Pepteditor: Replace MCOORD with an all-purpose atom/molecule addition feature.

[primaryodors]

Create a new feature in Pepteditor that can add an atom or molecule represented by any SDF file or any SMILES string to the protein, docking it in place near specified residues.

Make sure it can coordinate metal ions.

Give it also the ability to make covalent bonds to the protein, e.g. an aldehyde and a lysine residue to form a Schiff base. Can test using bovine rhodopsin (btRHO) and 11-cis retinal.

Once this is in place, add a deprecated notice to the MCOORD feature and recommend using the new feature in its place.