New quality checks

[RubenChM]

Some that needs to be implemented still. They come from the biocuration section from the deposition policies:

• Average distance between bonded atoms along the trajectory must be within an acceptable range
• Wrong atom charges - Atomic charges must be coherent according to chemical knowledge. If they are not between acceptable value ranges then the problem is reported to the author.
• Incoherent residues - All atoms which belong to the same residue must be bonded together. If they are not, then new residues are created to allocate the different groups of connected atoms from the incoherent residues.
• Stereoisomery checks? Amino-acids should be always L.

For more ideas we can use this documents from Bioexcel.