More tests passing after merge

Autodesk · Jun 20, 2017 · 7ef3bfa · 7ef3bfa
1 parent 0eab030
commit 7ef3bfa
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Showing 6 changed files with 17 additions and 14 deletions.
diff --git a/DockerMakefiles/buildfiles/ambertools/runsander.py b/DockerMakefiles/buildfiles/ambertools/runsander.py
@@ -81,9 +81,7 @@ def convert(q, units):
         10.0
     """
     quantity = q['value'] * ureg(q['units'])
-    return quantity.m_as(units)
-
-
+    return quantity.value_in(units)
 
 
 ##### helper routines below ######

diff --git a/moldesign/_tests/test_atoms_and_bonds.py b/moldesign/_tests/test_atoms_and_bonds.py
@@ -5,7 +5,7 @@
 
 from .test_ambertools_xface import protein_default_amber_forcefield, pdb1yu8
 from .molecule_fixtures import h2
-from .test_pyscf_xface import h2_rhfwfn
+from .test_qm_xfaces import h2_rhfwfn
 
 
 def test_forcefield_atom_term_access(protein_default_amber_forcefield):

diff --git a/moldesign/_tests/test_molecules.py b/moldesign/_tests/test_molecules.py
@@ -9,7 +9,7 @@
 
 from .object_fixtures import *
 from .test_ambertools_xface import protein_default_amber_forcefield
-from .test_pyscf_xface import h2_rhfwfn
+from .test_qm_xfaces import h2_rhfwfn
 
 
 def test_h2_protected_atom_arrays(h2):

diff --git a/moldesign/interfaces/openbabel.py b/moldesign/interfaces/openbabel.py
@@ -159,11 +159,9 @@ def mol_to_pybel(mdtmol):
         if atom.residue and atom.residue not in resmap:
             obres = obmol.NewResidue()
             resmap[atom.residue] = obres
-            obres.SetChain(str(
-                    mdt.utils.if_not_none(atom.chain.name, 'Z')[0]))
-            obres.SetName(str(
-                    mdt.utils.if_not_none(atom.residue.pdbname, 'UNL')))
-            obres.SetNum(mdt.utils.if_not_none(atom.residue.pdbindex, '0'))
+            obres.SetChain(str(atom.chain.pdbname)[0] if atom.chain.pdbname else 'Z')
+            obres.SetName(str(atom.residue.pdbname) if atom.residue.pdbname else 'UNL')
+            obres.SetNum(str(atom.residue.pdbindex) if atom.residue.pdbindex else 0)
         else:
             obres = resmap[atom.residue]
 

diff --git a/moldesign/models/jsonmodel.py b/moldesign/models/jsonmodel.py
@@ -116,7 +116,7 @@ def _make_wfn(self, state):
         return wfn
 
     @staticmethod
-    def _json_to_quantities(jsonprops):
+    def _json_to_quantities(jsonprops):  # TODO: handle this within JSON decoder
         props = {}
         for name, property in jsonprops.items():
             if isinstance(property, dict) and len(property) == 2 and \
@@ -142,7 +142,7 @@ def _make_minimization_job(self, nsteps):
         params['runType'] = 'minimization'
         if nsteps is not None:
             params['minimization_steps'] = 100
-        inputfiles['params.json'] = json.dumps(dict(params))
+        inputfiles['params.json'] = mdt.utils.json_dumps(dict(params))
 
         job = pyccc.Job(image=mdt.compute.get_image_path(self.IMAGE),
                         command='%s && %s' % (self.RUNNER, self.PARSER),

diff --git a/moldesign/utils/json_extension.py b/moldesign/utils/json_extension.py
@@ -17,11 +17,18 @@
 from . import args_from
 
 
+# TODO: defined JSON types that we can serialize directly into MDT objects OR
+#       use a JSON "pickling" library (only if there's more complexity than covered here already)
+
 class JsonEncoder(json.JSONEncoder):
     def default(self, obj):
         if hasattr(obj, 'to_json'):
-            obj = obj.to_json()
-        return obj
+            return obj.to_json()
+        elif hasattr(obj, 'tolist'):
+            return obj.tolist()
+        else:
+            raise TypeError('No seralizer for object "%s" (class: %s)'
+                            % (obj,obj.__class__.__name__))
 
 
 @args_from(json.dump)