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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.

Implemented private _addIons method that improves placement of ions in solvated box, specially for membrane systems

Has a much smaller effect compared to caching the improper search, but non-negligible and easy to do.

This reverts commit 5ef91d22.