Scripts for consensus protein design using pyRosetta
python3.8 design_scan.py --pdb --design_undef --db --n_designs --csv_out
--pdb = PDB structure of the protein to be designed
--alignment = Alignment file in clustal format. The first sequence of the alignment should perfetly match the structure
--csv_out = output csv file
--n_designs = number of designs for each combination of identity and consensus thresholds
--design_undef = yes or no. If "yes", residues without consensus will be designed by rosetta design function, if False they will be kept as found in the reference structure
get_consensus = generates a consensus sequence given an alignment, the structure and the consensus threshold
consensus_design = Given a structure and a consensus sequence, carries out the consensus design. Can be used with or without the design option. If design is set to True, all residues without consensus will be designed using Rosetta design
consensus_design runs clustal and blast locally