I have 2 tasks that I hope you can help with. Both of these require conjugation of a moiety to multiple places on a large, multi chain protein. Command line solutions are fine. 

Task 1. Conjugate some group like a tosyl to selected cystine residues. There could be about 200 residues needing conjugation across 4 chains of a protein PDB file.

Task 2. Conjugate a peptide chain to the N or C terminus of a multi chain protein PDB file.  

I am already familiar with build structure protein and smiles, but connecting models without severe steric hindrance is problematic. Also, given the number of needed conjugations, it would be great it I could do this via command line (or some other function that I am currently not aware of) so that the tosyl or peptide chains needing connecting do not have to be positioned prior to making the covalent bond.

Much thanks to everyone in advance.

Best, 

Scott