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Additional changes to support LocalCoordinatesSite

VS2013 compile errors

This reverts commit fa806957.

This reverts commit a3998cae.

This reverts commit 5dfab798.

Fixing some sphinx doc typos

Created a new type of virtual site

Add support for native CHARMM files

Magic bytes at the beginning of the checkpoint

the file name (not the path) for "top" and "par" to determine file type.  Often
enough, these files are stored in a "toppar" directory, so all of them will be
interpreted as RTF files.

correction maps in their calculations.

patched up by me).

boxVectors directly (which is how you would do it if you set up a PDB with a
CRYST1 record, for instance).

My test with a periodic system now works, but the interface to adding box
vectors should be improved.