Add create json file and correc creation of fasta file

app.py

@@ -11,6 +11,44 @@ from modal_app import app, chai1_inference, download_inference_dependencies, her
 
 # Definition of the tools for the MCP server 
 
+# Function to create a custom JSON config file
+def create_custom_config(
+    num_trunk_recycles: int = 3,
+    num_diffn_timesteps: int = 200,
+    seed: int = 42,
+    use_esm_embeddings: bool = True,
+    use_msa_server: bool = True,
+    output_file: Optional[str] = None
+) -> str:
+    """Create a custom JSON configuration file for Chai1 inference.
+    
+    Args:
+        num_trunk_recycles (int, optional): Number of trunk recycles. Defaults to 3.
+        num_diffn_timesteps (int, optional): Number of diffusion timesteps. Defaults to 200.
+        seed (int, optional): Random seed. Defaults to 42.
+        use_esm_embeddings (bool, optional): Whether to use ESM embeddings. Defaults to True.
+        use_msa_server (bool, optional): Whether to use MSA server. Defaults to True.
+        output_file (str, optional): Path to save the config file. If None, saves to default location.
+    
+    Returns:
+        str: Path to the created config file
+    """
+    config = {
+        "num_trunk_recycles": num_trunk_recycles,
+        "num_diffn_timesteps": num_diffn_timesteps,
+        "seed": seed,
+        "use_esm_embeddings": use_esm_embeddings,
+        "use_msa_server": use_msa_server
+    }
+    
+    if output_file is None:
+        output_file = here / "inputs" / "chai1_custom_inference.json"
+        
+    with open(output_file, "w") as f:
+        json.dump(config, f, indent=4)
+        
+    return str(output_file)
+
 # Function to compute Chai1 inference
 def compute_Chai1(
     fasta_file: Optional[str] = None,
@@ -37,7 +75,7 @@ def compute_Chai1(
             fasta_file = here / "inputs" / "chai1_default_input.fasta"
         else:
             name_file = here / "inputs" / "chai1_custom_input.fasta"
-            with open(fasta_file, "w") as f:
+            with open(fasta_file, "x") as f:
                 f.write(fasta_file)
             fasta_file = name_file