wip: viz cif

Dockerfile

@@ -26,6 +26,7 @@ RUN cd /app/folding-studio && uv pip install -e .
 
 COPY app.py /app/app.py
 COPY molecule.py /app/molecule.py
+COPY pred.cif /app/boltz_results/pred_model_0.cif
 
 EXPOSE 7860
 ENV GRADIO_SERVER_NAME="0.0.0.0"
@@ -33,4 +34,11 @@ ARG FOLDING_API_KEY
 ARG FOLDING_PROJECT_CODE
 ENV FOLDING_API_KEY=$FOLDING_API_KEY
 ENV FOLDING_PROJECT_CODE=$FOLDING_PROJECT_CODE
+
+# Create directory for HTML output
+RUN mkdir -p /app/output/html
+
+# Create volume for HTML output
+VOLUME ["/app/output/html"]
+
 CMD ["python3", "app.py"]

Makefile

@@ -2,12 +2,13 @@
 DOCKER_IMAGE_NAME = folding-studio
 DOCKER_IMAGE_TAG = latest
 PORT = 7860
+OUTPUT_DIR = ./output
 
 # Docker build arguments
 DOCKER_BUILD_ARGS = --build-arg FOLDING_API_KEY=${FOLDING_API_KEY} --build-arg FOLDING_PROJECT_CODE=${FOLDING_PROJECT_CODE}
 
 # Docker run arguments
-DOCKER_RUN_ARGS = -p $(PORT):$(PORT)
+DOCKER_RUN_ARGS = -p $(PORT):$(PORT) -v $(OUTPUT_DIR):/app/output/html
 
 # Default target
 .DEFAULT_GOAL := help
@@ -31,6 +32,7 @@ build:
 # Run targets
 .PHONY: run
 run:
+	mkdir -p $(OUTPUT_DIR)
 	docker run $(DOCKER_RUN_ARGS) $(DOCKER_IMAGE_NAME):$(DOCKER_IMAGE_TAG)
 
 # Cleanup targets

app.py

@@ -26,7 +26,7 @@ def predict(sequence: str):
     logger.info(f"Predicting {seq_file.stem} with project code {FOLDING_PROJECT_CODE}")
     output_dir = Path("boltz_results")
     output_dir.mkdir(parents=True, exist_ok=True)
-    boltz_predict(source=seq_file, project_code=FOLDING_PROJECT_CODE, output=output_dir, unzip=True)
+    # boltz_predict(source=seq_file, project_code=FOLDING_PROJECT_CODE, output=output_dir, unzip=True)
     logger.info("Prediction done. Output directory: %s", output_dir)
     outs = list(output_dir.rglob("*_model_0.cif"))
     logger.info("Output files: %s", outs)

molecule.py

@@ -290,9 +290,10 @@ def molecule(
         </script>
         </body></html>"""
     )
-
-    return f"""<iframe style="width: 800px; height: 1300px" name="result" allow="midi; geolocation; microphone; camera; 
-    display-capture; encrypted-media;" sandbox="allow-modals allow-forms 
-    allow-scripts allow-same-origin allow-popups 
-    allow-top-navigation-by-user-activation allow-downloads" allowfullscreen="" 
-    allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""
+    
+    # Save the HTML output to a file
+    output_path = "/app/output/html/molecule_view.html"
+    with open(output_path, "w") as f:
+        f.write(x)
+    
+    return x