Merge d7b9494 into 96c9d78

openpathsampling · Mar 12, 2016 · 70ffb67 · 70ffb67
2 parents 96c9d78 + d7b9494
commit 70ffb67
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Showing 5 changed files with 39 additions and 7 deletions.
diff --git a/openpathsampling/engines/features/base.py b/openpathsampling/engines/features/base.py
@@ -83,6 +83,24 @@ def _decorator(cls):
 
         __features__['classes'] += 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'):
+                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()
             # if '_reversed' not in __features__['lazy']:
@@ -91,7 +109,7 @@ def _decorator(cls):
         origin = dict()
         required = dict()
         # loop over all the features
-        for feature in features:
+        for feature in __features__['classes']:
 
             # add properties
             for prop in feature.attributes:
@@ -189,7 +207,11 @@ def _decorator(cls):
             ]
             code += [
                 "       cls.{0} : self._lazy[cls.{0}],".format(lazy)
-                for lazy in __features__['lazy']
+                for lazy in __features__['lazy'] if lazy not in __features__['numpy']
+            ]
+            code += [
+                "       cls.{0} : self._lazy[cls.{0}].copy(),".format(lazy)
+                for lazy in __features__['lazy'] if lazy in __features__['numpy']
             ]
             code += [
                 "    }"
@@ -202,7 +224,14 @@ def _decorator(cls):
         code += map(
             "    this.{0} = self.{0}".format,
             filter(
-                lambda x : x not in __features__['lazy'],
+                lambda x : x not in __features__['lazy'] and x not in __features__['numpy'],
+                __features__['parameters']
+            )
+        )
+        code += map(
+            "    this.{0} = self.{0}.copy()".format,
+            filter(
+                lambda x : x not in __features__['lazy'] and x in __features__['numpy'],
                 __features__['parameters']
             )
         )

diff --git a/openpathsampling/engines/features/coordinates.py b/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',

diff --git a/openpathsampling/engines/features/statics.py b/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())

diff --git a/openpathsampling/engines/openmm/snapshot.py b/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):

diff --git a/openpathsampling/engines/toy/snapshot.py b/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",