[WIP] Snapshot/System converters

gutis/.gitignore

@@ -0,0 +1 @@
+.coveragerc

gutis/converters.py

@@ -1,6 +1,46 @@
 """
 Functions to convert between OPS object and PyRETIS objects.
 """
+import pyretis
+import openpathsampling as paths
+import simtk.unit as unit
+import numpy as np
+
+
+def ops_box_vectors_to_pyretis(box_vectors):
+    """Convert OPS box_vectors (square numpy array) to PyRETIS ``Box``
+
+    Parameters
+    ----------
+    box_vectors: :class:`numpy.array` shape (n_dim, n_dim)
+        input box vectors from OpenPathSampling
+
+    Returns
+    -------
+    :class:`pyretis.core.Box`
+        PyRETIS ``Box`` object for the box vectors
+    """
+    if isinstance(box_vectors, unit.Quantity):
+        box_vectors = box_vectors._value
+    for i in range(len(box_vectors)):
+        for j in range(len(box_vectors[i])):
+            if i != j and box_vectors[i][j] != 0:
+                raise ValueError("PyRETIS requires rectangular boxes.")
+    box = pyretis.core.Box(size=[[0.0, box_vectors[i, i]]
+                                 for i in range(len(box_vectors))])
+    return box
+
+
+def pyretis_box_to_ops(box):
+    """Convert PyRETIS ``Box`` to OPS box_vectors (numpy array)
+    """
+    box_vectors = np.zeros(shape=(box.dim, box.dim))
+    for i in range(box.dim):
+        box_vectors[i, i] = box.length[i]
+
+    # TODO: may need to add units for OpenMM
+    return box_vectors
+
 
 def ops_snapshot_to_pyretis(snapshot):
     """Convert an OPS ``Snapshot`` to a PyRETIS ``System``
@@ -12,12 +52,37 @@ def ops_snapshot_to_pyretis(snapshot):
 
     Returns
     -------
-    :class:`pyretis.System`
+    :class:`pyretis.core.System`
         output system
     """
-    pass
+    box = ops_box_vectors_to_pyretis(snapshot.box_vectors)
+    system = pyretis.core.System(box=box)
+    load_system_with_snapshot(system, snapshot, update_box=False)
+    return system
 
-def pyretis_system_to_ops(system):
-    pass
 
+def load_system_with_snapshot(system, snapshot, update_box=True):
+    """Load a PyRETIS ``System`` object with data from an OPS ``Snapshot``
+    """
+    if update_box:
+        box = ops_box_vectors_to_pyretis(snapshot.box_vectors)
+        system.box = box
+
+    pos = snapshot.coordinates
+    vel = snapshot.velocities
 
+    # strip units if present
+    if isinstance(pos, unit.Quantity):
+        pos = pos._value
+    if isinstance(vel, unit.Quantity):
+        vel = vel._value
+
+    particles = pyretis.core.Particles(dim=system.box.dim)
+    particles.pos = pos
+    particles.vel = vel
+
+    system.particles = particles
+
+
+def pyretis_system_to_ops(system):
+    pass

gutis/tests/.gitignore

@@ -0,0 +1 @@
+.coveragerc