| 135 | |
| 136 | |
| 137 | def parse(): |
| 138 | parser = argparse.ArgumentParser(description='CDR design') |
| 139 | parser.add_argument('--ckpt', type=str, default='./checkpoints/ckpt/rabd_cdrh3_mean.ckpt', |
| 140 | help='Path to the checkpoint') |
| 141 | parser.add_argument('--cdr_type', type=str, choices=['H3'], default='H3', |
| 142 | help='Type of cdr to design. Note that this should be consistent with training objective of the checkpoint.') |
| 143 | |
| 144 | parser.add_argument('--pdb', type=str, required=True, nargs='+', help='Path to the pdb of the docked antigen-antibody complex') |
| 145 | parser.add_argument('--heavy_chain', type=str, required=True, nargs='+', help='Id of the heavy chain') |
| 146 | parser.add_argument('--light_chain', type=str, required=True, nargs='+', help='Id of the light chain') |
| 147 | parser.add_argument('--out_dir', type=str, default='./results', help='Path to save the generated antibodies') |
| 148 | |
| 149 | parser.add_argument('--gpu', type=int, default=0, help='GPU id') |
| 150 | return parser.parse_args() |
| 151 | |
| 152 | |
| 153 | if __name__ == '__main__': |