void associate_pir_alignment_from_file(int imol, std::string chain_id, std::string pir_alignment_file_name)
associate an alignment in a file with a chain in a model molecule
void associate_pir_alignment(int imol, std::string chain_id, std::string pir_alignment)
associate an alignment with a chain in a model molecule
void apply_pir_alignment(int imol, std::string chain_id)
apply the mutations of the associated alignment