fix boltz params

.gitignore

@@ -1,2 +1,3 @@
 .envrc
 
+boltz_results/

app.py

@@ -5,7 +5,7 @@ from Bio.PDB import MMCIFParser, PDBIO
 import logging
 import os
 from folding_studio.client import Client
-from folding_studio.query.boltz import BoltzQuery
+from folding_studio.query.boltz import BoltzQuery, BoltzParameters
 
 
 from molecule import molecule
@@ -37,13 +37,13 @@ def convert_cif_to_pdb(cif_path, pdb_path):
     io.set_structure(structure)
     io.save(pdb_path)
 
-def call_boltz(seq_file: Path, api_key: str, output_dir: Path) -> None:
+def call_boltz(seq_file: Path | str, api_key: str, output_dir: Path) -> None:
     """Call Boltz prediction."""
     # Initialize parameters with CLI-provided values
     parameters = {
         "recycling_steps": 3,
-        "sampling_steps": 1,
-        "diffusion_samples": 100,
+        "sampling_steps": 200,
+        "diffusion_samples": 1,
         "step_scale": 1.638,
         "msa_pairing_strategy": "greedy",
         "write_full_pae": False,
@@ -52,15 +52,17 @@ def call_boltz(seq_file: Path, api_key: str, output_dir: Path) -> None:
         "seed": 0,
         "custom_msa_paths": None,
     }
-
+    
     # Create a client using API key
     logger.info("Authenticating client with API key")
     client = Client.from_api_key(api_key=api_key)
 
     # Define query
-    query = BoltzQuery.from_file(seq_file, **parameters)
+    seq_file = Path(seq_file)
+    query = BoltzQuery.from_file(seq_file, query_name="gradio", parameters=BoltzParameters(**parameters))
     query.save_parameters(output_dir)
 
+    logger.info("Payload: %s", query.payload)
 
     # Send a request
     logger.info("Sending request to Folding Studio API")
@@ -84,12 +86,10 @@ def predict(sequence: str, api_key: str) -> str:
         str: HTML iframe containing 3D molecular visualization
     """
     
-    # Create FASTA file with sequence
-    seq_file = Path("sequence.fasta")
-    _write_fasta_file(seq_file, sequence)
-    
     # Set up unique output directory based on sequence hash
     seq_id = hashlib.sha1(sequence.encode()).hexdigest()
+    seq_file = Path(f"sequence_{seq_id}.fasta")
+    _write_fasta_file(seq_file, sequence)
     output_dir = Path(f"sequence_{seq_id}")
     output_dir.mkdir(parents=True, exist_ok=True)
     
@@ -103,8 +103,7 @@ def predict(sequence: str, api_key: str) -> str:
     else:
         logger.info("Prediction already exists. Output directory: %s", output_dir)
 
-    # # TODO: remove this
-    # output_dir = Path("boltz_results")
+    # output_dir = Path("boltz_results") # debug
     # Convert output CIF to PDB
     pred_cif = list(output_dir.rglob("*_model_0.cif"))[0]
     logger.info("Output file: %s", pred_cif)