Initial commit

Created liquidgen.tcl to provide liquidgen plugin for VMD
Added initial package requirements
Built basic GUI which works as extension in VMD

-PDB/PSF file browse/input
-Box dimensions (x,y,z) input
Removed old liquidgen.tcl file (forgot earlier)
Updated gui and fixed namespaces

-added num iterations
-added cube and early rejection check boxes
-added save directory field
-added populate button (only prints options right now)
Molecules loaded into viewer, some error handling

Also cleaned up gui code
Parameter checking in entries and proc populate
 -niter
 -box dimensions
Added reset button
PSF is now loaded into top molecule coordinate info
Replication is finally working! (no overlap checking yet)

-new molecules added as segments
-translated/rotated from parent molecule randomly within box
-added set_defaults proc to auto fill some values
-temporarily using num iterations to fill box with certain # molecules
Fixed bug in "Fill" button - now resets psf
Removed redundant code

-coordinates were being written twice
Implemented different populate method - only requires one write/reload to file

-generate # blank molecules using given density estimate (spheres/unit volume)
-write and reload pdb/psf
-move each molecule (scatter proc)
-some work on early rejection
Moved scattering to proc - overlap checking implemented

-molecules are rescattered if atomic radii overlap
Linked file saving to given filenames - not just tmp.pdb anymore
Implemented loops to adjust for PBC although they do not actually move atoms yet
Switched from using segments to residues to add molecules

-still need to work on PBC
Added some useful comments. Cleaned up some disorganized code.
Coordinates passed for overlap checking are now adjusted for PBC.

-coords written to PDB file are not wrapped as NAMD will do that
 during a run
Added proc to write xsc file. GUI layout tweaking.
Added proc to calculate density
Multiple updates:
-added small results section (report density, number molecules added)
-renamed some data variables for clarity
-fixed bug for non-cubic boxes boundary setup (missing $)
Added some error handling and overwrite file checking.
-reorganized some procs