/package/MDAnalysis/coordinates/base.py
+++ b/package/MDAnalysis/coordinates/base.py
@@ -1230,7 +1230,7 @@ def check_slice_indices(self, start, stop, step):
         ----------
         start, stop, step : int or None
           Values representing the slice indices.
-          Can use `None` to use defaults of (0, -1, and 1)
+          Can use `None` to use defaults of (0, n_frames, and 1)
           respectively.
 
         Returns

From 0649737a6780e9725c7f1d71297d275cc2bbeb1f Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Tue, 26 Jul 2016 17:35:06 -0700
Subject: [PATCH 04/28] Fixed analysis docs

---
 package/MDAnalysis/analysis/contacts.py     | 7 ++++---
 package/MDAnalysis/analysis/diffusionmap.py | 7 ++++---
 package/MDAnalysis/analysis/polymer.py      | 8 +++++---
 package/MDAnalysis/analysis/rms.py          | 3 ++-
 4 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/package/MDAnalysis/analysis/contacts.py b/package/MDAnalysis/analysis/contacts.py
index b8b5bbf00ff..6c03381ebcb 100644
--- a/package/MDAnalysis/analysis/contacts.py
+++ b/package/MDAnalysis/analysis/contacts.py
@@ -396,11 +396,12 @@ def __init__(self, u, selection, refgroup, method="hard_cut", radius=4.5,
             dictionary of additional kwargs passed to `method`. Check
             respective functions for reasonable values.
         start : int, optional
-            First frame of trajectory to analyse, Default: 0
+            First frame of trajectory to analyse, Default: None becomes 0.
         stop : int, optional
-            Last frame of trajectory to analyse, Default: -1
+            Frame index to stop analysis. Default: None becomes
+            n_frames. Iteration stops *before* this frame number.
         step : int, optional
-            Step between frames to analyse, Default: 1
+            Step between frames to analyse, Default: None becomes 1.
 
         """
         self.u = u
diff --git a/package/MDAnalysis/analysis/diffusionmap.py b/package/MDAnalysis/analysis/diffusionmap.py
index a4337b50fcc..b42be7f044f 100644
--- a/package/MDAnalysis/analysis/diffusionmap.py
+++ b/package/MDAnalysis/analysis/diffusionmap.py
@@ -227,11 +227,12 @@ def __init__(self, u, select='all', metric=rmsd, cutoff=1E0-5,
         weights : array, optional
             Weights to be given to coordinates for metric calculation
         start : int, optional
-            First frame of trajectory to analyse, Default: 0
+            First frame of trajectory to analyse, Default: None becomes 0.
         stop : int, optional
-            Last frame of trajectory to analyse, Default: -1
+            Frame index to stop analysis. Default: None becomes
+            n_frames. Iteration stops *before* this frame number.
         step : int, optional
-            Step between frames to analyse, Default: 1
+            Step between frames to analyse, Default: None becomes 1.
         """
         self._u = u
         traj = self._u.trajectory
diff --git a/package/MDAnalysis/analysis/polymer.py b/package/MDAnalysis/analysis/polymer.py
index 53e3044f40d..ce826f80b2d 100644
--- a/package/MDAnalysis/analysis/polymer.py
+++ b/package/MDAnalysis/analysis/polymer.py
@@ -59,11 +59,13 @@ def __init__(self, atomgroups, **kwargs):
             List of atomgroups.  Each atomgroup should represent a single
             polymer chain, ordered in the correct order.
         start : int, optional
-            First frame of trajectory to analyse, Default: 0
+            First frame of trajectory to analyse, Default: None becomes 0.
         stop : int, optional
-            Last frame of trajectory to analyse, Default: -1
+            Last frame of trajectory to analyse, Default: None becomes
+            n_frames.
         step : int, optional
-            Step between frames to analyse, Default: 1
+            Frame index to stop analysis. Default: None becomes
+            n_frames. Iteration stops *before* this frame number.
         """
         super(PersistenceLength, self).__init__(
             atomgroups[0].universe.trajectory, **kwargs)
diff --git a/package/MDAnalysis/analysis/rms.py b/package/MDAnalysis/analysis/rms.py
index c6170938d1e..f7227b620a8 100644
--- a/package/MDAnalysis/analysis/rms.py
+++ b/package/MDAnalysis/analysis/rms.py
@@ -567,7 +567,8 @@ def run(self, start=None, stop=None, step=None, progout=10, quiet=False):
         start : int (optional)
             starting frame, default None becomes 0.
         stop : int (optional)
-            stopping frame, default None becomes n_frames.
+            Frame index to stop analysis. Default: None becomes
+            n_frames. Iteration stops *before* this frame number.
         step : int (optional)
             step between frames, default None becomes 1.
         progout : int (optional)

From 9e7d439bde51cdb42190db70ae6cd95b1531ec4e Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Tue, 26 Jul 2016 17:40:25 -0700
Subject: [PATCH 05/28] Check_slice index fix

---
 package/MDAnalysis/analysis/rms.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/analysis/rms.py b/package/MDAnalysis/analysis/rms.py
index f7227b620a8..26be0ba8e13 100644
--- a/package/MDAnalysis/analysis/rms.py
+++ b/package/MDAnalysis/analysis/rms.py
@@ -584,9 +584,8 @@ def run(self, start=None, stop=None, step=None, progout=10, quiet=False):
            Calculating Corrected Sums of Squares and Products." Technometrics
            4(3):419-420.
         """
-        start, stop, step = self.atomgroup.universe.check_slice_indices(start,
-                                                                        stop,
-                                                                        step)
+        traj = self.atomgroup.universe.trajectory
+        start, stop, step = traj.check_slice_indices(start, stop, step)
         sumsquares = np.zeros((self.atomgroup.n_atoms, 3))
         means = np.array(sumsquares)
 

From e9b65862e4b17d10ec037fe22130a4d0a6475d62 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Tue, 26 Jul 2016 17:49:04 -0700
Subject: [PATCH 06/28] DCD fix

---
 package/MDAnalysis/coordinates/DCD.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py
index 47acfd1a740..98bfdb6c8a7 100644
--- a/package/MDAnalysis/coordinates/DCD.py
+++ b/package/MDAnalysis/coordinates/DCD.py
@@ -523,9 +523,9 @@ def timeseries(self, asel, start=None, stop=None, step=None, format='afc'):
         # 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, skip, format)
+        return self._read_timeseries(atom_numbers, start, stop, step, format)
 
-    def correl(self, timeseries, start=None, stop=None, skip=None):
+    def correl(self, timeseries, start=None, stop=None, step=None):
         """Populate a TimeseriesCollection object with timeseries computed from the trajectory
 
         :Arguments:
@@ -543,7 +543,7 @@ def correl(self, timeseries, start=None, stop=None, skip=None):
         atomcounts = timeseries._getAtomCounts()
         auxdata = timeseries._getAuxData()
         return self._read_timecorrel(atomlist, atomcounts, format, auxdata,
-                                     sizedata, lowerb, upperb, start, stop, skip)
+                                     sizedata, lowerb, upperb, start, stop, step)
 
     def close(self):
         if self.dcdfile is not None:

From 04dc85d1d8be6c8ccd9875fb396453b25738b7c9 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Tue, 26 Jul 2016 18:07:22 -0700
Subject: [PATCH 07/28] Changed RMSFarray to reflect correct data

---
 .../data/adk_oplsaa_CA_rmsf.npy               | Bin 1844 -> 1792 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/testsuite/MDAnalysisTests/data/adk_oplsaa_CA_rmsf.npy b/testsuite/MDAnalysisTests/data/adk_oplsaa_CA_rmsf.npy
index d28a8aa8fc182e78ca521ce41752051b7cb6db6d..34d754740a80aafbdcd41d2b04bb8d2685039a4d 100644
GIT binary patch
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From 1983709a197ef8d4be98734d481d62783521a8c5 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Tue, 26 Jul 2016 18:30:55 -0700
Subject: [PATCH 08/28] Updated changelog [skip ci]

---
 package/CHANGELOG | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index 9a1bb52719d..bd287842752 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -34,7 +34,8 @@ Fixes
   * Display of Deprecation warnings doesn't affect other modules anymore (Issue #754)
   * Changed nframes to n_frames in analysis modules for consistency (Issue #890)
   * fixed incompatibility with newer matplotlib in analysis.hole
-        
+  * Fixed modules that improperly documented and/or used frame slicing 
+    defaults (#914)
 Changes
   * Added protected variable _frame_index to to keep track of frame iteration
     number in AnalysisBase

From cb5852e9cea9fa1affdd04297e00a06b51a66d7e Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Wed, 27 Jul 2016 15:56:26 -0700
Subject: [PATCH 09/28] Added test for slicing, slowly changing DCD source for
 timeseries slicing.

---
 package/MDAnalysis/coordinates/src/dcd.c      | 49 ++++++++++++-------
 .../MDAnalysisTests/coordinates/test_dcd.py   |  9 ++++
 2 files changed, 41 insertions(+), 17 deletions(-)

diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index dea24b6884a..ebdbfaddcd1 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -435,7 +435,13 @@ __read_timeseries(PyObject *self, PyObject *args)
    int rc;
    int i, j, index;
    int n_atoms = 0, n_frames = 0;
+<<<<<<< HEAD
    int start = 0, stop = -1, skip = 1, numskip = 0;
+=======
+   /* Stop = -1 is incorrect and causes an error, look for a fix of this in line
+   469 */
+   int start = 0, stop = -1, skip = 1, numskip = 0, remaining_frames=0;
+>>>>>>> Added test for slicing, slowly changing DCD source for timeseries slicing.
    dcdhandle *dcd = NULL;
    int *atomlist = NULL;
    npy_intp dimensions[3];
@@ -464,8 +470,10 @@ __read_timeseries(PyObject *self, PyObject *args)
    Py_DECREF(temp);
 
    // Assume that start and stop are valid
-   if (stop == -1) { stop = dcd->nsets; }
-   n_frames = (stop-start+1) / skip;
+
+   if (stop == -1) { stop = dcd->nsets -1; }
+   n_frames = ((stop-start) / skip)+1;
+
    //n_frames = dcd->nsets / skip;
    n_atoms = PyList_Size((PyObject*)atoms);
    if (n_atoms == 0) {
@@ -497,20 +505,15 @@ __read_timeseries(PyObject *self, PyObject *args)
    // Figure out the format string
    if (strncasecmp(format, "afc", 3) == 0) {
       dimensions[0] = n_atoms; dimensions[1] = n_frames; dimensions[2] = 3;
-   } else
-   if (strncasecmp(format, "acf", 3) == 0) {
+   } else if (strncasecmp(format, "acf", 3) == 0) {
       dimensions[0] = n_atoms; dimensions[1] = 3; dimensions[2] = n_frames;
-   } else
-   if (strncasecmp(format, "fac", 3) == 0) {
+   } else if (strncasecmp(format, "fac", 3) == 0) {
       dimensions[0] = n_frames; dimensions[1] = n_atoms; dimensions[2] = 3;
-   } else
-   if (strncasecmp(format, "fca", 3) == 0) {
+   } else if (strncasecmp(format, "fca", 3) == 0) {
       dimensions[0] = n_frames; dimensions[1] = 3; dimensions[2] = n_atoms;
-   } else
-   if (strncasecmp(format, "caf", 3) == 0) {
+   } else if (strncasecmp(format, "caf", 3) == 0) {
       dimensions[0] = 3; dimensions[1] = n_atoms; dimensions[2] = n_frames;
-   } else
-   if (strncasecmp(format, "cfa", 3) == 0) {
+   } else if (strncasecmp(format, "cfa", 3) == 0) {
       dimensions[0] = 3; dimensions[1] = n_frames; dimensions[2] = n_atoms;
    }
 
@@ -534,32 +537,43 @@ __read_timeseries(PyObject *self, PyObject *args)
       goto error;
    }
 
-   for (i=0;i<n_frames;i++)
-   {
+   /*Should actually be number of frames, not true yet*/
+   remaining_frames = stop;
+   for (i=0;i<n_frames;i++) {
       if (skip > 1) {
          // Figure out how many steps to skip
-         numskip = skip - (dcd->setsread % skip) - 1;
+         numskip = skip-1;
+         if(remaining_frames < numskip){
+            numskip = 1;
+         }
+         printf("%d numskip, %d skip %d stop %d setsread %d n_frames %d i %d remaining_frames \n", numskip, skip, stop, dcd->setsread, n_frames, i, remaining_frames);
          rc = skip_dcdstep(dcd->fd, dcd->natoms, dcd->nfixed, dcd->charmm, numskip);
          if (rc < 0) {
             // return an exception
             PyErr_SetString(PyExc_IOError, "Error skipping frame from DCD file");
             goto error;
          }
-         dcd->setsread+=numskip;
       }
+      //now read from subset
       rc = read_dcdsubset(dcd->fd, dcd->natoms, lowerb, upperb, tempX, tempY, tempZ,
          unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
          dcd->reverse, dcd->charmm);
       dcd->first = 0;
-      dcd->setsread++;
+      dcd->setsread += numskip;
+      remaining_frames = stop - dcd->setsread++;
       if (rc < 0) {
          // return an exception
          PyErr_SetString(PyExc_IOError, "Error reading frame from DCD file");
          goto error;
+
+         }
+
       }
+
       // Copy into Numeric array only those atoms we are interested in
       for (j=0;j<n_atoms;j++) {
          index = atomlist[j]-lowerb;
+
          /*
          * coord[a][b][c] = *(float*)(coord->data + a*coord->strides[0] + b*coord->strides[1] + c*coord->strides[2])
          */
@@ -616,6 +630,7 @@ __read_timeseries(PyObject *self, PyObject *args)
    return NULL;
 }
 
+
 static PyObject *
 __read_next_frame(PyObject *self, PyObject *args)
 {
diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index 0e901ee87fb..7868e8c00f6 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -137,6 +137,15 @@ def test_volume(self):
                             err_msg="wrong volume for unitcell (no unitcell "
                             "in DCD so this should be 0)")
 
+    def test_timeseries_slicing(self):
+        # check that slicing behaves correctly
+        # should fail before issue #914 resolved
+        self.u = mda.Universe(PSF, DCD)
+        ts = self.u.trajectory.timeseries(self.u.atoms)
+        ts_skip = self.u.trajectory.timeseries(self.u.atoms, skip=10)
+        assert_array_almost_equal(ts[:,::10], ts_skip, 5)
+
+
 def test_DCDReader_set_dt(dt=100., frame=3):
     u = mda.Universe(PSF, DCD, dt=dt)
     assert_almost_equal(u.trajectory[frame].time, frame*dt,

From 1b1d4f28b33684277f56e33712a213f0b9f5a4f5 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Wed, 27 Jul 2016 15:57:04 -0700
Subject: [PATCH 10/28] DCD.py changes

---
 package/MDAnalysis/coordinates/DCD.py    | 11 ++++++++---
 package/MDAnalysis/coordinates/src/dcd.c | 10 +++-------
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py
index 98bfdb6c8a7..84bab725130 100644
--- a/package/MDAnalysis/coordinates/DCD.py
+++ b/package/MDAnalysis/coordinates/DCD.py
@@ -498,7 +498,8 @@ def _read_frame(self, frame):
         ts.frame = frame
         return ts
 
-    def timeseries(self, asel, start=None, stop=None, step=None, format='afc'):
+    def timeseries(self, asel, start=None, stop=-1, step=None, skip=None,
+                   format='afc'):
         """Return a subset of coordinate data for an AtomGroup
 
         :Arguments:
@@ -514,7 +515,11 @@ def timeseries(self, asel, start=None, stop=None, step=None, format='afc'):
                where the shape is (frame, number of atoms,
                coordinates)
         """
-        start, stop, skip = self.check_slice_indices(start, stop, step)
+        if skip is not None:
+            step = skip
+        start, stop, step = self.check_slice_indices(start, stop, step)
+        # for old cython _read_timeseries code
+        skip = step
         if len(asel) == 0:
             raise NoDataError("Timeseries requires at least one atom to analyze")
         if len(format) != 3 and format not in ['afc', 'acf', 'caf', 'cfa', 'fac', 'fca']:
@@ -523,7 +528,7 @@ def timeseries(self, asel, start=None, stop=None, step=None, format='afc'):
         # 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)
+        return self._read_timeseries(atom_numbers, start, stop, skip, format)
 
     def correl(self, timeseries, start=None, stop=None, step=None):
         """Populate a TimeseriesCollection object with timeseries computed from the trajectory
diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index ebdbfaddcd1..0e465cd7360 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -435,13 +435,10 @@ __read_timeseries(PyObject *self, PyObject *args)
    int rc;
    int i, j, index;
    int n_atoms = 0, n_frames = 0;
-<<<<<<< HEAD
-   int start = 0, stop = -1, skip = 1, numskip = 0;
-=======
+
    /* Stop = -1 is incorrect and causes an error, look for a fix of this in line
    469 */
    int start = 0, stop = -1, skip = 1, numskip = 0, remaining_frames=0;
->>>>>>> Added test for slicing, slowly changing DCD source for timeseries slicing.
    dcdhandle *dcd = NULL;
    int *atomlist = NULL;
    npy_intp dimensions[3];
@@ -542,7 +539,7 @@ __read_timeseries(PyObject *self, PyObject *args)
    for (i=0;i<n_frames;i++) {
       if (skip > 1) {
          // Figure out how many steps to skip
-         numskip = skip-1;
+         numskip = skip;
          if(remaining_frames < numskip){
             numskip = 1;
          }
@@ -560,7 +557,7 @@ __read_timeseries(PyObject *self, PyObject *args)
          dcd->reverse, dcd->charmm);
       dcd->first = 0;
       dcd->setsread += numskip;
-      remaining_frames = stop - dcd->setsread++;
+      remaining_frames = stop - dcd->setsread;
       if (rc < 0) {
          // return an exception
          PyErr_SetString(PyExc_IOError, "Error reading frame from DCD file");
@@ -568,7 +565,6 @@ __read_timeseries(PyObject *self, PyObject *args)
 
          }
 
-      }
 
       // Copy into Numeric array only those atoms we are interested in
       for (j=0;j<n_atoms;j++) {

From 320b1dcc7de8aec5d89d1e1abe0aaa825311b27a Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Wed, 27 Jul 2016 16:49:59 -0700
Subject: [PATCH 11/28] Everything working. Fixed logic error in code. Removed
 printing of debug statement.

---
 package/MDAnalysis/coordinates/src/dcd.c | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 0e465cd7360..4924a9c9b4f 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -535,15 +535,14 @@ __read_timeseries(PyObject *self, PyObject *args)
    }
 
    /*Should actually be number of frames, not true yet*/
-   remaining_frames = stop;
+   remaining_frames = stop-start;
    for (i=0;i<n_frames;i++) {
-      if (skip > 1) {
+      if (skip > 1 && i>0) {
          // Figure out how many steps to skip
-         numskip = skip;
+         numskip = skip -1;
          if(remaining_frames < numskip){
             numskip = 1;
          }
-         printf("%d numskip, %d skip %d stop %d setsread %d n_frames %d i %d remaining_frames \n", numskip, skip, stop, dcd->setsread, n_frames, i, remaining_frames);
          rc = skip_dcdstep(dcd->fd, dcd->natoms, dcd->nfixed, dcd->charmm, numskip);
          if (rc < 0) {
             // return an exception
@@ -551,12 +550,13 @@ __read_timeseries(PyObject *self, PyObject *args)
             goto error;
          }
       }
+      dcd->setsread += numskip;
       //now read from subset
       rc = read_dcdsubset(dcd->fd, dcd->natoms, lowerb, upperb, tempX, tempY, tempZ,
          unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
          dcd->reverse, dcd->charmm);
       dcd->first = 0;
-      dcd->setsread += numskip;
+      dcd->setsread += 1;
       remaining_frames = stop - dcd->setsread;
       if (rc < 0) {
          // return an exception

From 55910a0a279ca6e76998142355cf061345e14d8c Mon Sep 17 00:00:00 2001
From: jdetle <jdetle@gmail.com>
Date: Wed, 27 Jul 2016 21:49:21 -0700
Subject: [PATCH 12/28] Change to ++

Small fixes to make code work better
---
 package/MDAnalysis/coordinates/DCD.py             | 6 ++----
 package/MDAnalysis/coordinates/src/dcd.c          | 6 +++++-
 testsuite/MDAnalysisTests/coordinates/test_dcd.py | 2 +-
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py
index 84bab725130..ad1819b9a8e 100644
--- a/package/MDAnalysis/coordinates/DCD.py
+++ b/package/MDAnalysis/coordinates/DCD.py
@@ -498,7 +498,7 @@ def _read_frame(self, frame):
         ts.frame = frame
         return ts
 
-    def timeseries(self, asel, start=None, stop=-1, step=None, skip=None,
+    def timeseries(self, asel, start=None, stop=None, step=None, skip=None,
                    format='afc'):
         """Return a subset of coordinate data for an AtomGroup
 
@@ -518,8 +518,6 @@ def timeseries(self, asel, start=None, stop=-1, step=None, skip=None,
         if skip is not None:
             step = skip
         start, stop, step = self.check_slice_indices(start, stop, step)
-        # for old cython _read_timeseries code
-        skip = step
         if len(asel) == 0:
             raise NoDataError("Timeseries requires at least one atom to analyze")
         if len(format) != 3 and format not in ['afc', 'acf', 'caf', 'cfa', 'fac', 'fca']:
@@ -528,7 +526,7 @@ def timeseries(self, asel, start=None, stop=-1, step=None, skip=None,
         # 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, skip, format)
+        return self._read_timeseries(atom_numbers, start, stop, step, format)
 
     def correl(self, timeseries, start=None, stop=None, step=None):
         """Populate a TimeseriesCollection object with timeseries computed from the trajectory
diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 4924a9c9b4f..0498b548b04 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -467,8 +467,12 @@ __read_timeseries(PyObject *self, PyObject *args)
    Py_DECREF(temp);
 
    // Assume that start and stop are valid
+<<<<<<< HEAD
 
    if (stop == -1) { stop = dcd->nsets -1; }
+=======
+   if (stop == dcd->nsets) { stop = dcd->nsets -1; }
+>>>>>>> Change to ++
    n_frames = ((stop-start) / skip)+1;
 
    //n_frames = dcd->nsets / skip;
@@ -556,7 +560,7 @@ __read_timeseries(PyObject *self, PyObject *args)
          unitcell, dcd->nfixed, dcd->first, dcd->freeind, dcd->fixedcoords,
          dcd->reverse, dcd->charmm);
       dcd->first = 0;
-      dcd->setsread += 1;
+      dcd->setsread++;
       remaining_frames = stop - dcd->setsread;
       if (rc < 0) {
          // return an exception
diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index 7868e8c00f6..d915c3a739f 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -142,7 +142,7 @@ def test_timeseries_slicing(self):
         # should fail before issue #914 resolved
         self.u = mda.Universe(PSF, DCD)
         ts = self.u.trajectory.timeseries(self.u.atoms)
-        ts_skip = self.u.trajectory.timeseries(self.u.atoms, skip=10)
+        ts_skip = self.u.trajectory.timeseries(self.u.atoms, step=10)
         assert_array_almost_equal(ts[:,::10], ts_skip, 5)
 
 

From 83c7e4f962122b684074f9fa770115a724a5922c Mon Sep 17 00:00:00 2001
From: jdetle <jdetle@gmail.com>
Date: Wed, 27 Jul 2016 22:40:47 -0700
Subject: [PATCH 13/28] Elaborated on docs

---
 package/MDAnalysis/analysis/contacts.py     | 3 ++-
 package/MDAnalysis/analysis/diffusionmap.py | 3 ++-
 package/MDAnalysis/analysis/rms.py          | 3 ++-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/analysis/contacts.py b/package/MDAnalysis/analysis/contacts.py
index 6c03381ebcb..5a1f8cfb656 100644
--- a/package/MDAnalysis/analysis/contacts.py
+++ b/package/MDAnalysis/analysis/contacts.py
@@ -399,7 +399,8 @@ def __init__(self, u, selection, refgroup, method="hard_cut", radius=4.5,
             First frame of trajectory to analyse, Default: None becomes 0.
         stop : int, optional
             Frame index to stop analysis. Default: None becomes
-            n_frames. Iteration stops *before* this frame number.
+            n_frames. Iteration stops *before* this frame number,
+            which means that the trajectory would be read until the end.
         step : int, optional
             Step between frames to analyse, Default: None becomes 1.
 
diff --git a/package/MDAnalysis/analysis/diffusionmap.py b/package/MDAnalysis/analysis/diffusionmap.py
index b42be7f044f..a6300212cc0 100644
--- a/package/MDAnalysis/analysis/diffusionmap.py
+++ b/package/MDAnalysis/analysis/diffusionmap.py
@@ -230,7 +230,8 @@ def __init__(self, u, select='all', metric=rmsd, cutoff=1E0-5,
             First frame of trajectory to analyse, Default: None becomes 0.
         stop : int, optional
             Frame index to stop analysis. Default: None becomes
-            n_frames. Iteration stops *before* this frame number.
+            n_frames. Iteration stops *before* this frame number,
+            which means that the trajectory would be read until the end.
         step : int, optional
             Step between frames to analyse, Default: None becomes 1.
         """
diff --git a/package/MDAnalysis/analysis/rms.py b/package/MDAnalysis/analysis/rms.py
index 26be0ba8e13..16ed9ae815b 100644
--- a/package/MDAnalysis/analysis/rms.py
+++ b/package/MDAnalysis/analysis/rms.py
@@ -568,7 +568,8 @@ def run(self, start=None, stop=None, step=None, progout=10, quiet=False):
             starting frame, default None becomes 0.
         stop : int (optional)
             Frame index to stop analysis. Default: None becomes
-            n_frames. Iteration stops *before* this frame number.
+            n_frames. Iteration stops *before* this frame number,
+            which means that the trajectory would be read until the end.
         step : int (optional)
             step between frames, default None becomes 1.
         progout : int (optional)

From beffbeaa923c85598fc67a918d8dee8d7f2930b2 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Thu, 28 Jul 2016 11:02:28 -0700
Subject: [PATCH 14/28] Added generator but it appears to not be working,
 please help.

---
 testsuite/MDAnalysisTests/coordinates/test_dcd.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index d915c3a739f..0548933e281 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -140,10 +140,20 @@ def test_volume(self):
     def test_timeseries_slicing(self):
         # check that slicing behaves correctly
         # should fail before issue #914 resolved
+        x = []
+        for i in range(10):
+            for j in range(i+1, 11):
+                for k in range(j, 11):
+                    tuples = (i, j, k)
+                    x.append(tuples)
+        for start, stop, step in x:
+            yield self._slice_generation_test, start, stop, step
+
+    def _slice_generation_test(self, start, stop, step):
         self.u = mda.Universe(PSF, DCD)
         ts = self.u.trajectory.timeseries(self.u.atoms)
-        ts_skip = self.u.trajectory.timeseries(self.u.atoms, step=10)
-        assert_array_almost_equal(ts[:,::10], ts_skip, 5)
+        ts_skip = self.u.trajectory.timeseries(self.u.atoms, start, stop, step)
+        assert_array_almost_equal(ts[:, start:stop:step,:], ts_skip, 5)
 
 
 def test_DCDReader_set_dt(dt=100., frame=3):

From 8e24480f247759aeb05216ae5e6823d361e1e9f3 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Thu, 28 Jul 2016 15:43:12 -0700
Subject: [PATCH 15/28] Deprecated skip for step

---
 package/MDAnalysis/coordinates/DCD.py | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py
index ad1819b9a8e..92c4c711278 100644
--- a/package/MDAnalysis/coordinates/DCD.py
+++ b/package/MDAnalysis/coordinates/DCD.py
@@ -73,6 +73,7 @@
 import numpy as np
 import struct
 import types
+from numpy.lib.utils import deprecate
 
 from ..core import flags
 from .. import units as mdaunits  # use mdaunits instead of units to avoid a clash
@@ -498,6 +499,7 @@ def _read_frame(self, frame):
         ts.frame = frame
         return ts
 
+
     def timeseries(self, asel, start=None, stop=None, step=None, skip=None,
                    format='afc'):
         """Return a subset of coordinate data for an AtomGroup
@@ -514,9 +516,15 @@ def timeseries(self, asel, start=None, stop=None, step=None, skip=None,
                of 'a', 'f', 'c' are allowed ie "fac" - return array
                where the shape is (frame, number of atoms,
                coordinates)
+        :Deprecated:
+            *skip*
+                Skip has been deprecated in favor of the standard keyword step.
         """
         if skip is not None:
             step = skip
+
+            @deprecate(new_name="step",
+                       message="This parameter will be removed in 0.17")
         start, stop, step = self.check_slice_indices(start, stop, step)
         if len(asel) == 0:
             raise NoDataError("Timeseries requires at least one atom to analyze")
@@ -528,7 +536,7 @@ def timeseries(self, asel, 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):
+    def correl(self, timeseries, start=None, stop=None, step=None, skip=None):
         """Populate a TimeseriesCollection object with timeseries computed from the trajectory
 
         :Arguments:
@@ -537,7 +545,15 @@ def correl(self, timeseries, start=None, stop=None, step=None):
             *start, stop, step*
                A subset of the trajectory to use, with start being inclusive
                and stop being exclusive.
+        :Deprecated:
+            *skip*
+                Skip has been deprecated in favor of the standard keyword step.
         """
+        if skip is not None:
+            step = skip
+
+            @deprecate(new_name="step",
+                       message="This parameter will be removed in 0.17")
         start, stop, step = self.check_slice_indices(start, stop, step)
         atomlist = timeseries._getAtomList()
         format = timeseries._getFormat()

From d687cc7492b611c51517569bad1d74b32b95c77b Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Fri, 29 Jul 2016 08:00:41 -0700
Subject: [PATCH 16/28] Changed to warnings.warn() because decorator wasnt
 working

---
 package/MDAnalysis/coordinates/DCD.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py
index 92c4c711278..fce5df80de0 100644
--- a/package/MDAnalysis/coordinates/DCD.py
+++ b/package/MDAnalysis/coordinates/DCD.py
@@ -73,7 +73,7 @@
 import numpy as np
 import struct
 import types
-from numpy.lib.utils import deprecate
+import warnings
 
 from ..core import flags
 from .. import units as mdaunits  # use mdaunits instead of units to avoid a clash
@@ -86,6 +86,7 @@
 from . import dcdtimeseries
 
 
+
 class Timestep(base.Timestep):
     #: Indices into :attr:`Timestep._unitcell` (``[A, gamma, B, beta, alpha,
     #: C]``, provided by the :class:`DCDReader` C code) to pull out
@@ -499,7 +500,6 @@ def _read_frame(self, frame):
         ts.frame = frame
         return ts
 
-
     def timeseries(self, asel, start=None, stop=None, step=None, skip=None,
                    format='afc'):
         """Return a subset of coordinate data for an AtomGroup
@@ -522,9 +522,10 @@ def timeseries(self, asel, start=None, stop=None, step=None, skip=None,
         """
         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)
 
-            @deprecate(new_name="step",
-                       message="This parameter will be removed in 0.17")
         start, stop, step = self.check_slice_indices(start, stop, step)
         if len(asel) == 0:
             raise NoDataError("Timeseries requires at least one atom to analyze")
@@ -551,10 +552,10 @@ def correl(self, timeseries, start=None, stop=None, step=None, skip=None):
         """
         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)
 
-            @deprecate(new_name="step",
-                       message="This parameter will be removed in 0.17")
-        start, stop, step = self.check_slice_indices(start, stop, step)
         atomlist = timeseries._getAtomList()
         format = timeseries._getFormat()
         lowerb, upperb = timeseries._getBounds()

From 6893abdb220980432cb51c136036fc526d3376ea Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Fri, 29 Jul 2016 09:01:10 -0700
Subject: [PATCH 17/28] Fixed silly correl bug

Simple arg changes
---
 package/MDAnalysis/coordinates/DCD.py    |  1 +
 package/MDAnalysis/coordinates/src/dcd.c | 14 +++++++++-----
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py
index fce5df80de0..e121a098295 100644
--- a/package/MDAnalysis/coordinates/DCD.py
+++ b/package/MDAnalysis/coordinates/DCD.py
@@ -556,6 +556,7 @@ def correl(self, timeseries, start=None, stop=None, step=None, skip=None):
                           "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()
diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 0498b548b04..827b9411dc7 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -438,7 +438,7 @@ __read_timeseries(PyObject *self, PyObject *args)
 
    /* Stop = -1 is incorrect and causes an error, look for a fix of this in line
    469 */
-   int start = 0, stop = -1, skip = 1, numskip = 0, remaining_frames=0;
+   int start = 0, stop = -1, step = 1, numskip = 0, remaining_frames=0;
    dcdhandle *dcd = NULL;
    int *atomlist = NULL;
    npy_intp dimensions[3];
@@ -448,12 +448,12 @@ __read_timeseries(PyObject *self, PyObject *args)
    if (!self) {
       /* we were in fact called as a module function, try to retrieve
       a matching object from args */
-      if( !PyArg_ParseTuple(args, "OO!|iiis", &self, &PyList_Type, &atoms, &start, &stop, &skip, &format) )
+      if( !PyArg_ParseTuple(args, "OO!|iiis", &self, &PyList_Type, &atoms, &start, &stop, &step, &format) )
       return NULL;
    } else {
       /* we were obviously called as an object method so args should
       only have the int value. */
-      if( !PyArg_ParseTuple(args, "O!|iiis", &PyList_Type, &atoms, &start, &stop, &skip, &format) )
+      if( !PyArg_ParseTuple(args, "O!|iiis", &PyList_Type, &atoms, &start, &stop, &step, &format) )
       return NULL;
    }
 
@@ -472,9 +472,13 @@ __read_timeseries(PyObject *self, PyObject *args)
    if (stop == -1) { stop = dcd->nsets -1; }
 =======
    if (stop == dcd->nsets) { stop = dcd->nsets -1; }
+<<<<<<< HEAD
 >>>>>>> Change to ++
    n_frames = ((stop-start) / skip)+1;
 
+=======
+   n_frames = ((stop-start) / step)+1;
+>>>>>>> Fixed silly correl bug
    //n_frames = dcd->nsets / skip;
    n_atoms = PyList_Size((PyObject*)atoms);
    if (n_atoms == 0) {
@@ -541,9 +545,9 @@ __read_timeseries(PyObject *self, PyObject *args)
    /*Should actually be number of frames, not true yet*/
    remaining_frames = stop-start;
    for (i=0;i<n_frames;i++) {
-      if (skip > 1 && i>0) {
+      if (step > 1 && i>0) {
          // Figure out how many steps to skip
-         numskip = skip -1;
+         numskip = step -1;
          if(remaining_frames < numskip){
             numskip = 1;
          }

From 6b275882712faaea80e3ab14b6766281f4c38862 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Fri, 29 Jul 2016 16:13:14 -0700
Subject: [PATCH 18/28] Fixed issue caused by integer division, when stop-start
 / nframes has no remainder it should remain 1.

---
 package/MDAnalysis/coordinates/src/dcd.c      | 13 ++-----------
 .../MDAnalysisTests/coordinates/test_dcd.py   | 19 +++++++++++++++++--
 2 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 827b9411dc7..772bd2fb513 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -466,19 +466,10 @@ __read_timeseries(PyObject *self, PyObject *args)
    dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
    Py_DECREF(temp);
 
-   // Assume that start and stop are valid
-<<<<<<< HEAD
 
-   if (stop == -1) { stop = dcd->nsets -1; }
-=======
    if (stop == dcd->nsets) { stop = dcd->nsets -1; }
-<<<<<<< HEAD
->>>>>>> Change to ++
-   n_frames = ((stop-start) / skip)+1;
-
-=======
-   n_frames = ((stop-start) / step)+1;
->>>>>>> Fixed silly correl bug
+   n_frames = ((stop-start) / step)+ 1;
+   if ((stop-start) == step) { n_frames = 1;}
    //n_frames = dcd->nsets / skip;
    n_atoms = PyList_Size((PyObject*)atoms);
    if (n_atoms == 0) {
diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index 0548933e281..b336e5be3c1 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -55,7 +55,17 @@ def test_with_statement(self):
             err_msg="with_statement: DCDReader does not read all frames")
 
 
-class TestDCDReader(_TestDCD):
+class TestDCDReader(object):
+    def setUp(self):
+        self.universe = mda.Universe(PSF, DCD)
+        self.dcd = self.universe.trajectory
+        self.ts = self.universe.coord
+
+    def tearDown(self):
+        del self.universe
+        del self.dcd
+        del self.ts
+
     def test_rewind_dcd(self):
         self.dcd.rewind()
         assert_equal(self.ts.frame, 0, "rewinding to frame 0")
@@ -154,7 +164,12 @@ def _slice_generation_test(self, start, stop, step):
         ts = self.u.trajectory.timeseries(self.u.atoms)
         ts_skip = self.u.trajectory.timeseries(self.u.atoms, start, stop, step)
         assert_array_almost_equal(ts[:, start:stop:step,:], ts_skip, 5)
-
+    
+    def test_slice_generation_test(self):
+        self.u = mda.Universe(PSF, DCD)
+        ts = self.u.trajectory.timeseries(self.u.atoms)
+        ts_skip = self.u.trajectory.timeseries(self.u.atoms, 0, 4, 4)
+        assert_array_almost_equal(ts[:, 0:4:4,:], ts_skip, 5)
 
 def test_DCDReader_set_dt(dt=100., frame=3):
     u = mda.Universe(PSF, DCD, dt=dt)

From 32fce067fefbef6b569d7af2e78063472f98a8e8 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Fri, 29 Jul 2016 21:08:02 -0700
Subject: [PATCH 19/28] Reduced number of tests by a signifcant margin, removed
 test of test

---
 testsuite/MDAnalysisTests/coordinates/test_dcd.py | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index b336e5be3c1..c62ecb91776 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -151,9 +151,9 @@ def test_timeseries_slicing(self):
         # check that slicing behaves correctly
         # should fail before issue #914 resolved
         x = []
-        for i in range(10):
-            for j in range(i+1, 11):
-                for k in range(j, 11):
+        for i in range(5):
+            for j in range(i+1, 6):
+                for k in range(j, 6):
                     tuples = (i, j, k)
                     x.append(tuples)
         for start, stop, step in x:
@@ -165,11 +165,6 @@ def _slice_generation_test(self, start, stop, step):
         ts_skip = self.u.trajectory.timeseries(self.u.atoms, start, stop, step)
         assert_array_almost_equal(ts[:, start:stop:step,:], ts_skip, 5)
     
-    def test_slice_generation_test(self):
-        self.u = mda.Universe(PSF, DCD)
-        ts = self.u.trajectory.timeseries(self.u.atoms)
-        ts_skip = self.u.trajectory.timeseries(self.u.atoms, 0, 4, 4)
-        assert_array_almost_equal(ts[:, 0:4:4,:], ts_skip, 5)
 
 def test_DCDReader_set_dt(dt=100., frame=3):
     u = mda.Universe(PSF, DCD, dt=dt)

From 68ae89786ab022d73ca3b0575a4bc14b1d80c6e0 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Sat, 30 Jul 2016 13:13:06 -0700
Subject: [PATCH 20/28] Fixed incomplete logic

Changed tuples

Eliminated _testDCD
---
 package/MDAnalysis/coordinates/src/dcd.c      |  2 +-
 .../MDAnalysisTests/coordinates/test_dcd.py   | 24 ++++---------------
 2 files changed, 5 insertions(+), 21 deletions(-)

diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 772bd2fb513..88e09293530 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -469,7 +469,7 @@ __read_timeseries(PyObject *self, PyObject *args)
 
    if (stop == dcd->nsets) { stop = dcd->nsets -1; }
    n_frames = ((stop-start) / step)+ 1;
-   if ((stop-start) == step) { n_frames = 1;}
+   if ((stop-start) % step == 0) { n_frames--;}
    //n_frames = dcd->nsets / skip;
    n_atoms = PyList_Size((PyObject*)atoms);
    if (n_atoms == 0) {
diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index c62ecb91776..0000d447058 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -23,18 +23,6 @@ def TestDCD_Issue32():
     assert_raises(IOError, mda.Universe, PSF, DCD_empty)
 
 
-class _TestDCD(TestCase):
-    def setUp(self):
-        self.universe = mda.Universe(PSF, DCD)
-        self.dcd = self.universe.trajectory
-        self.ts = self.universe.coord
-
-    def tearDown(self):
-        del self.universe
-        del self.dcd
-        del self.ts
-
-
 class TestDCDReaderClass(TestCase):
     def test_with_statement(self):
         from MDAnalysis.coordinates.DCD import DCDReader
@@ -150,12 +138,8 @@ def test_volume(self):
     def test_timeseries_slicing(self):
         # check that slicing behaves correctly
         # should fail before issue #914 resolved
-        x = []
-        for i in range(5):
-            for j in range(i+1, 6):
-                for k in range(j, 6):
-                    tuples = (i, j, k)
-                    x.append(tuples)
+        x = [(0, 1, 1), (1,1,1), (1, 2, 1), (1, 2, 2), (1, 4, 2), (1, 4, 4),
+             (0, 5, 5), (3, 5, 1)]
         for start, stop, step in x:
             yield self._slice_generation_test, start, stop, step
 
@@ -164,7 +148,7 @@ def _slice_generation_test(self, start, stop, step):
         ts = self.u.trajectory.timeseries(self.u.atoms)
         ts_skip = self.u.trajectory.timeseries(self.u.atoms, start, stop, step)
         assert_array_almost_equal(ts[:, start:stop:step,:], ts_skip, 5)
-    
+
 
 def test_DCDReader_set_dt(dt=100., frame=3):
     u = mda.Universe(PSF, DCD, dt=dt)
@@ -445,7 +429,7 @@ def test_coordinates(self):
                 ts_orig.frame))
 
 
-class TestDCDCorrel(_TestDCD):
+class TestDCDCorrel(TestCase):
     def setUp(self):
         # Note: setUp is executed for *every* test !
         super(TestDCDCorrel, self).setUp()

From 6f9e57d874524887eee4e9fe96a3d4b6731b924e Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Sat, 30 Jul 2016 18:47:03 -0700
Subject: [PATCH 21/28] Changes to DCD correl functions

---
 .../MDAnalysis/coordinates/dcdtimeseries.pyx  | 25 +++++++++++++------
 package/MDAnalysis/coordinates/src/dcd.c      |  4 +--
 package/MDAnalysis/core/Timeseries.py         | 25 +++++++++++++++----
 .../MDAnalysisTests/coordinates/test_dcd.py   |  9 ++++---
 4 files changed, 45 insertions(+), 18 deletions(-)

diff --git a/package/MDAnalysis/coordinates/dcdtimeseries.pyx b/package/MDAnalysis/coordinates/dcdtimeseries.pyx
index c60e20589c8..db1c94fd9a4 100644
--- a/package/MDAnalysis/coordinates/dcdtimeseries.pyx
+++ b/package/MDAnalysis/coordinates/dcdtimeseries.pyx
@@ -59,7 +59,7 @@ cdef extern from "correl.h":
 
 import numpy as np
 
-def __read_timecorrel(object self, object atoms, object atomcounts, object format, object auxdata, int sizedata, int lowerb, int upperb, int start, int stop, int skip):
+def __read_timecorrel(object self, object atoms, object atomcounts, object format, object auxdata, int sizedata, int lowerb, int upperb, int start, int stop, int step):
     cdef dcdhandle* dcd
     cdef numpy.ndarray atomlist, atomcountslist, auxlist
     cdef numpy.ndarray data, temp
@@ -69,8 +69,10 @@ def __read_timecorrel(object self, object atoms, object atomcounts, object forma
 
     dcd = <dcdhandle*>PyCObject_AsVoidPtr(self._dcd_C_ptr)
     cdef int n_frames
-    if (stop == -1): stop = dcd.nsets
-    n_frames = (stop-start+1) / skip
+
+    if stop == dcd.nsets: stop -= 1;
+    n_frames = ((stop-start) / step) + 1;
+    if (stop-start) % step == 0: n_frames -= 1;
     cdef int numdata
     numdata = len(format)
     if numdata==0:
@@ -109,18 +111,25 @@ def __read_timecorrel(object self, object atoms, object atomcounts, object forma
     cdef int index, numskip
     cdef int i, j
     cdef float unitcell[6]
+    cdef int remaining_frames = stop-start
+    numskip = 0
+    print n_frames
     for i from 0 <= i < n_frames:
-        if (skip > 1):
+        if (step > 1 and i > 0):
             # Check if we have fixed atoms
             # XXX not done
-            numskip = skip - (dcd.setsread % skip) - 1
+            numskip = step - 1
+            if(remaining_frames < numskip):
+               numskip = 1
+
             rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip)
             if (rc < 0):
                 raise IOError("Error skipping frame from DCD file")
-            dcd.setsread = dcd.setsread + numskip
+        dcd.setsread = dcd.setsread + numskip
         rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm)
-        dcd.first=0
-        dcd.setsread = dcd.setsread + 1
+        dcd.first = 0
+        dcd.setsread += 1
+        remaining_frames = stop - dcd.setsread
         if (rc < 0):
             raise IOError("Error reading frame from DCD file")
         # Copy into data array based on format
diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 88e09293530..714e5f73cad 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -467,8 +467,8 @@ __read_timeseries(PyObject *self, PyObject *args)
    Py_DECREF(temp);
 
 
-   if (stop == dcd->nsets) { stop = dcd->nsets -1; }
-   n_frames = ((stop-start) / step)+ 1;
+   if (stop == dcd->nsets) { stop = dcd->nsets - 1; }
+   n_frames = ((stop-start) / step) + 1;
    if ((stop-start) % step == 0) { n_frames--;}
    //n_frames = dcd->nsets / skip;
    n_atoms = PyList_Size((PyObject*)atoms);
diff --git a/package/MDAnalysis/core/Timeseries.py b/package/MDAnalysis/core/Timeseries.py
index 45a3776f341..317b62a8cfd 100644
--- a/package/MDAnalysis/core/Timeseries.py
+++ b/package/MDAnalysis/core/Timeseries.py
@@ -1,5 +1,5 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #
 # MDAnalysis --- http://www.MDAnalysis.org
 # Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
@@ -52,6 +52,7 @@
 .. autoclass:: WaterDipole
 
 """
+import warnings
 
 from . import AtomGroup
 
@@ -104,16 +105,30 @@ def clear(self):
         '''clear the timeseries collection'''
         self.timeseries = []
 
-    def compute(self, trj, start=0, stop=-1, skip=1):
+    def compute(self, trj, start=None, stop=None, skip=None, step=None):
         '''Iterate through the trajectory *trj* and compute the time series.
 
          *trj*
             dcd trajectory object (i.e. :attr:`Universe.trajectory`)
+         *start*
+            First frame of trajectory to analyse, Default: None becomes 0.
+         *stop*
+            Frame index to stop analysis. Default: None becomes
+            n_frames. Iteration stops *before* this frame number,
+            which means that the trajectory would be read until the end.
+         *step*
+            Step between frames to analyse, Default: None becomes 1.
+         *Deprecated*
+            Skip is deprecated in favor of step.
 
-         *start, stop, skip*
-            Frames to calculate parts of the trajectory. It is important to
-            note that *start* and *stop* are inclusive
         '''
+        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 = trj.check_slice_indices(start, stop, skip)
         self.data = trj.correl(self, start, stop, skip)
         # Now remap the timeseries data to each timeseries
         typestr = "|f8"
diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index 0000d447058..0f058456697 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -432,9 +432,10 @@ def test_coordinates(self):
 class TestDCDCorrel(TestCase):
     def setUp(self):
         # Note: setUp is executed for *every* test !
-        super(TestDCDCorrel, self).setUp()
         import MDAnalysis.core.Timeseries as TS
-
+        self.universe = mda.Universe(PSF, DCD)
+        self.dcd = self.universe.trajectory
+        self.ts = self.universe.coord
         self.collection = TS.TimeseriesCollection()
         C = self.collection
         all = self.universe.atoms
@@ -458,7 +459,9 @@ def setUp(self):
 
     def tearDown(self):
         del self.collection
-        super(TestDCDCorrel, self).tearDown()
+        del self.universe
+        del self.dcd
+        del self.ts
 
     def test_correl(self):
         assert_equal(len(self.collection), 10, "Correl: len(collection)")

From e476ee5c2d913aabc936c7330f391f666f3fe6c1 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Sat, 30 Jul 2016 19:48:25 -0700
Subject: [PATCH 22/28] Changed to logic to take advantage of new default,
 simplify code.

---
 package/MDAnalysis/coordinates/dcdtimeseries.pyx | 6 ++----
 package/MDAnalysis/coordinates/src/dcd.c         | 6 ++----
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/package/MDAnalysis/coordinates/dcdtimeseries.pyx b/package/MDAnalysis/coordinates/dcdtimeseries.pyx
index db1c94fd9a4..d7c2ab4cb48 100644
--- a/package/MDAnalysis/coordinates/dcdtimeseries.pyx
+++ b/package/MDAnalysis/coordinates/dcdtimeseries.pyx
@@ -70,9 +70,8 @@ def __read_timecorrel(object self, object atoms, object atomcounts, object forma
     dcd = <dcdhandle*>PyCObject_AsVoidPtr(self._dcd_C_ptr)
     cdef int n_frames
 
-    if stop == dcd.nsets: stop -= 1;
-    n_frames = ((stop-start) / step) + 1;
-    if (stop-start) % step == 0: n_frames -= 1;
+    n_frames = ((stop-start) / step);
+    if (stop-start) % step > 0 : n_frames += 1;
     cdef int numdata
     numdata = len(format)
     if numdata==0:
@@ -113,7 +112,6 @@ def __read_timecorrel(object self, object atoms, object atomcounts, object forma
     cdef float unitcell[6]
     cdef int remaining_frames = stop-start
     numskip = 0
-    print n_frames
     for i from 0 <= i < n_frames:
         if (step > 1 and i > 0):
             # Check if we have fixed atoms
diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 714e5f73cad..9f3d6fe222f 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -466,10 +466,8 @@ __read_timeseries(PyObject *self, PyObject *args)
    dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp);
    Py_DECREF(temp);
 
-
-   if (stop == dcd->nsets) { stop = dcd->nsets - 1; }
-   n_frames = ((stop-start) / step) + 1;
-   if ((stop-start) % step == 0) { n_frames--;}
+   n_frames = ((stop-start) / step);
+   if ((stop-start) % step > 0) { n_frames++; }
    //n_frames = dcd->nsets / skip;
    n_atoms = PyList_Size((PyObject*)atoms);
    if (n_atoms == 0) {

From d036859610ca8253a179078e3c0e725e33f757e9 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Sat, 30 Jul 2016 20:55:44 -0700
Subject: [PATCH 23/28] I made a silly mistake in Timeseries

---
 package/MDAnalysis/core/Timeseries.py             |  4 ++--
 testsuite/MDAnalysisTests/coordinates/test_dcd.py | 10 ++++++++++
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/core/Timeseries.py b/package/MDAnalysis/core/Timeseries.py
index 317b62a8cfd..f73ab6a701b 100644
--- a/package/MDAnalysis/core/Timeseries.py
+++ b/package/MDAnalysis/core/Timeseries.py
@@ -128,8 +128,8 @@ def compute(self, trj, start=None, stop=None, skip=None, step=None):
                           "in 1.0. Use step instead.",
                           category=DeprecationWarning)
 
-        start, stop, step = trj.check_slice_indices(start, stop, skip)
-        self.data = trj.correl(self, start, stop, skip)
+        start, stop, step = trj.check_slice_indices(start, stop, step)
+        self.data = trj.correl(self, start, stop, step)
         # Now remap the timeseries data to each timeseries
         typestr = "|f8"
         start = 0
diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index 0f058456697..ee928803d35 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -437,7 +437,9 @@ def setUp(self):
         self.dcd = self.universe.trajectory
         self.ts = self.universe.coord
         self.collection = TS.TimeseriesCollection()
+        self.collection_slicing = TS.TimeseriesCollection()
         C = self.collection
+        C_step = self.collection_slicing
         all = self.universe.atoms
         ca = self.universe.s4AKE.CA
         ca_termini = mda.core.AtomGroup.AtomGroup([ca[0], ca[-1]])
@@ -454,11 +456,16 @@ def setUp(self):
         C.addTimeseries(TS.CenterOfGeometry(ca))  # 7
         C.addTimeseries(TS.CenterOfMass(all))  # 8
         C.addTimeseries(TS.CenterOfGeometry(all))  # 9
+
+        C_step.addTimeseries(TS.Atom('v', ca_termini))
+
         # cannot test WaterDipole because there's no water in the test dcd
         C.compute(self.dcd)
+        C_step.compute(self.dcd, step=10)
 
     def tearDown(self):
         del self.collection
+        del self.collection_slicing
         del self.universe
         del self.dcd
         del self.ts
@@ -526,6 +533,9 @@ def test_clear(self):
         C.clear()
         assert_equal(len(C), 0, "Correl: clear()")
 
+    def test_Atom_slicing(self):
+        assert_equal(self.collection_slicing[0].shape, (2, 3, 10),
+                     "Correl: Atom positions")
 
 # notes:
 def compute_correl_references():

From 0c268ed06c1034336a0c2dfc9ab07e0d3894bc62 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Sat, 30 Jul 2016 21:04:36 -0700
Subject: [PATCH 24/28] More testing

---
 testsuite/MDAnalysisTests/coordinates/test_dcd.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index ee928803d35..da17411aeb4 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -536,6 +536,8 @@ def test_clear(self):
     def test_Atom_slicing(self):
         assert_equal(self.collection_slicing[0].shape, (2, 3, 10),
                      "Correl: Atom positions")
+        assert_array_almost_equal(self.collection[0][:, :, ::10],
+                                  self.collection_slicing[0])
 
 # notes:
 def compute_correl_references():

From d3d4dadac56fef66101e461140d0856143198081 Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Sun, 31 Jul 2016 11:50:03 -0700
Subject: [PATCH 25/28] Added comments.

---
 package/MDAnalysis/coordinates/dcdtimeseries.pyx | 10 ++++++++--
 package/MDAnalysis/coordinates/src/dcd.c         | 10 ++++++++--
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/coordinates/dcdtimeseries.pyx b/package/MDAnalysis/coordinates/dcdtimeseries.pyx
index d7c2ab4cb48..aaec810c54a 100644
--- a/package/MDAnalysis/coordinates/dcdtimeseries.pyx
+++ b/package/MDAnalysis/coordinates/dcdtimeseries.pyx
@@ -115,15 +115,21 @@ def __read_timecorrel(object self, object atoms, object atomcounts, object forma
     for i from 0 <= i < n_frames:
         if (step > 1 and i > 0):
             # Check if we have fixed atoms
-            # XXX not done
+            # Figure out how many steps to step over, if step = n, np array
+            # slicing treats this as skip over n-1, read the nth.
             numskip = step - 1
+            # If the number to skip is greater than the number of frames left
+            # to be jumped over, just take one more step to reflect np slicing
+            # if there is a remainder, guaranteed to have at least one more
+            # frame.
             if(remaining_frames < numskip):
                numskip = 1
 
             rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip)
             if (rc < 0):
                 raise IOError("Error skipping frame from DCD file")
-        dcd.setsread = dcd.setsread + numskip
+        # on first iteration, numskip = 0, first set is always read.
+        dcd.setsread += numskip
         rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm)
         dcd.first = 0
         dcd.setsread += 1
diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 9f3d6fe222f..6b898e3c897 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -531,12 +531,17 @@ __read_timeseries(PyObject *self, PyObject *args)
       goto error;
    }
 
-   /*Should actually be number of frames, not true yet*/
    remaining_frames = stop-start;
    for (i=0;i<n_frames;i++) {
       if (step > 1 && i>0) {
-         // Figure out how many steps to skip
+         /* Figure out how many steps to step over, if step = n, np array
+            slicing treats this as skip over n-1, read the nth. */
          numskip = step -1;
+         /* If the number to skip is greater than the number of frames left
+            to be jumped over, just take one more step to reflect np slicing
+            if there is a remainder, guaranteed to have at least one more
+            frame.
+         */
          if(remaining_frames < numskip){
             numskip = 1;
          }
@@ -547,6 +552,7 @@ __read_timeseries(PyObject *self, PyObject *args)
             goto error;
          }
       }
+      // on first iteration, numskip == 0, first set is always read.
       dcd->setsread += numskip;
       //now read from subset
       rc = read_dcdsubset(dcd->fd, dcd->natoms, lowerb, upperb, tempX, tempY, tempZ,

From 6833e3a772be12069a9953f667fd395b9893c55a Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Sun, 31 Jul 2016 14:53:17 -0700
Subject: [PATCH 26/28] Undo comment removal [skip ci]

---
 package/MDAnalysis/coordinates/dcdtimeseries.pyx | 1 +
 package/MDAnalysis/coordinates/src/dcd.c         | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/package/MDAnalysis/coordinates/dcdtimeseries.pyx b/package/MDAnalysis/coordinates/dcdtimeseries.pyx
index aaec810c54a..1f1d4f585e8 100644
--- a/package/MDAnalysis/coordinates/dcdtimeseries.pyx
+++ b/package/MDAnalysis/coordinates/dcdtimeseries.pyx
@@ -115,6 +115,7 @@ def __read_timecorrel(object self, object atoms, object atomcounts, object forma
     for i from 0 <= i < n_frames:
         if (step > 1 and i > 0):
             # Check if we have fixed atoms
+            # XXX not done
             # Figure out how many steps to step over, if step = n, np array
             # slicing treats this as skip over n-1, read the nth.
             numskip = step - 1
diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 6b898e3c897..0edc7abd29d 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -534,6 +534,8 @@ __read_timeseries(PyObject *self, PyObject *args)
    remaining_frames = stop-start;
    for (i=0;i<n_frames;i++) {
       if (step > 1 && i>0) {
+         // Check if we have fixed atoms
+-        // XXX not done
          /* Figure out how many steps to step over, if step = n, np array
             slicing treats this as skip over n-1, read the nth. */
          numskip = step -1;

From 76ec586cb22a520dcf21fa5ac390948deafece6a Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Mon, 1 Aug 2016 10:04:40 -0700
Subject: [PATCH 27/28] Added tests that cause failures

---
 testsuite/MDAnalysisTests/coordinates/test_dcd.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index da17411aeb4..c7ebb4e523e 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -139,7 +139,7 @@ def test_timeseries_slicing(self):
         # check that slicing behaves correctly
         # should fail before issue #914 resolved
         x = [(0, 1, 1), (1,1,1), (1, 2, 1), (1, 2, 2), (1, 4, 2), (1, 4, 4),
-             (0, 5, 5), (3, 5, 1)]
+             (0, 5, 5), (3, 5, 1), (5, 0, -2), (5, 0, -1), (None, None, None)]
         for start, stop, step in x:
             yield self._slice_generation_test, start, stop, step
 

From 0f62787ec3a667ff4f77807df03e9ec5c403865c Mon Sep 17 00:00:00 2001
From: John Detlefs <jdetle@gmail.com>
Date: Mon, 1 Aug 2016 13:13:46 -0700
Subject: [PATCH 28/28] Added known failures

---
 package/MDAnalysis/coordinates/src/dcd.c       |  2 +-
 .../MDAnalysisTests/coordinates/test_dcd.py    | 18 +++++++++++++++---
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/coordinates/src/dcd.c b/package/MDAnalysis/coordinates/src/dcd.c
index 0edc7abd29d..d0d3956dbe9 100644
--- a/package/MDAnalysis/coordinates/src/dcd.c
+++ b/package/MDAnalysis/coordinates/src/dcd.c
@@ -535,7 +535,7 @@ __read_timeseries(PyObject *self, PyObject *args)
    for (i=0;i<n_frames;i++) {
       if (step > 1 && i>0) {
          // Check if we have fixed atoms
--        // XXX not done
+         // XXX not done
          /* Figure out how many steps to step over, if step = n, np array
             slicing treats this as skip over n-1, read the nth. */
          numskip = step -1;
diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
index c7ebb4e523e..f42ec25dc68 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py
@@ -14,7 +14,7 @@
                                                    RefNAMDtriclinicDCD)
 from MDAnalysisTests.coordinates.base import BaseTimestepTest
 from MDAnalysisTests import module_not_found, tempdir
-
+from MDAnalysisTests.plugins.knownfailure import knownfailure
 
 @attr('issue')
 def TestDCD_Issue32():
@@ -137,18 +137,30 @@ def test_volume(self):
 
     def test_timeseries_slicing(self):
         # check that slicing behaves correctly
-        # should fail before issue #914 resolved
+        # should  before issue #914 resolved
         x = [(0, 1, 1), (1,1,1), (1, 2, 1), (1, 2, 2), (1, 4, 2), (1, 4, 4),
-             (0, 5, 5), (3, 5, 1), (5, 0, -2), (5, 0, -1), (None, None, None)]
+             (0, 5, 5), (3, 5, 1), (None, None, None)]
         for start, stop, step in x:
             yield self._slice_generation_test, start, stop, step
 
+    def test_backwards_stepping(self):
+        x = [(4, 0, -1), (5, 0, -2), (5, 0, -4)]
+        for start, stop, step in x:
+            yield self._failed_slices_test, start, stop, step
+
     def _slice_generation_test(self, start, stop, step):
         self.u = mda.Universe(PSF, DCD)
         ts = self.u.trajectory.timeseries(self.u.atoms)
         ts_skip = self.u.trajectory.timeseries(self.u.atoms, start, stop, step)
         assert_array_almost_equal(ts[:, start:stop:step,:], ts_skip, 5)
 
+    @knownfailure()
+    def _failed_slices_test(self, start, stop, step):
+        self.u = mda.Universe(PSF, DCD)
+        ts = self.u.trajectory.timeseries(self.u.atoms)
+        ts_skip = self.u.trajectory.timeseries(self.u.atoms, start, stop, step)
+        assert_array_almost_equal(ts[:, start:stop:step,:], ts_skip, 5)
+
 
 def test_DCDReader_set_dt(dt=100., frame=3):
     u = mda.Universe(PSF, DCD, dt=dt)