fix: obabel bin resolve

PaddlePaddle · Aug 17, 2024 · 5aae769 · 5aae769
1 parent ae9146a
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diff --git a/apps/protein_folding/helixfold3/FOLDING.md b/apps/protein_folding/helixfold3/FOLDING.md
@@ -1,7 +1,12 @@
 # FOLD GUIDE
 
 ## Quick example
+Run from default config
 ```shell
 LD_LIBRARY_PATH=/mnt/data/envs/conda_env/envs/helixfold/lib/:$LD_LIBRARY_PATH helixfold input=/repo/PaddleHelix/apps/protein_folding/helixfold3/data/demo_8ecx.json  output=. CONFIG_DIFFS.preset=allatom_demo
+```
 
+Run with customized configuration dir and name:
+```shell
+LD_LIBRARY_PATH=/mnt/data/envs/conda_env/envs/helixfold/lib/:$LD_LIBRARY_PATH helixfold --config-dir=. --config-name=myfold input=/repo/PaddleHelix/apps/protein_folding/helixfold3/data/demo_6zcy_smiles.json  output=. CONFIG_DIFFS.preset=allatom_demo
 ```
diff --git a/apps/protein_folding/helixfold3/helixfold/inference.py b/apps/protein_folding/helixfold3/helixfold/inference.py
@@ -457,7 +457,6 @@ def main(cfg: DictConfig):
     print(f'>>> FLAGS_new_einsum: {new_einsum}')
     print(f'>>> config:\n{cfg}')
 
-    all_entitys = preprocess_json_entity(cfg.input, cfg.output)
     ## check maxit binary path
     maxit_binary=resolve_bin_path(cfg.other.maxit_binary,'maxit')
 
@@ -468,6 +467,8 @@ def main(cfg: DictConfig):
     obabel_bin=resolve_bin_path(cfg.bin.obabel,'obabel')
     os.environ['OBABEL_BIN']=obabel_bin
 
+    all_entitys = preprocess_json_entity(cfg.input, cfg.output)
+
     ### Set seed for reproducibility
     seed = cfg.seed
     if seed is None: