GitLab

The following lipid were added to the addMembrane() method: DLPC,
DLPE, DMPC, DOPC, DPPC.

Original pdb files were taken from
http://www.fos.su.se/~sasha/SLipids/Downloads.html .

Original files were obtained at temperatures between 293K and 303K.
NPT MD simulations were run for all the systems at 298K for ~10 ns
and the last simulation  step was used to create the pdb files.

Within Modeller.addExtraParticles(), add the ability to pass down
an option to modify compiled.matchResidueToTemplate() 's
ignoreExternalBonds parameter.

https://simtk.org/plugins/phpBB/viewtopicPhpbb.php?f=161&t=11264&p=0&start=0&view=&sid=e384beeb08f3bfd767dcfb546006ad63

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

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.

Adding alternative names of terminal nucleic acids (5' and 3' as DG5 and DG3). Adding alternative names of atoms H2', H2'', H5' and H5'' for nucleic acids.