sdf for non-cannonical residues

[alejandrovr]

Code to show how SDFs can be used as replacement of the templating code.

Because SDFs can be "drawn" with pymol, it can be more convinient and it does not need the templating code, which can cause issues in some edge cases: See PDB code 2VAG

Maybe we can add the SDF path as an option, so users can pick smiles templating or SDF?

[stefdoerr]

The issue is that you need to obtain an SDF with the exact coordinates of your molecule which is not always very easy or user-friendly. Another issue is if you have two copies of the residue, the second one would not match, then we need a way to assign for specific residues (and not residue names) an SDF. I think we need something more clever. The SMILES templating is an issue though because if you have something looking like backbone in the sidechain it can often mess up.