Tidying of topology related things

Changed Universe._psf to Universe._topology

topology.base.TopologyReader now has keyword 'universe' which
gets saved as self._u.  This is then passed to Atoms on creation.

Atoms can now be passed their Universe as kwarg.

All '_things' renamed to 'things' in Universe._topology.

Renamed __is_guessed to _is_guessed in Bond (death to double
underscores)

Added absolute_import from future to all topology modules (Issues #132 #216)

Updated tests to reflect new names

package/MDAnalysis/core/AtomGroup.py

@@ -386,7 +386,7 @@ class Atom(object):
 
     def __init__(self, number, name, type, resname, resid, segid, mass, charge,
                  residue=None, segment=None, radius=None, bfactor=None,
-                 resnum=None, serial=None, altLoc=None):
+                 resnum=None, serial=None, altLoc=None, universe=None):
         self.number = number
         self.name = name
         self.altLoc = altLoc
@@ -402,7 +402,7 @@ def __init__(self, number, name, type, resname, resid, segid, mass, charge,
         self.radius = radius
         self.bfactor = bfactor
         self.serial = serial
-        self.__universe = None
+        self.__universe = universe
 
     def __repr__(self):
         return ("<Atom {idx}: {name} of type {t} of resname {rname}, "
@@ -2964,7 +2964,8 @@ class Universe(object):
       :attr:`Universe.trajectory.ts` is the current time step
     - :attr:`Universe.dimensions`: current system dimensions (simulation unit cell, if
       set in the trajectory)
-    - bonds, angles, dihedrals, impropers (low level access through :attr:`Universe._psf`)
+    - bonds, angles, dihedrals, impropers
+      (low level access through :attr:`Universe._topology`)
 
     .. Note::
 
@@ -3120,9 +3121,9 @@ def __init__(self, *args, **kwargs):
                                     permissive=perm,
                                     tformat=topology_format)
         try:
-            with parser(self.filename,
+            with parser(self.filename, universe=self,
                         guess_bonds_mode=kwargs.get('bonds', False)) as p:
-                self._psf = p.parse()
+                self._topology = p.parse()
         except IOError as err:
             raise IOError("Failed to load from the topology file {}"
                           " with parser {}.\n"
@@ -3162,17 +3163,15 @@ def _fill_cache(self, name, value):
         self._cache[name] = value
 
     def _init_topology(self):
-        """Populate Universe attributes from the structure dictionary *_psf*."""
-        self.atoms = AtomGroup(self._psf["_atoms"])
+        """Populate Universe attributes from the structure dictionary
+        *_topology*.
+        """
+        self.atoms = AtomGroup(self._topology['atoms'])
 
         # XXX: add H-bond information here if available from psf (or other sources)
         # segment instant selectors
         self._build_segments()
 
-        # Let atoms access the universe
-        for a in self.atoms:
-            a.universe = self
-
     def _build_segments(self):
         """Parse list of atoms into segments.
 
@@ -3201,7 +3200,7 @@ def _build_segments(self):
         self.universe = self  # for Writer.write(universe), see Issue 49
 
     def _init_bonds(self):
-        """Set bond information from u._psf['_bonds']
+        """Set bond information from u._topology['bonds']
 
         .. versionchanged 0.9.0
            Now returns a :class:`~MDAnalysis.topology.core.TopologyGroup`
@@ -3216,11 +3215,11 @@ def fix_order(bondset):
 
         bondlist = set()
 
-        defined_bonds = fix_order(self._psf.get('_bonds', set()))
-        guessed_bonds = fix_order(self._psf.get('_guessed_bonds', set()))
+        defined_bonds = fix_order(self._topology.get('bonds', set()))
+        guessed_bonds = fix_order(self._topology.get('guessed_bonds', set()))
         # Some topologies define an order for bonds, this is stored
         # as dict of bondtuple:value
-        bondorder = self._psf.get('_bondorder', False)
+        bondorder = self._topology.get('bondorder', False)
         # Defined bonds take priority, remove bonds in 'guessed' that are in 'defined'
         guessed_bonds.difference_update(defined_bonds)
 
@@ -3246,14 +3245,14 @@ def fix_order(bondset):
             return None
 
     def _init_angles(self):
-        """Builds angle information from u._psf['_angles']
+        """Builds angle information from u._topology['angles']
 
         Returns ``None`` if no angle information is present, otherwise
         returns a :class:`~MDAnalysis.topology.core.TopologyGroup`
 
         .. versionadded 0.9.0
         """
-        angle_entries = self._psf.get('_angles', None)
+        angle_entries = self._topology.get('angles', None)
         if angle_entries is None:
             return None
         else:
@@ -3267,14 +3266,14 @@ def _init_angles(self):
                 return None
 
     def _init_torsions(self):
-        """Builds torsion information from u._psf['_dihe']
+        """Builds torsion information from u._topology['torsions']
 
         Returns ``None`` if no torsion information is present, otherwise
         returns a :class:`~MDAnalysis.topology.core.TopologyGroup`
 
         .. versionadded 0.9.0
         """
-        torsion_entries = self._psf.get('_dihe', None)
+        torsion_entries = self._topology.get('torsions', None)
         if torsion_entries is None:
             return None
         else:
@@ -3288,14 +3287,14 @@ def _init_torsions(self):
                 return None
 
     def _init_impropers(self):
-        """Build improper torsion information from u._psf['_impr']
+        """Build improper torsion information from u._topology['impropers']
 
         Returns ``None`` if no improper torsion information is present,
         otherwise returns a :class:`~MDAnalysis.topology.core.TopologyGroup`
 
         .. versionadded 0.9.0
         """
-        torsion_entries = self._psf.get('_impr', None)
+        torsion_entries = self._topology.get('impropers', None)
         if torsion_entries is None:
             return None
         else:
@@ -3518,7 +3517,7 @@ def bonds(self, bondlist):
         .. versionadded:: 0.9.0
         """
         del self.bonds
-        self._psf['_bonds'] = bondlist
+        self._topology['bonds'] = bondlist
         self._fill_cache('bonds', self._init_bonds())
 
     @bonds.deleter
@@ -3547,7 +3546,7 @@ def angles(self):
     @angles.setter
     def angles(self, bondlist):
         del self.angles
-        self._psf['_angles'] = bondlist
+        self._topology['angles'] = bondlist
         self._fill_cache('angles', self._init_angles())
 
     @angles.deleter
@@ -3570,7 +3569,7 @@ def torsions(self):
     @torsions.setter
     def torsions(self, bondlist):
         del self.torsions
-        self._psf['_dihe'] = bondlist
+        self._topology['torsions'] = bondlist
         self._fill_cache('torsions', self._init_torsions())
 
     @torsions.deleter
@@ -3593,7 +3592,7 @@ def impropers(self):
     @impropers.setter
     def impropers(self, bondlist):
         del self.impropers
-        self._psf['_impr'] = bondlist
+        self._topology['impropers'] = bondlist
         self._fill_cache('impropers', self._init_impropers())
 
     @impropers.deleter

package/MDAnalysis/topology/CRDParser.py

@@ -29,10 +29,11 @@
    :inherited-members:
 
 """
+from __future__ import absolute_import
 
-from MDAnalysis.core.AtomGroup import Atom
-from MDAnalysis.core.util import openany, FORTRANReader
-from MDAnalysis.topology.core import guess_atom_type, guess_atom_mass, guess_atom_charge
+from ..core.AtomGroup import Atom
+from ..core.util import openany, FORTRANReader
+from .core import guess_atom_type, guess_atom_mass, guess_atom_charge
 from .base import TopologyReader
 
 
@@ -75,10 +76,11 @@ def parse(self):
                 atomtype = guess_atom_type(name)
                 mass = guess_atom_mass(name)
                 charge = guess_atom_charge(name)
-                atoms.append(Atom(atom_serial, name, atomtype, resName, TotRes, chainID, mass, charge))
+                atoms.append(Atom(atom_serial, name, atomtype, resName,
+                                  TotRes, chainID, mass, charge, universe=self._u))
                 atom_serial += 1
 
         structure = {}
-        structure["_atoms"] = atoms
+        structure['atoms'] = atoms
 
         return structure

package/MDAnalysis/topology/DMSParser.py

@@ -32,12 +32,13 @@
    :inherited-members:
 
 """
+from __future__ import absolute_import
 
 import sqlite3
 import os
 
-from MDAnalysis.core.AtomGroup import Atom
-from MDAnalysis.topology.core import guess_atom_type
+from ..core.AtomGroup import Atom
+from .core import guess_atom_type
 from .base import TopologyReader
 
 
@@ -92,7 +93,8 @@ def dict_factory(cursor, row):
                     atoms = [Atom(p["id"], p["name"].strip(),
                                   guess_atom_type(p["name"].strip()),
                                   p["resname"].strip(), p["resid"],
-                                  p["segid"].strip(), p["mass"], p["charge"])
+                                  p["segid"].strip(), p["mass"], p["charge"],
+                                  universe=self._u)
                              for p in particles]
                 except KeyError:
                     raise ValueError("Failed reading atom information")
@@ -112,6 +114,8 @@ def dict_factory(cursor, row):
         # All the records below besides donors and acceptors can be contained in a DMS file.
         # In addition to the coordinates and bonds, DMS may contain the entire force-field
         # information (terms+parameters),
-        structure = {"_atoms": atoms, "_bonds": tuple(bondlist), "_bondorder": bondorder}
+        structure = {"atoms": atoms,
+                     "bonds": tuple(bondlist),
+                     "bondorder": bondorder}
 
         return structure

package/MDAnalysis/topology/ExtendedPDBParser.py

@@ -51,9 +51,9 @@
    :inherited-members:
 
 """
+from __future__ import absolute_import
 
-import MDAnalysis.coordinates.PDB
-import PrimitivePDBParser
+from . import PrimitivePDBParser
 
 
 class ExtendedPDBParser(PrimitivePDBParser.PrimitivePDBParser):
@@ -69,4 +69,5 @@ class ExtendedPDBParser(PrimitivePDBParser.PrimitivePDBParser):
     """
     def __init__(self, filename, **kwargs):
         super(ExtendedPDBParser, self).__init__(filename, **kwargs)
-        self.PDBReader = MDAnalysis.coordinates.PDB.ExtendedPDBReader
+        from ..coordinates.PDB import ExtendedPDBReader
+        self.PDBReader = ExtendedPDBReader

package/MDAnalysis/topology/GMSParser.py

@@ -39,11 +39,12 @@
 """
 from __future__ import absolute_import
 
+import re
+
 from ..core.AtomGroup import Atom
 from ..core.util import openany
 from .core import get_atom_mass, guess_atom_charge, guess_atom_element
 from .base import TopologyReader
-import re
 
 
 class GMSParser(TopologyReader):
@@ -82,10 +83,10 @@ def parse(self):
                 mass = get_atom_mass(elem)
                 #TODO: may be use coordinates info from _m.group(3-5) ??
                 at = Atom(i, name, elem, resname, resid,
-                          segid, mass, charge)
+                          segid, mass, charge, universe=self._u)
                 atoms.append(at)
                 i += 1
 
-        struc = {"_atoms": atoms}
+        struc = {"atoms": atoms}
 
         return struc

package/MDAnalysis/topology/GROParser.py

@@ -31,9 +31,10 @@
    :inherited-members:
 
 """
+from __future__ import absolute_import
 
-from MDAnalysis.core.util import openany
-from MDAnalysis.core.AtomGroup import Atom
+from ..core.util import openany
+from ..core.AtomGroup import Atom
 from .core import get_atom_mass, guess_atom_charge, guess_atom_element
 from .base import TopologyReader
 
@@ -89,8 +90,8 @@ def parse(self):
                     # Just use the atom_iter (counting from 0) rather than
                     # the number in the .gro file (which wraps at 99999)
                     atoms.append(Atom(atom_iter, name, atype, resname, resid,
-                                      segid, mass, charge))
+                                      segid, mass, charge, universe=self._u))
                     atom_iter += 1
-        structure = {'_atoms':atoms}
+        structure = {'atoms': atoms}
 
         return structure