InstantiationException: Error in call to target when using sequence with D-amino acid #23
Description
Using the following json input, I get an error that stems from how modelforge is trying to parse the (DTY) code for D-Tyrosine in my sequence. The error is not produced when I use the single letter Y for L-Tyrosine. I used the CCD code for this residue [https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/DTY]. Have I formatted the sequence string wrong in my json file?
JSON input
[
{
"name": "2GB1_31_108",
"components": [
{
"seq": "LVFKLVVQFSTLKGETTTEAVDAATLIKVVKQYLNDNGLSGKVTQNPSKGFEIRL(DTY)",
"chain_id": "A",
"msa_path": "docs/rf3/2GB1/2GB1.a3m"
}
]
}
]
Error Output
│ /gpfs/gsfs12/users/samdintd/modelforge/.venv/lib/python3.12/site-packages/hydra/_internal/instantiate/_instantiate2.py:226 in instantiate │
│ ││ 223 │ │ convert = config.pop(_Keys.CONVERT, ConvertMode.NONE) │
│ 224 │ │ partial = config.pop(_Keys.PARTIAL, False) ││ 225 │ │ │
│ ❱ 226 │ │ return instantiate_node( ││ 227 │ │ │ config, args, recursive=recursive, convert=convert, partial=partial │
│ 228 │ │ ) ││ 229 │ elif OmegaConf.is_list(config): │
│ ││ ╭──────────────────────────────────────────────────────────────────── locals ────────────────────────────────────────────────────────────────────╮ │
│ │ convert = 'partial' │ ││ │ partial = False │ │
│ │ recursive = False │ ││ │ args = () │ │
│ │ config = {'ckpt_path': 'rf3_latest.pt', 'inputs': 'docs/rf3/2GB1/31_108_single_D.json', 'out_dir': './', 'num_nodes': 1, │ ││ │ 'devices_per_node': 1, 'target': 'modelhub.inference_engines.rf3.RF3InferenceEngine', 'n_recycles': 10, │ │
│ │ 'diffusion_batch_size': 5, 'num_steps': 50, 'solver': 'af3', 'early_stopping_plddt_threshold': 0.5, 'residue_renaming_dict': │ ││ │ None, 'template_selection': None, 'ground_truth_conformer_selection': None, 'seed': None, 'skip_existing': False, │ │
│ │ 'print_config': True, 'raise_if_missing_msa_for_protein_of_length_n': None, 'dump_predictions': True, 'dump_trajectories': │ ││ │ False, 'one_model_per_file': False, 'annotate_b_factor_with_plddt': True, 'metrics_cfg': {'ptm': {'target': │ │
│ │ 'modelhub.metrics.predicted_error.ComputePTM'}, 'iptm': {'target': 'modelhub.metrics.predicted_error.ComputeIPTM'}, │ ││ │ 'count_clashing_chains': {'target': 'modelhub.metrics.clashing_chains.CountClashingChains'}}, 'temp_dir': │ │
│ │ PosixPath('/tmp/tmp22l2ihqh')} │ ││ │ config_copy = {'ckpt_path': 'rf3_latest.pt', 'inputs': 'docs/rf3/2GB1/31_108_single_D.json', 'out_dir': './', 'num_nodes': 1, │ │
│ │ 'devices_per_node': 1, 'target': 'modelhub.inference_engines.rf3.RF3InferenceEngine', 'n_recycles': 10, │ ││ │ 'diffusion_batch_size': 5, 'num_steps': 50, 'solver': 'af3', 'early_stopping_plddt_threshold': 0.5, 'residue_renaming_dict': │ │
│ │ None, 'template_selection': None, 'ground_truth_conformer_selection': None, 'seed': None, 'skip_existing': False, │ │
│ │ 'print_config': True, 'raise_if_missing_msa_for_protein_of_length_n': None, 'dump_predictions': True, 'dump_trajectories': │ │
│ │ False, 'one_model_per_file': False, 'annotate_b_factor_with_plddt': True, 'metrics_cfg': {'ptm': {'target': │ │
│ │ 'modelhub.metrics.predicted_error.ComputePTM'}, 'iptm': {'target': 'modelhub.metrics.predicted_error.ComputeIPTM'}, │ │
│ │ 'count_clashing_chains': {'target': 'modelhub.metrics.clashing_chains.CountClashingChains'}}} │ │
│ │ kwargs = {'temp_dir': PosixPath('/tmp/tmp22l2ihqh'), 'convert': 'partial', 'recursive': False} │ │
│ ╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ │
│ │
│ /gpfs/gsfs12/users/samdintd/modelforge/.venv/lib/python3.12/site-packages/hydra/_internal/instantiate/_instantiate2.py:347 in instantiate_node │
│ │
│ 344 │ │ │ │ │ │ ) │
│ 345 │ │ │ │ │ kwargs[key] = _convert_node(value, convert) │
│ 346 │ │ │ │
│ ❱ 347 │ │ │ return _call_target(target, partial, args, kwargs, full_key) │
│ 348 │ │ else: │
│ 349 │ │ │ # If ALL or PARTIAL non structured or OBJECT non structured, │
│ 350 │ │ │ # instantiate in dict and resolve interpolations eagerly. │
│ │
│ ╭──────────────────────────────────────────────────────────────────── locals ────────────────────────────────────────────────────────────────────╮ │
│ │ args = () │ │
│ │ convert = 'partial' │ │
│ │ exclude_keys = {'convert', 'partial', 'recursive', 'target'} │ │
│ │ full_key = '' │ │
│ │ is_partial = False │ │
│ │ key = 'temp_dir' │ │
│ │ kwargs = { │ │
│ │ │ 'ckpt_path': 'rf3_latest.pt', │ │
│ │ │ 'inputs': 'docs/rf3/2GB1/31_108_single_D.json', │ │
│ │ │ 'out_dir': './', │ │
│ │ │ 'num_nodes': 1, │ │
│ │ │ 'devices_per_node': 1, │ │
│ │ │ 'n_recycles': 10, │ │
│ │ │ 'diffusion_batch_size': 5, │ │
│ │ │ 'num_steps': 50, │ │
│ │ │ 'solver': 'af3', │ │
│ │ │ 'early_stopping_plddt_threshold': 0.5, │ │
│ │ │ ... +13 │ │
│ │ } │ │
│ │ node = {'ckpt_path': 'rf3_latest.pt', 'inputs': 'docs/rf3/2GB1/31_108_single_D.json', 'out_dir': './', 'num_nodes': 1, │ │
│ │ 'devices_per_node': 1, 'target': 'modelhub.inference_engines.rf3.RF3InferenceEngine', 'n_recycles': 10, │ │
│ │ 'diffusion_batch_size': 5, 'num_steps': 50, 'solver': 'af3', 'early_stopping_plddt_threshold': 0.5, 'residue_renaming_dict': │ │
│ │ None, 'template_selection': None, 'ground_truth_conformer_selection': None, 'seed': None, 'skip_existing': False, │ │
│ │ 'print_config': True, 'raise_if_missing_msa_for_protein_of_length_n': None, 'dump_predictions': True, 'dump_trajectories': │ │
│ │ False, 'one_model_per_file': False, 'annotate_b_factor_with_plddt': True, 'metrics_cfg': {'ptm': {'target': │ │
│ │ 'modelhub.metrics.predicted_error.ComputePTM'}, 'iptm': {'target': 'modelhub.metrics.predicted_error.ComputeIPTM'}, │ │
│ │ 'count_clashing_chains': {'target': 'modelhub.metrics.clashing_chains.CountClashingChains'}}, 'temp_dir': │ │
│ │ PosixPath('/tmp/tmp22l2ihqh')} │ │
│ │ partial = False │ │
│ │ recursive = False │ │
│ │ value = PosixPath('/tmp/tmp22l2ihqh') │ │
│ ╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ │
│ │
│ /gpfs/gsfs12/users/samdintd/modelforge/.venv/lib/python3.12/site-packages/hydra/_internal/instantiate/instantiate2.py:97 in call_target │
│ │
│ 94 │ │ │ msg = f"Error in call to target '{_convert_target_to_string(target)}':\n{r │
│ 95 │ │ │ if full_key: │
│ 96 │ │ │ │ msg += f"\nfull_key: {full_key}" │
│ ❱ 97 │ │ │ raise InstantiationException(msg) from e │
│ 98 │
│ 99 │
│ 100 def convert_target_to_string(t: Any) -> Any: │
│ │
│ ╭────────────────────────────────────────────── locals ───────────────────────────────────────────────╮ │
│ │ partial = False │ │
│ │ args = () │ │
│ │ full_key = '' │ │
│ │ kwargs = { │ │
│ │ │ 'ckpt_path': 'rf3_latest.pt', │ │
│ │ │ 'inputs': 'docs/rf3/2GB1/31_108_single_D.json', │ │
│ │ │ 'out_dir': './', │ │
│ │ │ 'num_nodes': 1, │ │
│ │ │ 'devices_per_node': 1, │ │
│ │ │ 'n_recycles': 10, │ │
│ │ │ 'diffusion_batch_size': 5, │ │
│ │ │ 'num_steps': 50, │ │
│ │ │ 'solver': 'af3', │ │
│ │ │ 'early_stopping_plddt_threshold': 0.5, │ │
│ │ │ ... +13 │ │
│ │ } │ │
│ │ msg = "Error in call to target 'modelhub.inference_engines.rf3.RF3InferenceEngine':\nVal"+390 │ │
│ │ v = PosixPath('/tmp/tmp22l2ihqh') │ │
│ ╰─────────────────────────────────────────────────────────────────────────────────────────────────────╯ │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
**InstantiationException: Error in call to target 'modelhub.inference_engines.rf3.RF3InferenceEngine':
ValueError("Invalid chain_type=<ChainType.POLYPEPTIDE_L: 6> for chem_comp_types={np.str('PEPTIDE LINKING'), np.str('D-PEPTIDE LINKING'),
np.str('L-PEPTIDE LINKING')}. Valid are valid_chem_comp_types=frozenset({'L-PEPTIDE LINKING', 'L-PEPTIDE NH3 AMINO TERMINUS', 'L-GAMMA-PEPTIDE,
C-DELTA LINKING', 'PEPTIDE LINKING', 'L-BETA-PEPTIDE, C-GAMMA LINKING', 'L-PEPTIDE COOH CARBOXY TERMINUS'})")*