Path sampling for ligand binding/unbinding kinetics

Using path sampling to study ligand binding/unbinding kinetics

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openpathsampling errors

@jhprinz : I've created a very basic attempt at ligand unbinding for a simple CB7:B2 host-guest system (using openmmtools >=0.8.0):
https://github.com/choderalab/ligand-binding-pathsampling/tree/master/host-guest/cb7-b2

The current script dies with the error

[LSKI1497:ligand-binding-pathsampling/host-guest/cb7-b2] choderaj% python -i run-ops.py
Creating host-guest system...
Creating template...
Creating an integrator...
Selecting a platform...
Creating engine...
Creating a "hot" engine...
Initializing storage...
(store.engines[DynamicsEngine], 11, UUID('137432cf-5ab5-11e6-9087-000000000010'))
(store.engines[DynamicsEngine], 11, UUID('137432cf-5ab5-11e6-9087-000000000014'))
CPU
CPU
<openpathsampling.engines.openmm.topology.MDTrajTopology object at 0x119cf75d0>
Traceback (most recent call last):
  File "run-ops.py", line 111, in <module>
    storage.save([compute_contacts])
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/netcdfplus.py", line 617, in save
    return [self.save(part, idx) for part in obj]
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/netcdfplus.py", line 628, in save
    return store, store_idx, store.save(obj, idx)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/objects.py", line 1371, in save
    reference = super(UniqueNamedObjectStore, self).save(obj, idx)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/objects.py", line 1183, in save
    reference = super(NamedObjectStore, self).save(obj)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/objects.py", line 853, in save
    self._save(obj, n_idx)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/storage/stores/collectivevariable.py", line 18, in _save
    self.add_diskcache(cv)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/storage/stores/collectivevariable.py", line 96, in add_diskcache
    chunksize=chunksize
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/storage/stores/snapshot.py", line 939, in add_cv
    params = NetCDFPlus.get_value_parameters(cv(template))
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 231, in __getitem__
    return self._post[items]
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 244, in __getitem__
    return np.array(self._post[items])
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 277, in __getitem__
    return self._post[[items]][0]
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 72, in __getitem__
    rep = self._post[nones]
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 65, in __getitem__
    results = self._get_list(items)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 360, in _get_list
    if self.scalarize_numpy_singletons and results.shape[-1] == 1:
AttributeError: 'tuple' object has no attribute 'shape'

Any ideas?

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