Rosetta EnzDes: Enzyme Design with Constraints and Interface Detection

-s 'inputs/1q91_CHGW_d1_mod.pdb' -extra_res_fa 'inputs/D2N_aX.params' -enzdes -detect_design_interface -cut1 6.0 -cut2 8.0 -cut3 10.0 -cut4 12.0 -cst_opt -cst_design -cst_min -cstfile 'inputs/Est_CHba_d2n.cst' -bb_min -chi_min -lig_packer_weight 1.8 -final_repack_without_ligand -additional_packing_ligand_rb_confs 4 #-ex_catalytic_rot 5 #-design_min_cycles 2 -include_catres_in_interface_detection -packing:soft_rep_design -out:file:o 'enz_score.out' -nblist_autoupdate -unboundrot 'inputs/1q91_CHGW_d1_mod.pdb' -mute 'core.io.database core.scoring.NeighborList' -restore_talaris_behavior

The space before '-detect_design_interface' and subsequent options is necessary for proper command-line parsing. In a command-line interface, each option and its parameter are separated by a space. This allows the program to recognize and interpret each option and its associated value correctly. For instance, '-detect_design_interface' is an option, and '-cut1', '-cut2', '-cut3', '-cut4', '-cst_opt', '-cst_design', '-cst_min', '-cstfile', '-bb_min', '-chi_min', '-lig_packer_weight', '-final_repack_without_ligand', '-additional_packing_ligand_rb_confs', and '-include_catres_in_interface_detection' are parameters. Therefore, a space is crucial between them for correct parsing.