rmcgibbo/mdtraj — pull request #432 by swails (2014-05-01 18:27:56+00:00)
Title: Fix TINKER arc parser (WIP)

```
/.../mdtraj/formats/arc.pyc in load_arc(filename, top, stride, atom_indices)
73 mdtraj.ArcTrajectoryFile : Low level interface to TINKER .arc files
74 """
---> 75 from mdtraj.trajectory import _parse_topology, Trajectory
76
77 # we make it not required in the signature, but required here. although this

ImportError: No module named trajectory
```
and
```
/.../mdtraj/formats/arc.pyc in load_arc(filename, top, stride, atom_indices)
87
88 topology = _parse_topology(top)
---> 89 atom_indices = _cast_indices(atom_indices)
90 if atom_indices is not None:
91 topology = topology.subset(atom_indices)

NameError: global name '_cast_indices' is not defined
```

This nominally fixes the parser as it was. However, the ARC file format (as well as TINKER XYZ) has changed. I'm working on implementing the changes, but had to get the original working first. Not ready for merge yet.