Rename IMP.mmcif.Convert to IMP.mmcif.Writer

modules/mmcif/pyext/src/util.py

@@ -41,7 +41,7 @@ def __getitem__(self, ind):
         return "".join(reversed(ids))
 
 
-class Convert(object):
+class Writer(object):
     """Convert one or more IMP Models and/or RMF frames to mmCIF
        or BinaryCIF.
 

modules/mmcif/test/standards_exceptions

@@ -1,4 +1,4 @@
 value_object_exceptions=[]
-function_name_exceptions=['System.report', 'Convert.report']
+function_name_exceptions=['System.report', 'Writer.report']
 show_exceptions=[]
 spelling_exceptions=['rmf']

modules/mmcif/test/test_convert.py

@@ -76,7 +76,7 @@ def test_parse_sel_tuple(self):
         m = IMP.Model()
         top = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
         self.add_chains(m, top)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
 
         all_foo = c._parse_sel_tuple("foo")
@@ -93,7 +93,7 @@ def test_no_chains(self):
         """Trying to add a Hierarchy with no chains should give an error"""
         m = IMP.Model()
         top = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         self.assertIsNone(c.system.title)
         self.assertRaises(ValueError, c.add_model, [top], [])
 
@@ -103,7 +103,7 @@ def test_no_state_node(self):
         top = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
         top.set_name("Top node")
         self.add_chains(m, top)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
         self.assertEqual([x.description for x in c.system.entities],
                          ['foo', 'baz'])
@@ -131,7 +131,7 @@ def test_dna_rna(self):
         chain1 = top.get_child(1).get_child(0)
         self.assertTrue(IMP.atom.Chain.get_is_setup(chain1))
         IMP.atom.Chain(chain1).set_chain_type(IMP.atom.DNA)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
         self.assertIsInstance(c.system.entities[0].sequence[0],
                               ihm.RNAChemComp)
@@ -145,7 +145,7 @@ def test_duplicate_chain_ids(self):
         top.set_name("Top node")
         self.add_chains(m, top,
                         chains = (('foo', 'ACGT', 'X'), ('baz', 'ACCT', 'X')))
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
         self.assertEqual([x.id for x in c.system.asym_units],
                          ['A', 'B'])
@@ -158,7 +158,7 @@ def test_duplicate_molecule_names(self):
         self.add_chains(m, top,
                         chains = (('foo', 'ACGT', 'X'), ('foo', 'ACCT', 'Y'),
                                   ('foo', 'ACGT', 'Z')))
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
         self.assertEqual([x.id for x in c.system.asym_units],
                          ['X', 'Y', 'Z'])
@@ -188,7 +188,7 @@ def make_rmf(fname):
         fname = self.get_tmp_file_name("test_add_rmf.rmf3")
         make_rmf(fname)
 
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_rmf(fname)
         self.assertEqual(len(c.system.entities), 2)
         self.assertEqual(len(c.system.asym_units), 3)
@@ -203,7 +203,7 @@ def test_two_states(self):
         self.add_chains(m, state0)
         state1 = self.add_state(m, top, 1, "State_1")
         self.add_chains(m, state1)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
         # Entities/asyms should not be duplicated
         self.assertEqual([x.description for x in c.system.entities],
@@ -229,16 +229,16 @@ def test_filter_states(self):
         self.add_chains(m, state1)
 
         # No filtering -> two states
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
         self.assertEqual(len(c.system.state_groups[0]), 2)
 
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [], states=["State_0"])
         self.assertEqual(len(c.system.state_groups[0]), 1)
 
         # No states selected (and so no groups either)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [], states=["State_99"])
         self.assertEqual(len(c.system.state_groups), 0)
 
@@ -248,24 +248,24 @@ def test_group_ensembles(self):
         top = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
         self.add_chains(m, top)
 
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
         c.add_model([top], [])
         # No grouping -> ensemble for each model
         self.assertEqual(len(c.system.ensembles), 2)
 
         # Group into single ensemble
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         ens = c.add_model([top], [])
         c.add_model([top], [], ensembles=ens)
         self.assertEqual(len(c.system.ensembles), 1)
 
     def test_write(self):
-        """Test Convert.write() method"""
+        """Test Writer.write() method"""
         m = IMP.Model()
         top = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
         self.add_chains(m, top)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
         fname = 'test_write.cif'
         c.write(fname)
@@ -276,12 +276,12 @@ def test_write(self):
         os.unlink(fname)
 
     def test_report(self):
-        """Test Convert.report() method"""
+        """Test Writer.report() method"""
         sio = StringIO()
         m = IMP.Model()
         top = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
         self.add_chains(m, top)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
         c.report(sio)
 
@@ -307,7 +307,7 @@ def test_sampcon_ensemble(self):
         self.add_protocol(m, state0, sampcon=True)
 
         for top in (top1, top2, top3):
-            c = IMP.mmcif.Convert()
+            c = IMP.mmcif.Writer()
             c.add_model([top], [])
 
             e, = c.system.ensembles
@@ -350,7 +350,7 @@ def add_software(m, top):
         add_software(m, state0)
 
         for top in (top1, top2, top3):
-            c = IMP.mmcif.Convert()
+            c = IMP.mmcif.Writer()
             c.add_model([top], [])
 
             soft, = c.system.software
@@ -385,7 +385,7 @@ def add_script(m, top):
         add_script(m, state0)
 
         for top in (top1, top2, top3):
-            c = IMP.mmcif.Convert()
+            c = IMP.mmcif.Writer()
             c.add_model([top], [])
 
             loc, = c.system.locations
@@ -400,7 +400,7 @@ def test_same_assembly(self):
         top2 = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
         self.add_chains(m, top2)
 
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top1, top2], [])
         self.assertEqual(len(c.system.orphan_assemblies), 1)
         self.assertEqual(len(c.system.orphan_assemblies[0]), 3)
@@ -415,7 +415,7 @@ def test_different_assembly(self):
         self.add_chains(m, top2,
                         chains = (('foo', 'ACGT', 'X'), ('bar', 'ACGT', 'Y')))
 
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top1, top2], [])
         self.assertEqual(len(c.system.orphan_assemblies), 2)
         self.assertEqual(len(c.system.orphan_assemblies[0]), 3)
@@ -426,7 +426,7 @@ def test_model_creation(self):
         m = IMP.Model()
         top = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
         self.add_chains(m, top)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         chain0 = top.get_child(0).get_child(0)
         self.assertTrue(IMP.atom.Chain.get_is_setup(chain0))
         # Test that IMP residue numbering (11-14) maps to IHM (1-4)
@@ -510,7 +510,7 @@ def test_starting_models(self):
         frag.add_child(residue)
         chain1.add_child(frag)
 
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
         # Both models should have same representation, with same starting model
         state0_model, = c.system.state_groups[0][0][0]
@@ -525,7 +525,7 @@ def test_em3d_restraint(self):
         top = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
         self.add_chains(m, top)
         self.add_protocol(m, top)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         chain0 = top.get_child(0).get_child(0)
         r1 = self.add_structured_residue(m, chain0, 1)
         self.add_structured_residue(m, chain0, 2)

modules/mmcif/test/test_dumper.py

@@ -104,7 +104,7 @@ def test_software_dumper(self):
         m = IMP.Model()
         h = self.make_model(m)
         IMP.core.add_imp_provenance(h)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([h], [], name="model1")
 
         # Assign ID to IMP citation
@@ -161,7 +161,7 @@ def test_assembly_all_modeled(self):
         self.add_structured_residue(m, chain2, 3)
         self.add_structured_residue(m, chain3, 1)
         self.add_structured_residue(m, chain3, 2)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([h], [])
 
         foo, bar, baz = c.system.asym_units
@@ -235,7 +235,7 @@ def test_model_representation_dumper(self):
         frag1 = IMP.atom.Fragment.setup_particle(IMP.Particle(m), [3, 4])
         self.add_structure(frag1)
         chain.add_child(frag1)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([h], [])
 
         self._assign_entity_ids(c)
@@ -336,7 +336,7 @@ def _internal_test_starting_model_dumper(self, cif):
         h2 = self._make_residue_chain('Nup85', 'B', m)
         state2h.add_child(h2)
 
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([top], [])
 
         self._assign_entity_ids(c)
@@ -413,7 +413,7 @@ def test_workflow(self):
         prov = IMP.core.ScriptProvenance.setup_particle(m, IMP.Particle(m),
                                                         __file__)
         IMP.core.add_provenance(m, h, prov)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([h], [], name="model1")
 
         root = os.path.dirname(__file__)
@@ -451,7 +451,7 @@ def test_modeling_protocol(self):
         """Test ProtocolDumper"""
         m = IMP.Model()
         h = self.make_model_with_protocol(m)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([h], [], name="model1")
 
         self._assign_entity_ids(c)
@@ -498,7 +498,7 @@ def test_post_process(self):
         """Test PostProcessDumper"""
         m = IMP.Model()
         h = self.make_model_with_protocol(m)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([h], [], name="model1")
 
         self._assign_entity_ids(c)
@@ -534,7 +534,7 @@ def test_ensemble_info(self):
         """Test EnsembleDumper"""
         m = IMP.Model()
         h = self.make_model(m)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         ens = c.add_model([h], [], name="model1")
         ens[None].name = 'cluster 1'
 
@@ -567,7 +567,7 @@ def test_model_list(self):
         """Test ModelListDumper"""
         m = IMP.Model()
         h = self.make_model(m)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         ens = c.add_model([h], [], name="model1")
         ens[None].model_group.name = 'cluster 1'
         c.add_model([h], [], name="model2", ensembles=ens)
@@ -615,7 +615,7 @@ def test_em3d_dumper(self):
         em_filename = self.get_input_file_name('test.gmm.txt')
         r = MockGaussianEMRestraint(m, em_filename, [res1.get_particle()])
         r.set_was_used(True)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([h], [r], name="model1")
 
         # Assign dataset ID (=2 since the gmm is derived from an MRC)
@@ -668,7 +668,7 @@ def test_site_dumper_spheres_only(self):
         xyzr.set_radius(9.2)
         chains[1].add_child(pfrag)
 
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         ens = c.add_model([h], [], name="model1")
         ens[None].model_group.name = 'cluster 1'
 
@@ -725,7 +725,7 @@ def test_no_localization_densities(self):
         """Test DensityDumper with no density information"""
         m = IMP.Model()
         h = self.make_model_with_protocol(m)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         c.add_model([h], [], name="model1")
 
         dumper = ihm.dumper._DensityDumper()
@@ -737,7 +737,7 @@ def test_sampcon_localization_densities(self):
         """Test DensityDumper with IMP.sampcon output"""
         m = IMP.Model()
         h = self.make_model_with_protocol(m, sampcon=True)
-        c = IMP.mmcif.Convert()
+        c = IMP.mmcif.Writer()
         ens = c.add_model([h], [], name="model1")
         e = ens[None]
 

modules/mmcif/test/test_restraints.py

@@ -246,7 +246,7 @@ def test_all_restraints_saxs(self):
 
     def test_all_restraints_cross_link(self):
         """Test _AllRestraints with cross-link restraint"""
-        conv = IMP.mmcif.Convert()
+        conv = IMP.mmcif.Writer()
         m = IMP.Model()
         h = make_model(m, chains=[("Rpb1", "AMT", "X"),
                                   ("Rpb2", "ACC", "Z")])