Final 0.3 changes

README.rst

@@ -164,6 +164,16 @@ The ``Xyz`` object itself can also be saved:
 Changelog
 ---------
 
+Release 0.3.0
+~~~~~~~~~~~~~
+
+`11 August 2017`
+
+* Added classes for Molecules, Chains, Residues, and their interfaces.
+* Added charges to atoms and structures.
+* Add ability to create AtomicStructures from AtomicStructures.
+
+
 Release 0.2.0
 ~~~~~~~~~~~~~
 

atomium/structures/chains.py

@@ -92,17 +92,18 @@ def verify(sequence):
         residues = set()
         for atom in sequence.atoms():
             residues.add(atom.residue())
-        seq = [list(residues)[0]]
-        while seq[-1].next() is not None and seq[-1].next() in residues:
-            seq.append(seq[-1].next())
-        while seq[-1].previous() is not None and seq[-1].previous() in residues:
-            seq.append(seq[-1].previous())
-        if set(seq) != residues:
-            raise SequenceConnectivityError(
-             "{} missing from sequence {} - check connections".format(
-              residues, residues - set(seq)
-             )
-            )
+        if residues:
+            seq = [list(residues)[0]]
+            while seq[-1].next() is not None and seq[-1].next() in residues:
+                seq.append(seq[-1].next())
+            while seq[-1].previous() is not None and seq[-1].previous() in residues:
+                seq.append(seq[-1].previous())
+            if set(seq) != residues:
+                raise SequenceConnectivityError(
+                 "{} missing from sequence {} - check connections".format(
+                  residues, residues - set(seq)
+                 )
+                )
         return True
 
 

atomium/structures/models.py

@@ -94,7 +94,9 @@ def molecules(self, molecule_id=None, name=None, generic=False):
              lambda m: not isinstance(m, (Residue, Chain)), molecules
             ))
         if molecule_id:
-            molecules = set(filter(lambda m: m.molecule_id() == molecule_id, molecules))
+            molecules = set(filter(
+             lambda m: m.molecule_id() == molecule_id, molecules
+            ))
         if name:
             molecules = set(filter(lambda m: m.name() == name, molecules))
         return molecules

docs/source/changelog.rst

@@ -1,6 +1,16 @@
 Changelog
 ---------
 
+Release 0.3.0
+~~~~~~~~~~~~~
+
+`11 August 2017`
+
+* Added classes for Molecules, Chains, Residues, and their interfaces.
+* Added charges to atoms and structures.
+* Add ability to create AtomicStructures from AtomicStructures.
+
+
 Release 0.2.0
 ~~~~~~~~~~~~~
 

tests/structure_tests/test_residue_sequences.py

@@ -137,6 +137,11 @@ def test_can_reject_unconnected_residues(self):
             ResidueSequence.verify(self.sequence)
 
 
+    def test_empty_sequences_pass(self):
+        self.sequence.atoms = lambda: set()
+        self.assertTrue(ResidueSequence.verify(self.sequence))
+
+
 
 class ResidueSequenceLengthTests(ResidueSequenceTest):