Check for missing translation or rotation

When writing out transformations (for geometric
objects or datasets) report an error if the
transformation is missing either a rotation or
a translation. Skip this check if so requested.

ihm/dumper.py

@@ -62,10 +62,15 @@ def dump(self, system, writer):
 def _get_transform(rot_matrix, tr_vector):
     """Return a dict encoding a transform, suitable for passing to
        loop.write()"""
-    # mmCIF writer usually outputs floats to 3 decimal
-    # places, but we need more precision for rotation
-    # matrices
-    rm = [["%.6f" % e for e in rot_matrix[i]] for i in range(3)]
+    if rot_matrix in (None, ihm.unknown):
+        rm = [[rot_matrix for _ in range(3)] for _ in range(3)]
+    else:
+        # mmCIF writer usually outputs floats to 3 decimal
+        # places, but we need more precision for rotation
+        # matrices
+        rm = [["%.6f" % e for e in rot_matrix[i]] for i in range(3)]
+    if tr_vector in (None, ihm.unknown):
+        tr_vector = [tr_vector for _ in range(3)]
 
     return {'rot_matrix11': rm[0][0], 'rot_matrix21': rm[1][0],
             'rot_matrix31': rm[2][0], 'rot_matrix12': rm[0][1],
@@ -1242,6 +1247,8 @@ def dump_related_transform(self, system, writer):
                  "rot_matrix[1][3]", "rot_matrix[2][3]", "rot_matrix[3][3]",
                  "tr_vector[1]", "tr_vector[2]", "tr_vector[3]"]) as lp:
             for t in self._transform_by_id:
+                if self._check:
+                    util._check_transform(t)
                 lp.write(id=t._dtid,
                          **_get_transform(t.rot_matrix, t.tr_vector))
 
@@ -2085,6 +2092,8 @@ def dump_transformations(self, writer):
                  "rot_matrix[1][3]", "rot_matrix[2][3]", "rot_matrix[3][3]",
                  "tr_vector[1]", "tr_vector[2]", "tr_vector[3]"]) as lp:
             for t in self._transformations_by_id:
+                if self._check:
+                    util._check_transform(t)
                 lp.write(id=t._id, **_get_transform(t.rot_matrix, t.tr_vector))
 
     def dump_generic(self, writer):

ihm/util/__init__.py

@@ -92,6 +92,13 @@ def _check_residue(r):
                          % (r.seq_id, r.entity, len(r.entity.sequence)))
 
 
+def _check_transform(t):
+    if t.rot_matrix in (None, ihm.unknown):
+        raise ValueError("Transformation %s is missing rotation" % t)
+    if t.tr_vector in (None, ihm.unknown):
+        raise ValueError("Transformation %s is missing translation" % t)
+
+
 def _invert_ranges(ranges, end, start=1):
     """Given a sorted list of non-overlapping ranges, yield a new list which
        contains every range in the range start-end which was not in the

test/test_dumper.py

@@ -1694,6 +1694,29 @@ def test_dataset_dumper_dump(self):
 #
 """)
 
+    def test_dataset_dumper_dump_invalid_transform(self):
+        """Test DatasetDumper.dump() with invalid transformed dataset"""
+        system = ihm.System()
+
+        loc = ihm.location.PDBLocation('1cdf', version='foo', details='bar')
+        loc._id = 1
+        dst = ihm.dataset.Dataset(loc, details='baz')
+        t = ihm.geometry.Transformation(
+            rot_matrix=None, tr_vector=[1., 2., 3.])
+        td = ihm.dataset.TransformedDataset(dst, transform=t)
+
+        loc = ihm.location.InputFileLocation(repo='foo', path='bar')
+        loc._id = 2
+        ds2 = ihm.dataset.CXMSDataset(loc)
+        ds2.parents.append(td)
+        system.orphan_datasets.append(ds2)
+
+        d = ihm.dumper._DatasetDumper()
+        d.finalize(system)  # Assign IDs
+        self.assertRaises(ValueError, _get_dumper_output, d, system)
+        # OK if checks are disabled
+        _ = _get_dumper_output(d, system, check=False)
+
     def test_model_representation_dump(self):
         """Test ModelRepresentationDumper"""
         system = ihm.System()
@@ -3576,6 +3599,39 @@ def test_geometric_object_dumper(self):
 #
 """)
 
+    def test_geometric_object_dumper_invalid_rotation(self):
+        """Test GeometricObjectDumper with invalid rotation"""
+        system = ihm.System()
+        center = ihm.geometry.Center(1., 2., 3.)
+        trans = ihm.geometry.Transformation(None, [1., 2., 3.])
+        sphere = ihm.geometry.Sphere(center=center, transformation=trans,
+                                     radius=2.2, name='my sphere',
+                                     description='a test sphere')
+        system.orphan_geometric_objects.append(sphere)
+
+        dumper = ihm.dumper._GeometricObjectDumper()
+        dumper.finalize(system)
+        self.assertRaises(ValueError, _get_dumper_output, dumper, system)
+        # OK if checks are disabled
+        _ = _get_dumper_output(dumper, system, check=False)
+
+    def test_geometric_object_dumper_invalid_translation(self):
+        """Test GeometricObjectDumper with invalid translation"""
+        system = ihm.System()
+        center = ihm.geometry.Center(1., 2., 3.)
+        trans = ihm.geometry.Transformation([[1, 0, 0], [0, 1, 0], [0, 0, 1]],
+                                            ihm.unknown)
+        sphere = ihm.geometry.Sphere(center=center, transformation=trans,
+                                     radius=2.2, name='my sphere',
+                                     description='a test sphere')
+        system.orphan_geometric_objects.append(sphere)
+
+        dumper = ihm.dumper._GeometricObjectDumper()
+        dumper.finalize(system)
+        self.assertRaises(ValueError, _get_dumper_output, dumper, system)
+        # OK if checks are disabled
+        _ = _get_dumper_output(dumper, system, check=False)
+
     def test_feature_dumper(self):
         """Test FeatureDumper"""
         system = ihm.System()