Standalone PDB reader

[GiovanniBussi]

@plumed/all

@sreisser reported some problems reading PDBs with --mf_pdb:

• CRYST with sides 1/1/1 and angles 90/90/90 is read as is. That is, the parser does not know that all NMR structures have these sides hardcoded.
• The parser is ignoring atom numbers.

Actually, I personally try to avoid the --mf_ plugins as much as I can since they ofter have problems. Fox xtc/trr I recommend the xdrfile library. For gro file we have our own parser.

Our own pdb parser used in MOLFILE seems already sort of better than the mf_ one.

Should we implement a driver --pdb which uses our parser?

Giovanni