demo_6zcy: ccd prediction (demo_6zcy.json) by helixfold3 is ok, but smiles (demo_6zcy_smiles.json) failed #337
Description
Great work !
I've successfully predict protein-SM complex structure using demo_6zcy.json, just similar with given predicted structure in demo_output. However, use of demo_6zcy_smiles.json failed. Please help to give a solution. Using "sh run_infer.sh", and
error message is like：
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PaddlePaddle commit: fbf852dd832bc0e63ae31cd4aa37defd829e4c03
FLAGS_new_einsum: True
args:
Namespace(bf16_infer=False, seed=None, logging_level='DEBUG', model_name='allatom_demo', init_ model='init_models/HelixFold3-240814.pdparams', precision='fp32', amp_level='O1', infer_times= 1, diff_batch_size=1, input_json='data/demo_6zcy_smiles.json', output_dir='./output', ccd_prep rocessed_path='/data/database/ccd_preprocessed_etkdg.pkl.gz', jackhmmer_binary_path='/home/gwb /miniconda3/envs/helixfold/bin/jackhmmer', hhblits_binary_path='/home/gwb/miniconda3/envs/heli xfold/bin/hhblits', hhsearch_binary_path='/home/gwb/miniconda3/envs/helixfold/bin/hhsearch', k align_binary_path='/home/gwb/miniconda3/envs/helixfold/bin/kalign', hmmsearch_binary_path='/ho me/gwb/miniconda3/envs/helixfold/bin/hmmsearch', hmmbuild_binary_path='/home/gwb/miniconda3/en vs/helixfold/bin/hmmbuild', nhmmer_binary_path='/home/gwb/miniconda3/envs/helixfold/bin/nhmmer ', uniprot_database_path='/data/database/uniprot/uniprot.fasta', pdb_seqres_database_path='/da ta/database/pdb_seqres/pdb_seqres.txt', uniref90_database_path='/data/database/uniref90/uniref 90.fasta', mgnify_database_path='/data/database/mgnify/mgy_clusters_2022_05.fa', bfd_database_ path='/data/database/small_bfd/bfd-first_non_consensus_sequences.fasta', small_bfd_database_pa th='/data/database/small_bfd/bfd-first_non_consensus_sequences.fasta', uniclust30_database_pat h='/data/database/uniclust30/uniclust30_2018_08/uniclust30_2018_08', rfam_database_path='/data /database/Rfam-14.9_rep_seq.fasta', template_mmcif_dir='/data/database/pdb_mmcif/mmcif_files', max_template_date='2020-05-14', obsolete_pdbs_path='/data/database/pdb_mmcif/obsolete.dat', p reset='reduced_dbs', maxit_binary='/home/gwb/RationalDesign/helixfold3/maxit-v11.100-prod-src/ bin/maxit')
[OBABEL] Temporary file created: /tmp/tmpjptejgmh.mol2
Failed to convert ligand entity 1: {'type': 'ligand', 'smiles': 'CNC(=O)c1nn(C)c2ccc(Nc3nccc(n 3)n4cc(N[C@@h]5CCNC5)c(C)n4)cc12', 'count': 1}, Python argument types in
rdkit.Chem.rdmolops.RemoveAllHs(NoneType)
did not match C++ signature:
RemoveAllHs(RDKit::ROMol mol, bool sanitize=True)
Traceback (most recent call last):
File "/home/gwb/RationalDesign/helixfold3/inference.py", line 637, in
main(args)
File "/home/gwb/RationalDesign/helixfold3/inference.py", line 442, in main
all_entitys = preprocess_json_entity(args.input_json, args.output_dir)
File "/home/gwb/RationalDesign/helixfold3/inference.py", line 87, in preprocess_json_entity
all_entitys = preprocess.online_json_to_entity(json_path, out_dir)
File "/home/gwb/RationalDesign/helixfold3/infer_scripts/preprocess.py", line 290, in online_ json_to_entity
raise RuntimeError(f'[Error] Failed to convert {len(error_ids)}/{len(entities)} entities')
RuntimeError: [Error] Failed to convert 1/2 entities
(helixfold) gwb@node01:/RationalDesign/helixfold3$ vi /home/gwb/RationalDesign/helixfold3/inf erence.py/RationalDesign/helixfold3$ vi /home/gwb/RationalDesign/helixfold3/inf er_scripts/preprocess.py
(helixfold) gwb@node01:
(helixfold) gwb@node01:~/RationalDesign/helixfold3$ python
Python 3.9.19 | packaged by conda-forge | (main, Mar 20 2024, 12:50:21)
[GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
from rdkit import Chemsmiles = 'CNC(=O)c1nn(C)c2ccc(Nc3nccc(n3)n4cc(N[C@@h]5CCNC5)c(C)n4)cc12'
mol = Chem.MolFromSmiles(smiles)
if mol is None:
... print("Failed to create molecule from SMILES")
... else:
... print("Molecule created successfully")
...
Molecule created successfully
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