From c00fd5f70dcc3ab28693210755212a44ad0156be Mon Sep 17 00:00:00 2001 From: David Wong Date: Fri, 15 Nov 2024 15:46:30 +0800 Subject: [PATCH 1/2] Update README.md There are two identical 'bfd_database_path' arguments in the 'run_infer.sh' script, which would lead to error when set 'full_dbs' for 'preset' argument. --- apps/protein_folding/helixfold3/README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/apps/protein_folding/helixfold3/README.md b/apps/protein_folding/helixfold3/README.md index 22266973..71f03935 100644 --- a/apps/protein_folding/helixfold3/README.md +++ b/apps/protein_folding/helixfold3/README.md @@ -147,7 +147,6 @@ CUDA_VISIBLE_DEVICES=0 "$PYTHON_BIN" inference.py \ --preset='reduced_dbs' \ --bfd_database_path "$DATA_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt" \ --small_bfd_database_path "$DATA_DIR/small_bfd/bfd-first_non_consensus_sequences.fasta" \ - --bfd_database_path "$DATA_DIR/small_bfd/bfd-first_non_consensus_sequences.fasta" \ --uniclust30_database_path "$DATA_DIR/uniclust30/uniclust30_2018_08/uniclust30_2018_08" \ --uniprot_database_path "$DATA_DIR/uniprot/uniprot.fasta" \ --pdb_seqres_database_path "$DATA_DIR/pdb_seqres/pdb_seqres.txt" \ From 30d43ec08439ba923494eef069b3fb6d77c3a1f6 Mon Sep 17 00:00:00 2001 From: David Wong Date: Fri, 15 Nov 2024 16:50:25 +0800 Subject: [PATCH 2/2] Update run_infer.sh There are two identical bfd_database_path arguments in the run_infer.sh script, which would lead to error when set 'full_dbs' for 'preset' argument. --- apps/protein_folding/helixfold3/run_infer.sh | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/apps/protein_folding/helixfold3/run_infer.sh b/apps/protein_folding/helixfold3/run_infer.sh index 5b0644e5..44541730 100644 --- a/apps/protein_folding/helixfold3/run_infer.sh +++ b/apps/protein_folding/helixfold3/run_infer.sh @@ -19,7 +19,6 @@ CUDA_VISIBLE_DEVICES=0 "$PYTHON_BIN" inference.py \ --preset='reduced_dbs' \ --bfd_database_path "$DATA_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt" \ --small_bfd_database_path "$DATA_DIR/small_bfd/bfd-first_non_consensus_sequences.fasta" \ - --bfd_database_path "$DATA_DIR/small_bfd/bfd-first_non_consensus_sequences.fasta" \ --uniclust30_database_path "$DATA_DIR/uniclust30/uniclust30_2018_08/uniclust30_2018_08" \ --uniprot_database_path "$DATA_DIR/uniprot/uniprot.fasta" \ --pdb_seqres_database_path "$DATA_DIR/pdb_seqres/pdb_seqres.txt" \ @@ -36,4 +35,4 @@ CUDA_VISIBLE_DEVICES=0 "$PYTHON_BIN" inference.py \ --init_model init_models/HelixFold3-240814.pdparams \ --infer_times 1 \ --diff_batch_size 1 \ - --precision "fp32" \ No newline at end of file + --precision "fp32"