Update

Dockerfile

@@ -19,6 +19,10 @@ RUN conda install pytorch::faiss-gpu --yes
 RUN wget 'https://drive.usercontent.google.com/download?id=1B_9t3n_nlj8Y3Kpc_mMjtMdY0OPYa7Re&export=download&authuser=0' -O /tmp/foldseek
 RUN chmod +x /tmp/foldseek
 
+# Download TMalign
+RUN wget 'https://drive.google.com/file/d/1waxLyL2MLCxyHyIlQe7zkeHy8lzuDThu/view?usp=sharing' -O /tmp/TMalign
+RUN chmod +x /tmp/TMalign
+
 # Download ProTrek model
 RUN huggingface-cli download westlake-repl/ProTrek_650M_UniRef50 --repo-type model --local-dir /tmp/ProTrek_650M_UniRef50
 

demo/config.yaml

@@ -7,7 +7,7 @@ sequence_index_dir:
 
 structure_index_dir:
   - name: Swiss-Prot
-    index_dir: /tmp/ProTrek-faiss-index/ProTrek_650M_UniRef50/Swiss-Prot/sequence
+    index_dir: /tmp/ProTrek-faiss-index/ProTrek_650M_UniRef50/Swiss-Prot/structure
 
 text_index_dir:
   - name: Swiss-Prot

demo/modules/tmalign.py

@@ -37,7 +37,7 @@ def tmalign(structure_1: str, structure_type_1: str, structure_2: str, structure
     structure_path_1 = get_structure_path(structure_1, structure_type_1)
     structure_path_2 = get_structure_path(structure_2, structure_type_2)
     
-    cmd = f"bin/TMalign {structure_path_1} {structure_path_2}"
+    cmd = f"/tmp/TMalign {structure_path_1} {structure_path_2}"
     
     r = os.popen(cmd)
     text = r.read()

requirements.txt

@@ -1,8 +1,12 @@
 torch==2.0.1
-gradio==4.16.0
+torchvision==0.15.2
+torchaudio==2.0.2
+gradio==4.37.1
 torchmetrics==0.9.3
 pytorch-lightning==2.1.3
 transformers==4.28.0
 scikit-learn==1.4.0
 tabulate==0.9.0
-easydict
+biopython==1.83
+easydict==1.13
+lmdb==1.4.1