Update app.py

app.py

@@ -144,8 +144,9 @@ def update_protGPT2(inp, length,repetitionPenalty, top_k_poolsize, max_seqs):
     sequencestxt = ""
     for i, seq in enumerate(gen_seqs):
         s = seq.replace("\n","")
+        seqlen = len(s)
         s = "\n".join([s[i:i+70] for i in range(0, len(s), 70)])
-        sequencestxt +=f">seq{i}\n{s}\n"
+        sequencestxt +=f">seq{i}, {seqlen} residues \n{s}\n\n"
     return sequencestxt
 
 
@@ -349,7 +350,7 @@ with proteindream:
     gr.Markdown("# GradioFold")
     gr.Markdown(
         """GradioFold is a web-based tool that combines a large language model trained on natural protein sequence (protGPT2) with structure prediction using AlphaFold. 
-    Type a start sequence that protGPT2 can complete or let protGPT2 generate a complete sequence."""
+    Type a start sequence that protGPT2 can complete or let protGPT2 generate a complete sequence without a start token."""
     )
     gr.Markdown("## protGPT2")
     gr.Markdown(
@@ -364,7 +365,7 @@ with proteindream:
         with gr.Row():
             repetitionPenalty = gr.Slider(minimum=1, maximum=5,value=1.2, label="Repetition penalty")
             top_k_poolsize = gr.Slider(minimum=700, maximum=52056,value=950, label="Top-K sampling pool size")
-            max_seqs = gr.Slider(minimum=2, maximum=20,value=5, label="Number of sequences to generate")
+            max_seqs = gr.Slider(minimum=2, maximum=20,value=5, step=1, label="Number of sequences to generate")
         btn = gr.Button("Predict sequences using protGPT2")
 
     results = gr.Textbox(label="Results", lines=15)
@@ -372,7 +373,7 @@ with proteindream:
 
     gr.Markdown("## AlphaFold")
     gr.Markdown(
-        "Select a generated sequence above and copy it in the field below for structure prediction using AlphaFold2."
+        "Select a generated sequence above and copy it in the field below for structure prediction using AlphaFold2. You can also edit the sequence. Predictions will take around 2-5 minutes to be processed. Proteins larger than about 1000 residues will not fit into memory."
     )
     with gr.Group():
         chosenSeq = gr.Textbox(label="Chosen sequence")
@@ -384,7 +385,7 @@ with proteindream:
             plot = gr.Plot(label="pLDDT")
     gr.Markdown(
         """## Acknowledgements
-         This was a fun demo using Gradio, Huggingface Spaces and ColabFold as inspiration. More information about the used algorithms can be found below. 
+         More information about the used algorithms can be found below. 
 
          All code is available on [Huggingface](https://huggingface.co/spaces/simonduerr/protGPT2_gradioFold/blob/main) and licensed under MIT license.
 
@@ -394,6 +395,7 @@ with proteindream:
         - 3Dmol.js: Rego & Koes 📄[Paper](https://academic.oup.com/bioinformatics/article/31/8/1322/213186)  💻 [Code](https://github.com/3dmol/3Dmol.js)
         
         Created by [@simonduerr](https://twitter.com/simonduerr)
+        Thanks to Hugginface team for sponsoring a free GPU for this demo.
     """
     )
     #seqChoice.change(fn=update_seqs, inputs=seqChoice, outputs=chosenSeq)