Fixes in light of MDAnalysis 0.11.0.

Fixed resnum functionality, and made updates to use the new APIs in
MDAnalysis for internal Universe handling.

docs/Sim.rst

@@ -12,7 +12,8 @@ also give it a topology and/or trajectory files as we would to an MDAnalysis
 **Universe** ::
     
     >>> from mdsynthesis import Sim
-    >>> s = Sim('scruffy', universe=['path/to/topology', 'path/to/trajectory'])
+    >>> s = Sim('scruffy')
+    >>> s.universes.add('main', 'path/to/topology', 'path/to/trajectory')
 
 This will create a directory ``scruffy`` that contains a single file
 (``Sim.<uuid>.h5``).  That file is a persistent representation of the **Sim** on disk.
@@ -81,8 +82,8 @@ but they should actually go from 10 to 223. If we can't change the topology to r
 this, we could set the resnums for these residues to the canonical values ::
 
     >>> prot = s.universe.selectAtoms('protein')
-    >>> prot.residues.set_resnum(prot.residues.resids() + 9)
-    >>> prot.residues.resnums()
+    >>> prot.residues.set_resnum(prot.residues.resids + 9)
+    >>> prot.residues.resnums
     array([ 10,  11,  12,  13,  14,  15,  16,  17,  18,  19,  20,  21,  22,
             23,  24,  25,  26,  27,  28,  29,  30,  31,  32,  33,  34,  35,
             36,  37,  38,  39,  40,  41,  42,  43,  44,  45,  46,  47,  48,
@@ -109,7 +110,7 @@ and we might save selections using resnums as well. However, resnums aren't
 stored in the topology, so to avoid having to reset resnums manually each time
 we load the **Universe**, we can just store the resnum definition with ::
 
-    >>> s.universes.resnums('main', s.universe.residues.resnums())
+    >>> s.universes.resnums('main', s.universe.residues.resnums)
 
 and the resnum definition will be applied to the **Universe** both now and every
 time it is activated.

mdsynthesis/aggregators.py

@@ -406,7 +406,7 @@ def add(self, handle, *selection):
         # Conversion function, leave strings alone,
         # turn AtomGroups into their indices
         def conv(x):
-            return x if isinstance(x, basestring) else x.indices()
+            return x if isinstance(x, basestring) else x.indices
 
         self._backend.add_selection(
             self._treant._uname, handle, *map(conv, selection))
@@ -459,7 +459,7 @@ def asAtomGroup(self, handle):
         # - a list of strings
         # - a numpy array of indices
         if isinstance(selstring[0], basestring):
-            return self._treant.universe.selectAtoms(*selstring)
+            return self._treant.universe.select_atoms(*selstring)
         else:
             return self._treant.universe.atoms[selstring]
 

mdsynthesis/tests/test_treants.py

@@ -100,29 +100,29 @@ def test_set_resnums(self, treant):
             """Test that we can add resnums to a universe."""
             treant.universes.add('lolcats', GRO, XTC)
 
-            protein = treant.universe.selectAtoms('protein')
-            resids = protein.residues.resids()
+            protein = treant.universe.select_atoms('protein')
+            resids = protein.residues.resids
             protein.residues.set_resnum(resids + 3)
 
             treant.universes.resnums('lolcats',
-                                     treant.universe.atoms.resnums())
+                                     treant.universe.residues.resnums)
 
             treant.universes['lolcats']
 
-            protein = treant.universe.selectAtoms('protein')
-            assert (resids + 3 == protein.residues.resnums()).all()
+            protein = treant.universe.select_atoms('protein')
+            assert (resids + 3 == protein.residues.resnums).all()
 
-            # BUG IN MDANALYSIS PREVENTS RESETTING OF RESNUMS
-            # protein.residues.set_resnum(resids + 6)
+            # test resetting of resnums
+            protein.residues.set_resnum(resids + 6)
 
-            # assert (protein.residues.resnums == resids + 6).all()
-            # treant.universes.resnums('lolcats',
-            #                            treant.universe.atoms.resnums())
+            assert (protein.residues.resnums == resids + 6).all()
+            treant.universes.resnums('lolcats',
+                                     treant.universe.residues.resnums)
 
-            # treant.universes['lolcats']
+            treant.universes['lolcats']
 
-            # protein = treant.universe.selectAtoms('protein')
-            # assert (resids + 6 == protein.residues.resnums()).all()
+            protein = treant.universe.select_atoms('protein')
+            assert (resids + 6 == protein.residues.resnums).all()
 
         def test_KeyError(self, treant):
             """Test that a KeyError raised when trying to activate a Universe
@@ -151,12 +151,12 @@ def test_add_selection(self, treant):
             treant.selections.add('CA', 'protein and name CA')
             treant.selections.add('someres', 'resid 12')
 
-            CA = treant.universe.selectAtoms('protein and name CA')
-            someres = treant.universe.selectAtoms('resid 12')
+            CA = treant.universe.select_atoms('protein and name CA')
+            someres = treant.universe.select_atoms('resid 12')
 
-            assert (CA.indices() == treant.selections['CA'].indices()).all()
-            assert (someres.indices() ==
-                    treant.selections['someres'].indices()).all()
+            assert (CA.indices == treant.selections['CA'].indices).all()
+            assert (someres.indices ==
+                    treant.selections['someres'].indices).all()
 
         def test_remove_selection(self, treant):
             """Test universe removal"""
@@ -206,18 +206,18 @@ def test_add_selections_multiple_strings_via_add(self, treant):
             treant.selections.add('funky town', 'name N', 'name CA')
             assert 'funky town' in treant.selections
 
-            ref = treant.universe.selectAtoms('name N', 'name CA')
+            ref = treant.universe.select_atoms('name N', 'name CA')
             sel = treant.selections['funky town']
-            assert (ref.indices() == sel.indices()).all()
+            assert (ref.indices == sel.indices).all()
 
         def test_add_selections_multiple_strings_via_setitem(self, treant):
             """Add a selection that has multiple selection strings"""
             treant.selections['funky town 2'] = 'name N', 'name CA'
             assert 'funky town 2' in treant.selections
 
-            ref = treant.universe.selectAtoms('name N', 'name CA')
+            ref = treant.universe.select_atoms('name N', 'name CA')
             sel = treant.selections['funky town 2']
-            assert (ref.indices() == sel.indices()).all()
+            assert (ref.indices == sel.indices).all()
 
         def test_add_selection_as_atomgroup_via_add(self, treant):
             """Make an arbitrary AtomGroup then save selection as AG"""
@@ -227,7 +227,7 @@ def test_add_selection_as_atomgroup_via_add(self, treant):
             assert 'ag sel' in treant.selections
 
             ag2 = treant.selections['ag sel']
-            assert (ag.indices() == ag2.indices()).all()
+            assert (ag.indices == ag2.indices).all()
 
         def test_add_selection_as_atomgroup_via_setitem(self, treant):
             """Make an arbitrary AtomGroup then save selection as AG"""
@@ -237,7 +237,7 @@ def test_add_selection_as_atomgroup_via_setitem(self, treant):
             assert 'ag sel 2' in treant.selections
 
             ag2 = treant.selections['ag sel 2']
-            assert (ag.indices() == ag2.indices()).all()
+            assert (ag.indices == ag2.indices).all()
 
 
 class TestReadOnly:

setup.py

@@ -25,7 +25,7 @@
                 'pandas>=0.16.1',
                 'tables>=3.2.0',
                 'h5py>=2.5.0',
-                'MDAnalysis<=0.10.0',
+                'MDAnalysis>=0.11.0',
                 'scandir>=1.0',
                 'PyYAML>=3.11'
                 ],