add final

.gradio/cached_examples/13/indices.csv

@@ -1,2 +1,4 @@
 4
 1
+0
+5

.gradio/cached_examples/13/log.csv

@@ -1,3 +1,5 @@
 Generated Molecule,timestamp
 "{""path"": "".gradio/cached_examples/13/Generated Molecule/96624d241f3ceaf7652e/MITOCHONDRIAL_9.pdb"", ""url"": ""/gradio_api/file=/tmp/gradio/dfeb6cce50c7d0cb5ab8f1fcbc0ed91e88c6f502e6abf12023254e663fafee05/MITOCHONDRIAL_9.pdb"", ""size"": 2031480, ""orig_name"": ""MITOCHONDRIAL_9.pdb"", ""mime_type"": null, ""is_stream"": false, ""meta"": {""_type"": ""gradio.FileData""}}",2024-11-20 21:18:05.776535
 "{""path"": "".gradio/cached_examples/13/Generated Molecule/4f0e0b233c39c3b226f9/Armadillo_6.pdb"", ""url"": ""/gradio_api/file=/tmp/gradio/e9e42deb7d9ea5c72c0bd60fb8f2bbed6357d48e775667232dc67eddc7886d87/Armadillo_6.pdb"", ""size"": 1271295, ""orig_name"": ""Armadillo_6.pdb"", ""mime_type"": null, ""is_stream"": false, ""meta"": {""_type"": ""gradio.FileData""}}",2024-11-20 22:28:22.665771
+"{""path"": "".gradio/cached_examples/13/Generated Molecule/2dacb41b06297c98890e/boltz_0.pdb"", ""url"": ""/gradio_api/file=/tmp/gradio/2ab77757589b1fd365f7221f92918cd369c77ddd8251942bc03a023821578dcd/boltz_0.pdb"", ""size"": 493208, ""orig_name"": ""boltz_0.pdb"", ""mime_type"": null, ""is_stream"": false, ""meta"": {""_type"": ""gradio.FileData""}}",2024-11-21 06:37:15.944530
+"{""path"": "".gradio/cached_examples/13/Generated Molecule/72c05e00d37b5c2010bd/Monkeypox_4.pdb"", ""url"": ""/gradio_api/file=/tmp/gradio/dddfb893d502b267dcc8eef503e040c3b0a274cf678df53be49614c61cb1c603/Monkeypox_4.pdb"", ""size"": 453357, ""orig_name"": ""Monkeypox_4.pdb"", ""mime_type"": null, ""is_stream"": false, ""meta"": {""_type"": ""gradio.FileData""}}",2024-11-21 06:50:24.876272

app.py

@@ -6,7 +6,7 @@ import subprocess
 import glob
 
 
-# Directory to store cached outputs
+# directory to store cached outputs
 CACHE_DIR = "gradio_cached_examples"
 
 
@@ -61,55 +61,27 @@ def on_example_click(fasta_file: str) -> str:
     return load_cached_example_outputs(fasta_file)
 
 # run predictions
-# @spaces.GPU(duration=120)
-def predict(data, out_dir, cache="~/.boltz", checkpoint=None, devices=1,
-            accelerator="gpu", recycling_steps=3, sampling_steps=50,
-            diffusion_samples=1, output_format="pdb", num_workers=2,
-            override=False):
+@spaces.GPU(duration=120)
+def predict(data,
+            accelerator="gpu", sampling_steps=50,
+            diffusion_samples=1):
 
     print("Arguments passed to `predict` function:")
     print(f"  data: {data}")
-    print(f"  out_dir: {out_dir}")
-    print(f"  cache: {cache}")
-    print(f"  checkpoint: {checkpoint}")
-    print(f"  devices: {devices}")
     print(f"  accelerator: {accelerator}")
-    print(f"  recycling_steps: {recycling_steps}")
     print(f"  sampling_steps: {sampling_steps}")
     print(f"  diffusion_samples: {diffusion_samples}")
-    print(f"  output_format: {output_format}")
-    print(f"  num_workers: {num_workers}")
-    print(f"  override: {override}")
-    # Construct the base command
+    # we construct the base command
     command = [
         "boltz", "predict",
-        "--out_dir", out_dir,
-        "--cache", cache,
-        "--devices", str(devices),
+        "--out_dir", "./",
         "--accelerator", accelerator,
-        "--recycling_steps", str(recycling_steps),
         "--sampling_steps", str(sampling_steps),
         "--diffusion_samples", str(diffusion_samples),
-        "--output_format", output_format,
-        "--num_workers", str(num_workers)
+        "--output_format", "pdb",
     ]
-
-    
-    # Add optional arguments if provided
-    if checkpoint:
-        command.extend(["--checkpoint", checkpoint])
-    if override:
-        command.append("--override")
-    
-
-    # Add the data argument (path to the input file)
+    command.extend(["--checkpoint", "./ckpt/boltz1.ckpt"])
     command.append(data)
-
-    # print("Constructed subprocess command:")
-    # print("  " + " ".join(command))
-
-
-    # Run the command using subprocess
     result = subprocess.run(command, capture_output=True, text=True)
     if result.returncode == 0:
         print("Prediction completed successfully...!")
@@ -118,39 +90,29 @@ def predict(data, out_dir, cache="~/.boltz", checkpoint=None, devices=1,
         print("Prediction failed :(")
         print("Error:", result.stderr)
 
-# @spaces.GPU(duration=60)
-def run_prediction(input_file, cache, accelerator, sampling_steps,
-                   diffusion_samples, output_format, checkpoint="./ckpt/boltz1.ckpt"):
-    # Assuming `input_file` is a path to the .fasta file
-    data = input_file.name  # Path to the uploaded .fasta file
+def run_prediction(input_file, accelerator, sampling_steps,
+                   diffusion_samples):
+    data = input_file.name
     print("the data : ", data)
-    # Update the `reps` settings with the chosen style and color
-
-    # Call your predict function
     predict(
         data=data,
-        out_dir="./",
-        cache=cache,
         accelerator=accelerator,
         sampling_steps=sampling_steps,
-        diffusion_samples=diffusion_samples,
-        output_format=output_format,
-        checkpoint=checkpoint
+        diffusion_samples=diffusion_samples
     )
 
-    # Search for the latest .pdb file in the predictions folder
+    # search for the latest .pdb file in the predictions folder
+    out_dir = "./"
     search_path = os.path.join(out_dir, "boltz_results*/predictions/**/*.pdb")
-    pdb_files = glob.glob(search_path, recursive=True)  # Enable recursive search
+    pdb_files = glob.glob(search_path, recursive=True)
     
     if not pdb_files:
         print("No .pdb files found in the predictions folder.")
         return None
 
-    # Get the latest .pdb file based on modification time
+    # some manual logic
+    # get the latest .pdb file based on modification time
     latest_pdb_file = max(pdb_files, key=os.path.getmtime)
-
-    
-    # Return the latest PDB file path
     return latest_pdb_file
 
 
@@ -189,4 +151,3 @@ with gr.Blocks() as demo:
 
 if __name__ == "__main__":
     demo.launch(share=True, debug=True)
-