updated changelog

package/CHANGELOG

@@ -13,8 +13,9 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/16 jandom, abhinavgupta94, orbeckst, kain88-de, hainm, jbarnoud, dotsdl,
-   jdetle
+??/??/16 jandom, abhinavgupta94, orbeckst, kain88-de, hainm, jbarnoud,
+         dotsdl, richardjgowers, jdetle
+
   * 0.15.0
 
 Metadata
@@ -39,12 +40,31 @@ Fixes
   * change_release now finds number and dev (Issue #776)
   * test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
   * HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
+  * MOL2 files without substructure section can now be read (Issue #816)
+  * MOL2 files can be written without substructure section (Issue #816)
 
 Changes
 
   * PDB parsers/readers/writers replaced by permissive counterparts (Issue #777)
   * Generalized contact analysis class added. (Issue #702)
 
+Deprecations (Issue #599)
+
+  * Deprecated all `get_*` and `set_*` methods of Groups.
+  * Deprecation warnings for accessing atom attributes from Residue,
+    ResidueGroup, Segment, SegmentGroup. Will not be present or will
+    give per-level results.
+  * Deprecation warnings for accessing plural residue attributes from
+    Residue or Segment (will disappear), or from SegmentGroup (will give
+    per-Segment results).
+  * Deprecation warnings for accessing plural segment attributes from Segment
+    (will disappear).
+  * Deprecated Atom number, pos, centroid, universe setter
+  * Deprecated AtomGroup serials, write_selection
+  * Deprecated Residue name, id
+  * Deprecated Segment id, name
+  * Deprecated as_Universe function; not needed
+
 02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
          manuel.nuno.melo, Balasubra, Saxenauts, mattihappy
 

package/MDAnalysis/coordinates/MOL2.py

@@ -59,6 +59,8 @@ def __init__(self, filename, **kwargs):
         """Read coordinates from *filename*."""
         super(MOL2Reader, self).__init__(filename, **kwargs)
 
+        self.n_atoms = None
+
         blocks = []
 
         with util.openany(filename) as f:
@@ -93,16 +95,26 @@ def parse_block(self, block):
         if not len(atom_lines):
             raise Exception("The mol2 (starting at line {0}) block has no atoms"
                             "".format(block["start_line"]))
+        elif self.n_atoms is None:
+            # First time round, remember the number of atoms
+            self.n_atoms = len(atom_lines)
+        elif len(atom_lines) != self.n_atoms:
+            raise ValueError(
+                "MOL2Reader assumes that the number of atoms remains unchanged"
+                " between frames; the current "
+                "frame has {0}, the next frame has {1} atoms"
+                "".format(self.n_atoms, len(atom_lines)))
+
         if not len(bond_lines):
             raise Exception("The mol2 (starting at line {0}) block has no bonds"
                             "".format(block["start_line"]))
 
-        coords = []
-        for a in atom_lines:
+        coords = np.zeros((self.n_atoms, 3), dtype=np.float32)
+        for i, a in enumerate(atom_lines):
             aid, name, x, y, z, atom_type, resid, resname, charge = a.split()
-            x, y, z = float(x), float(y), float(z)
-            coords.append((x, y, z))
-        coords = np.array(coords, dtype=np.float32)
+            #x, y, z = float(x), float(y), float(z)
+            coords[i, :] = x, y, z
+
         return sections, coords
 
     def _read_next_timestep(self, ts=None):
@@ -124,16 +136,11 @@ def _read_frame(self, frame):
 
         sections, coords = self.parse_block(block)
 
-        self.ts.data['molecule'] = sections["molecule"]
-        self.ts.data['substructure'] = sections["substructure"]
-
-        # check if atom number changed
-        if len(coords) != self.n_atoms:
-            raise ValueError(
-                "MOL2Reader assumes that the number of atoms remains unchanged"
-                " between frames; the current "
-                "frame has {0}, the next frame has {1} atoms"
-                "".format(self.n_atoms, len(coords)))
+        for sect in ['molecule', 'substructure']:
+            try:
+                self.ts.data[sect] = sections[sect]
+            except KeyError:
+                pass
 
         self.ts.positions = np.array(coords, dtype=np.float32)
         self.ts.unitcell = unitcell
@@ -277,10 +284,9 @@ def encode_block(self, obj):
         atom_lines = "\n".join(atom_lines)
 
         try:
-            substructure = ["@<TRIPOS>SUBSTRUCTURE\n"]
-            substructure.extend(ts.data['substructure'])
+            substructure = ["@<TRIPOS>SUBSTRUCTURE\n"] + ts.data['substructure']
         except KeyError:
-            raise NotImplementedError("No MOL2 substructure type found in traj")
+            substructure = ""
 
         molecule = ts.data['molecule']
         check_sums = molecule[1].split()