SMILES with uncertain stereochemistry

[jchodera]

Our SMILES-based setup pipeline will fail if the stereochemistry is not specified for molecules with chiral atoms or bonds. We should probably either:

• Require users specify molecules with certain stereochemistry and issue a failure quickly with a clear error message about how to correct this. We can use the OpenEye stereochemistry perception here.
• Automatically expand stereochemically uncertain molecules as a sort of !Combinatorial, maybe if expand_stereochemistry: yes option is enabled for the molecules: description for that molecule.

For now, the only major issue is that sometimes we don't get the current error message and YANK hangs. cc: https://github.com/choderalab/yank-examples/pull/31#issuecomment-260192892

[jchodera]

I've just discovered that a misconfigured wall clock time limit was the source of the lack of error message for one of the simulations.