revert: script links

apps/protein_folding/helixfold3/helixfold/config/helixfold.yaml

@@ -34,7 +34,7 @@ nproc_msa:
 input: null  # Input file/Directory, required field. If it's a directory, run HF3 against all files under input directory.
 output: null  # Corresponds to --output_dir, required field
 override: false # Set true to override existing msa output directory
-
+ 
 
 # Binary tool paths, leave them as null to find proper ones under PATH or conda bin path
 bin:

apps/protein_folding/helixfold3/helixfold/inference.py

@@ -45,8 +45,8 @@
 from helixfold.data.tools.utils import timing
 from helixfold.utils.utils import get_custom_amp_list
 from typing import Dict, Mapping
-from helixfold.infer_scripts import feature_processing_aa, preprocess
-from helixfold.infer_scripts.tools import mmcif_writer
+from helixfold.utils import feature_processing_aa, preprocess
+from helixfold.utils import mmcif_writer
 
 
 script_path=os.path.dirname(__file__)
@@ -495,7 +495,7 @@ def split_prediction(pred, rank):
     return prediction
 
 @dataclass
-class HelixFold:
+class HelixFoldRunner:
 
     cfg: DictConfig
 
@@ -580,11 +580,16 @@ def fold(self, entity: str):
         init_seed(seed)
 
 
-
-
         print(f"============ Data Loading ============")
         job_base = pathlib.Path(entity).stem
         output_dir_base = pathlib.Path(self.cfg.output).joinpath(job_base)
+
+        expected_res=os.path.join(self.cfg.output, job_base, f'{job_base}-rank1','all_results.json')
+        if os.path.isfile(expected_res):
+            logging.warning(f'Skip {job_base} because {expected_res} exists')
+            return
+
+
         msa_output_dir = output_dir_base.joinpath('msas')
         msa_output_dir.mkdir(parents=True, exist_ok=True)
 
@@ -659,36 +664,31 @@ def cleanup_ramdisk(self, ramdisk_path: str = "/dev/shm"):
 @hydra.main(version_base=None, config_path=os.path.join(script_path,'config',),config_name='helixfold')
 def main(cfg: DictConfig):
 
-    hf_runner=HelixFold(cfg=cfg)
+    hf_runner=HelixFoldRunner(cfg=cfg)
 
-    try:
 
-        if os.path.isfile(cfg.input):
-            logging.info(f'Starting inference on {cfg.input}')
+
+    if os.path.isfile(cfg.input):
+        logging.info(f'Starting inference on {cfg.input}')
+        try:
             hf_runner.fold(cfg.input)
-            return 
-        elif os.path.isdir(cfg.input):
-            logging.info(f'Starting inference on all files in {cfg.input}')
-            for f in [i for i in os.listdir(cfg.input) if any(i.endswith(p) for p in ['json', 'jsonl', 'json.gz', 'jsonl.gz'])]:
-                logging.info(f'Processing  {f}')
-                try:
-                    hf_runner.fold(os.path.join(cfg.input,f))
-                except (ValueError, AssertionError, RuntimeError, FileNotFoundError, MemoryError) as e :
-                    logging.error(f'Error processing {f}: {e}')
-                    continue
+        except (ValueError, AssertionError, RuntimeError, FileNotFoundError, MemoryError) as e :
+            logging.error(f'Error processing {cfg.input}: {e}')
+    elif os.path.isdir(cfg.input):
+        logging.info(f'Starting inference on all files in {cfg.input}')
+        for f in [i for i in os.listdir(cfg.input) if any(i.endswith(p) for p in ['json', 'jsonl', 'json.gz', 'jsonl.gz'])]:
+            logging.info(f'Processing  {f}')
+            try:
+                hf_runner.fold(os.path.join(cfg.input,f))
+            except (ValueError, AssertionError, RuntimeError, FileNotFoundError, MemoryError, OSError) as e :
+                logging.error(f'Error processing {f}: {e}')
+                continue
 
-
-    except Exception as e:
-        logging.error(f'Error processing {cfg.input}: {e}')
 
-    finally:
-        hf_runner.cleanup_ramdisk()
+    return hf_runner.cleanup_ramdisk()
 
 
 
-    raise ValueError(f'Invalid input file/dir: {cfg.input}')
-
-
 @hydra.main(version_base=None, config_path=os.path.join(script_path,'config',),config_name='helixfold')
 def show_atom_id_ccd(cfg: DictConfig):
 

apps/protein_folding/helixfold3/infer_scripts/feature_processing_aa.py

@@ -0,0 +1 @@
+../helixfold/utils/feature_processing_aa.py

apps/protein_folding/helixfold3/infer_scripts/preprocess.py

@@ -0,0 +1 @@
+../helixfold/utils/preprocess.py

apps/protein_folding/helixfold3/infer_scripts/tools/mmcif_writer.py

@@ -0,0 +1 @@
+../../helixfold/utils/mmcif_writer.py