Preparing for aria integration

.gitignore

@@ -9,4 +9,4 @@ ariaec.egg-info/
 docs/_static/
 docs/_templates/
 .svn/
-examples*
+examples-dev

ariaec/converter.py

@@ -629,7 +629,7 @@ assign (resid {res1} and name n) (resid {res1} and name ca) (resid {res1} and na
 
 class AriaEcXMLConverter(AriaXMLConverter):
     """XML converter ariaec to aria"""
-
+    # TODO: use aria api instead to generate xml files
     def __init__(self, *args, **kwargs):
         self.restraint_list = []
         super(AriaEcXMLConverter, self).__init__(*args, **kwargs)

ariaec/reader.py

@@ -16,6 +16,7 @@ from .protmap import (ResMap, ResAtmMap)
 
 LOG = logging.getLogger(__name__)
 # TODO: check if Atom is still used ...
+# TODO: Should use conkit in the future
 Atom = collections.namedtuple("Atom", ["name", "coords"])