Added unwrap and wrap transformations

package/.pylintrc

@@ -200,7 +200,6 @@ enable=abstract-class-instantiated,
        xrange-builtin,
        zip-builtin-not-iterating,
        map-builtin-not-iterating,
-       range-builtin-not-iterating,
 
 # Things we'd like to try.
 # Procedure:

package/CHANGELOG

@@ -14,12 +14,20 @@ The rules for this file:
 
 ------------------------------------------------------------------------------
 ??/??/18 tylerjereddy, richardjgowers, palnabarun, orbeckst, kain88-de, zemanj,
-         VOD555, davidercruz, jbarnoud, ayushsuhane, hfmull
+         VOD555, davidercruz, jbarnoud, ayushsuhane, hfmull, micaela-matta
 
   * 0.18.1
 
 Enhancements
 
+  * Added wrap/unwrap transformations
+  * Modified around selections to work with KDTree and periodic boundary
+    conditions.  Should reduce memory usage (#974 PR #2022)
+  * Modified topology.guessers.guess_bonds to automatically select the
+    fastest method for guessing bonds using
+    lib.distance.self_capped_distance (PR # 2006)
+  * Added lib.distances.self_capped_distance to internally select the
+    optimized method for distance evaluations of coordinates with itself. (PR # 2006)
   * Added augment functionality to create relevant images of particles 
     in the vicinity of central cell to handle periodic boundary
     conditions (PR #1977) 
@@ -68,6 +76,7 @@ Fixes
   * PDBWriter now properly sets start value
   * Zero length TopologyGroup now return proper shape array via to_indices
     (Issue #1974)
+  * Added periodic boundary box support to the Tinker file reader (Issue #2001)
 
 Changes
   * TopologyAttrs are now statically typed (Issue #1876)

package/MDAnalysis/coordinates/TXYZ.py

@@ -74,12 +74,19 @@ def __init__(self, filename, **kwargs):
         root, ext = os.path.splitext(self.filename)
         self.xyzfile = util.anyopen(self.filename)
         self._cache = dict()
-
+        # Check if file has box information saved
+        with util.openany(self.filename) as inp:
+           inp.readline()
+           line = inp.readline()
+           # If second line has float at second position, we have box info
+           try:
+               float(line.split()[1])
+           except ValueError:
+               self.periodic = False
+           else:
+               self.periodic = True
         self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
-        # Haven't quite figured out where to start with all the self._reopen()
-        # etc.
-        # (Also cannot just use seek() or reset() because that would break
-        # with urllib2.urlopen() streams)
+
         self._read_next_timestep()
 
     @property
@@ -103,6 +110,8 @@ def _read_xyz_n_frames(self):
         # the number of lines in the XYZ file will be 1 greater than the
         # number of atoms
         linesPerFrame = self.n_atoms + 1
+        if self.periodic:
+            linesPerFrame += 1
         counter = 0
         offsets = []
 
@@ -134,6 +143,8 @@ def _read_next_timestep(self, ts=None):
         try:
             # we assume that there is only one header line per frame
             f.readline()
+            if self.periodic:
+                ts.dimensions = f.readline().split() 
             # convert all entries at the end once for optimal speed
             tmp_buf = []
             for i in range(self.n_atoms):

package/MDAnalysis/core/selection.py

@@ -243,9 +243,6 @@ def __init__(self):
             self.apply = self._apply_distmat
 
         self.periodic = flags['use_periodic_selections']
-        # KDTree doesn't support periodic
-        if self.periodic:
-            self.apply = self._apply_distmat
 
     def validate_dimensions(self, dimensions):
         r"""Check if the system is periodic in all three-dimensions.
@@ -282,6 +279,9 @@ def _apply_KDTree(self, group):
         # All atoms in group that aren't in sel
         sys = group[~np.in1d(group.indices, sel.indices)]
 
+        if not sys:
+            return sys[[]]
+
         box = self.validate_dimensions(group.dimensions)
 
         cut = self.cutoff if box is not None else None
@@ -321,7 +321,8 @@ def _apply_KDTree(self, group):
         """
         sel = self.sel.apply(group)
         box = self.validate_dimensions(group.dimensions)
-        ref = sel.center_of_geometry(pbc=self.periodic)
+        periodic = box is not None
+        ref = sel.center_of_geometry(pbc=periodic)
         kdtree = PeriodicKDTree(box=box)
 
         cutoff = self.exRadius if box is not None else None
@@ -363,7 +364,8 @@ def _apply_KDTree(self, group):
         """
         sel = self.sel.apply(group)
         box = self.validate_dimensions(group.dimensions)
-        ref = sel.center_of_geometry(pbc=self.periodic)
+        periodic = box is not None
+        ref = sel.center_of_geometry(pbc=periodic)
 
         cut = self.cutoff if box is not None else None
         kdtree = PeriodicKDTree(box=box)
@@ -483,7 +485,7 @@ def __init__(self, parser, tokens):
         self.cutoff = float(tokens.popleft())
 
     def _apply_KDTree(self, group):
-        box = group.dimensions if self.periodic else None
+        box = self.validate_dimensions(group.dimensions)
         kdtree = PeriodicKDTree(box=box)
         cut = self.cutoff if box is not None else None
         kdtree.set_coords(group.positions, cutoff=cut)
@@ -496,7 +498,7 @@ def _apply_distmat(self, group):
         ref_coor = self.ref[np.newaxis, ...]
 
         ref_coor = np.asarray(ref_coor, dtype=np.float32)
-        box = group.dimensions if self.periodic else None
+        box = self.validate_dimensions(group.dimensions)
 
         dist = distances.distance_array(group.positions, ref_coor, box)
         mask = (dist <= self.cutoff).any(axis=1)