add dependent feature loading

openpathsampling/engines/features/base.py

@@ -73,7 +73,7 @@ def _decorator(cls):
             __features__ = dict()
 
         for name in ['attributes', 'minus', 'reversal', 'properties',
-                     'flip', 'numpy', 'lazy', 'required', 'classes', 'provides']:
+                     'flip', 'numpy', 'lazy', 'required', 'classes']:
             if name not in __features__:
                 __features__[name] = []
 
@@ -83,10 +83,23 @@ def _decorator(cls):
 
         __features__['classes'] += features
 
-        for feature in features:
+        # add provided additional feature and run though the added ones
+        # recursively until nothing is added
+        feat_no = 0
+        while feat_no < len(__features__['classes']):
+            feature = __features__['classes'][feat_no]
+
             # add provides additional features
             if hasattr(feature, 'provides'):
-                __features__['classes'] += feature.provides
+                if type(feature.provides) is list:
+                    for c in feature.provides:
+                        if c not in __features__['classes']:
+                            __features__['classes'].append(c)
+                else:
+                    if feature.provides not in __features__['classes']:
+                        __features__['classes'].append(feature.provides)
+
+            feat_no += 1
 
         if use_lazy_reversed:
             cls._reversed = DelayedLoader()

openpathsampling/engines/features/coordinates.py

@@ -5,10 +5,13 @@
     atomic coordinates
 """
 
+from openpathsampling.engines.features import xyz
 
 attributes = ['coordinates']
 numpy = ['coordinates']
 
+provides = [xyz]
+
 
 def netcdfplus_init(store):
     store.create_variable('coordinates', 'numpy.float32',

openpathsampling/engines/features/statics.py

@@ -2,9 +2,13 @@
 from shared import StaticContainerStore
 import mdtraj
 
+from openpathsampling.engines.features import xyz
+
 attributes = ['statics', 'box_vectors', 'md', 'coordinates']
 lazy = ['statics']
 
+provides = [xyz]
+
 
 def netcdfplus_init(store):
     store.storage.create_store('statics', StaticContainerStore())

openpathsampling/engines/openmm/snapshot.py

@@ -12,7 +12,6 @@
     features.velocities,
     features.coordinates,
     features.box_vectors,
-    features.xyz,
     features.topology
 ])
 class MDSnapshot(BaseSnapshot):
@@ -28,7 +27,6 @@ class MDSnapshot(BaseSnapshot):
 #         features.velocities,
 #         features.coordinates,
 #         features.box_vectors,
-#         features.xyz,
 #         features.topology
 #     ],
 #     description="A fast MDSnapshot",
@@ -39,7 +37,6 @@ class MDSnapshot(BaseSnapshot):
 @features.base.attach_features([
     features.statics,
     features.kinetics,
-    features.xyz,
     features.topology  # for compatibility
 ])
 class Snapshot(BaseSnapshot):

openpathsampling/engines/toy/snapshot.py

@@ -27,7 +27,6 @@
     features=[
         features.velocities,
         features.coordinates,
-        features.xyz,
         features.topology
     ],
     description="Simulation snapshot. Only references to coordinates and velocities",