Cosmetics

app.py

@@ -95,7 +95,7 @@ def create_fasta_file(file_content: str, name: Optional[str] = None, seq_name: O
     
     # Generate a unique file name
     unique_id = hashlib.sha256(uuid4().bytes).hexdigest()[:8]
-    file_name = f"{name if name else unique_id}"
+    file_name = f"{name if name else "chai1_"+unique_id+".fasta"}"
     file_path = here / "inputs/fasta" / file_name
     
     # Write the FASTA file
@@ -137,7 +137,7 @@ def create_json_config(
     }
     
     # Generate file name based on provided name or unique ID
-    file_name = f"{name if name else hashlib.sha256(uuid4().bytes).hexdigest()[:8]}"
+    file_name = f"{name if name else "chai1_"+hashlib.sha256(uuid4().bytes).hexdigest()[:8]+".json"}"
     file_path = here / "inputs/config" / file_name
     
     # Write the JSON file 
@@ -279,12 +279,12 @@ with gr.Blocks(theme=theme) as demo:
     gr.Markdown(
     """
     # Protein Folding Simulation Interface
-    This interface provides you the tools to fold any FASTA chain based on Chai-1 model. Also, this is a MCP server to provide all the tools to automate the process of folding proteins with LLMs.     
+    This interface provides the tools to fold any FASTA chain based on Chai-1 model. Also, this is a MCP server to provide all the tools to automate the process of folding proteins with LLMs.     
     """) 
     
     with gr.Tab("Introduction 🔭"):
         
-        gr.Image("images/logo1.png", show_label=False,width=400)
+        gr.Image("images/logo1.png", show_label=False, width=600, show_download_button=False, show_fullscreen_button=False)
         
         gr.Markdown(
         """
@@ -307,7 +307,13 @@ with gr.Blocks(theme=theme) as demo:
         )
         
         gr.HTML(
-            """<iframe width="600" height="338" 
+            """<style> 
+                iframe { 
+                display: block; 
+                margin: 0 auto; 
+            } 
+            </style>
+            <iframe width="600" height="338" 
             src="https://www.youtube.com/embed/P9cAKxJ9Zh8" 
             frameborder="0" allowfullscreen></iframe>""",
             label="MCP demonstration video"
@@ -316,7 +322,22 @@ with gr.Blocks(theme=theme) as demo:
         with open("introduction_page.md", "r") as f:
             intro_md = f.read()
         gr.Markdown(intro_md)
+        
+        gr.Markdown(
+        """
+        # Result example
+        The following image shows an example of a protein folding simulation using the Chai-1 model. 
+        The simulation was run with the default configuration and the image is 3D view from the Gradio interface.
+        """)    
+        
+        gr.Image("images/protein.png", show_label=True, width=400, label="Protein Folding example", show_download_button=False, show_fullscreen_button=False)
     
+        gr.Markdown(
+        """
+        # Contact
+        For any issues or questions, please contact the developer or refer to the documentation.
+        """)    
+
     
     with gr.Tab("Configuration 📦"):
         
@@ -353,18 +374,18 @@ with gr.Blocks(theme=theme) as demo:
        
        
     with gr.Tab("Run folding simulation 🚀"):     
-        with gr.Row():
-            with gr.Column(scale=1):
-                inp1 = gr.FileExplorer(root_dir=here / "inputs/fasta", 
-                                value="chai1_default_input.fasta",
-                                label="Input Fasta file", 
-                                file_count='single')     
-                
+        with gr.Row():                
             with gr.Column(scale=1):
                 inp2 = gr.FileExplorer(root_dir=here / "inputs/config", 
                                 value="chai1_quick_inference.json",
                                 label="Configuration file", 
                                 file_count='single')    
+                
+            with gr.Column(scale=1):
+                inp1 = gr.FileExplorer(root_dir=here / "inputs/fasta", 
+                                value="chai1_default_input.fasta",
+                                label="Input Fasta file", 
+                                file_count='single')     
         btn_refresh = gr.Button("Refresh available files")
         
         # Only workaround I found to update the file explorer
@@ -394,7 +415,7 @@ with gr.Blocks(theme=theme) as demo:
         )
     
     
-    with gr.Tab("Show protein from a cif file 💻"):     
+    with gr.Tab("Show molecule from a CIF file 💻"):     
         
         gr.Markdown(
         """

introduction_page.md

@@ -10,10 +10,10 @@ code[class*="language-bash"], pre[class*="language-bash"] {
 
 <div style="background-color:#f5f5f5; border-radius:8px; padding:18px 24px; margin-bottom:24px; border:1px solid #cccccc;">
 
-### 1. <span style="color:#2563eb;">(Optional) Create your JSON configuration file</span>
+### 1. <span style="color:#e98935;">Create your JSON configuration file (Optional)</span>
 <small>Default configuration is available if you skip this step.</small>
 
-- Set your simulation parameters and generate the JSON config file. A unique identifier will be assigned (e.g., `chai_{run_id}_config.json`).
+- In the `Configuration 📦` window, set your simulation parameters and generate the JSON config file. You can provide a file name in the dedicated box that will appear in the list of available configuration files. If you don't, a unique identifier will be assigned (e.g., `chai_{run_id}_config.json`).
 - **Parameters:**
   - <b>Number of diffusion time steps:</b> 1 to 500
   - <b>Number of trunk recycles:</b> 1 to 5
@@ -21,22 +21,28 @@ code[class*="language-bash"], pre[class*="language-bash"] {
   - <b>ESM_embeddings:</b> Include or not
   - <b>MSA_server:</b> Include or not
 
-### 2. <span style="color:#2563eb;">(Optional) Upload a FASTA file with your molecule sequence</span>
+### 2. <span style="color:#e98935;">Upload a FASTA file with your molecule sequence (Optional)</span>
 <small>Default FASTA files are available if you skip this step.</small>
 
-- Write your FASTA content and create the file. A unique identifier will be assigned (e.g., `chai_{run_id}_input.fasta`).
+- In the `Configuration 📦` window, write your FASTA content and create the file. You can provide a file name in the dedicated box that will appear in the list of available configuration files. If you don't provide a file name a unique identifier will be assigned (e.g., `chai_{run_id}_input.fasta`). Also, if you don't provide a fasta content a default sequence will be written in the file.
 - <b style="color:#b91c1c;">Warning:</b> The header must be well formatted for Chai1 to process it.
 
 **FASTA template:**
+<div style="background-color:#ffffff; border-radius:8px; padding:18px 24px; margin-bottom:24px; border:1px solid #cccccc;">
+
 ```fasta
 >{molecule_type}|{molecule_name}
 Sequence (for protein/RNA/DNA) or SMILES for ligand
 ```
 
+</div>
+
 **Accepted  molecule types:** 
  `protein`/ `rna`/  `dna` / `ligand`
 
 **Default input (provided by Chai1):**
+<div style="background-color:#ffffff; border-radius:8px; padding:18px 24px; margin-bottom:24px; border:1px solid #cccccc;">
+
 ```fasta
 >protein|name=example-of-long-protein
 AGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQWMFGCDLGPDGRLLRGYDQSAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKETLQRAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQWDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP
@@ -50,40 +56,35 @@ GAAL
 >ligand|name=example-ligand-as-smiles
 CCCCCCCCCCCCCC(=O)O
 ```
+
+</div>
 <small>For a peptide, use `protein` as the molecule type.</small>
 
 **Other example:**
+<div style="background-color:#ffffff; border-radius:8px; padding:18px 24px; margin-bottom:24px; border:1px solid #cccccc;">
+
 ```fasta
 >protein|lysozyme
 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPDLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCAAINQVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPDRAKRVITTFRTGTWDAYKNL
 ```
-### 3. <span style="color:#2563eb;">Select your config and FASTA files</span>
+
+</div>
+
+### 3. <span style="color:#e98935;">Select your config and FASTA files</span>
 <small>Files are stored in your working directory as you create them.</small>
 
-### 4. <span style="color:#2563eb;">Click the "Run" button to start the simulation</span>
+In the `Run folding simulation 🚀` window, refresh the file list by clicking on the `Refresh available files`. Then select the configuration and fasta file you want.
 
-### 5. <span style="color:#2563eb;">View the 3D visualization of your molecule</span>
-</div>
+### 4. <span style="color:#e98935;">Run the simulation</span>
 
-## Simulation parameters choice       
-If no config or fasta files are created, default values are chosen:
-- chai1_default_input.fasta
-- chai1_quick_inference.json
-
-The files content is diplayed at the bottom of the page.
-The default json configuration makes the computation fast (about 2min) but results can be disappointing. 
-Please use chai1_default_inference.json to have a wonderful protein 😃.
-
-- chai1_quick_inference.json
-```json
-{
-    "num_trunk_recycles": 1,
-    "num_diffn_timesteps": 10,
-    "seed": 42,
-    "use_esm_embeddings": true
-    "use_msa_server": false
-}
-```
+Press the `Run Simulation` button to start de folding Simulation. Five protein folding simulations will be performed. Unfortunately, this parameter is hard coded in Chai-1. The simulation time is expected to be from 2min to 10min depending on the molecule.
+
+### 5. <span style="color:#e98935;">Analyse the results of your simulation</span>
+
+To analyse the results of the simulation, two outputs are provided:
+- A table showing the score of the 5 folding performed
+- Interactive 3D visualization of the molecule
+
+Finally, you can get to the `Show molecule from a CIF file 💻` window to watch the cif files. This is mainly used to visualize CIF files after using this tool as an MCP server.
 
-# Contact
-For any issues or questions, please contact the developer or refer to the documentation.
+</div>