GitLab

Fixes writing invalid PDBx/mmCIF files when residue insertion codes are blank (not empty) in Topology

From @peastman:

> Test cases are failing. I believe it's because the parent for a ScaledUnit needs to be a Unit, not another ScaledUnit. So in the line
>
> ```
>  hartree_base_unit = ScaledUnit(4.3597447222071e-18, joule_base_unit, "hartree", "Ha")
> ```
>
> replace joule_base_unit with joule.

This is of immediate need to QCEngine, in particular MolSSI/QCEngine#151

Improve the performance of sending the AmoebaVdwLambda to Cuda using pinned host memory; Updated the AmoebaVdwForceProxy to version 3, and added backward compatibility to version 2; updated TestAPIUnits.py to handle the per particle lambda flag

Fixed units in swigInputConfig.py for new Alchemical AMOEBA vdW methods exposed in the OpenMM API; implemented the getDefaultParameters() on the AmoebaVdwForceImpl to return 1.0 for AmoebaVdwAlpha; Use AmoebaVdwForce::Lambda() to refer to this parameter rather than the String AmoebaVdwAlpha

when the number of molecules does not agree
with the number of holders.

Don't parse resid, since we don't do anything with it anyway and it is not required to be an integer.