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ivorobyev commited on 27 days ago

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50bf798

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1 Parent(s): 2550c12

Update app.py

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app.py +89 -149

app.py CHANGED Viewed

@@ -1,3 +1,6 @@
 import gradio as gr
 from igfold import IgFoldRunner
 import os
@@ -5,177 +8,114 @@ import random
 import base64
 import socket
 import re
 def read_mol(molpath):
-    with open(molpath, "r") as fp:
-        lines = fp.readlines()
-    mol = ""
-    for l in lines:
-        mol += l
-    return mol
 def molecule(input_pdb, h_seq, l_seq):
-    mol = read_mol(input_pdb)
-    byte_content = mol.encode('utf-8')
-    base64_content = base64.b64encode(byte_content).decode('utf-8')
-    x = (
-        """<!DOCTYPE html>
-        <html>
-        <head>
-    <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
-    <style>
-    body{
-        font-family:sans-serif
-    }
-    .mol-container {
-    width: 100%;
-    height: 600px;
-    position: relative;
-    }
-    .mol-container select{
-        background-image:None;
-    }
-    </style>
-     <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.3/jquery.min.js" integrity="sha512-STof4xm1wgkfm7heWqFJVn58Hm3EtS31XFaagaa8VMReCXAkQnJZ+jEy8PCC/iT18dFy95WcExNHFTqLyp72eQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
-     <script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
-    </head>
-    <body>
-    <div id="container" class="mol-container"></div>
         <script>
-        let h_seq = `"""
-        + h_seq
-        + """`
-        let l_seq = `"""
-        + l_seq
-        + """`
-        let pdb = `"""
-        + mol
-        + """`
-             $(document).ready(function () {
-                let element = $("#container");
-                let config = { backgroundColor: "white" };
-                let viewer = $3Dmol.createViewer(element, config);
-                viewer.addModel(pdb, "pdb");
-                viewer.getModel(0).setStyle({chain: "H"}, {cartoon:{color:"red"}});
-                viewer.getModel(0).setStyle({chain: "L"}, {cartoon:{color:"blue"}});
-                viewer.addSurface($3Dmol.SurfaceType.VDW, {opacity: 0.4, color: "lightblue"});
-                viewer.zoomTo();
-                viewer.render();
-                viewer.zoom(0.8, 2000);
-              })
-        </script>
-        </body></html>"""
-    )
-    return f"""<iframe style="width: 100%; height: 600px" 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>
-  <div style="position: absolute; top: 10px; right: 10px; background-color: white; padding: 10px; border: 1px solid black;">
-        <div style="width: 20px; height: 20px; background-color: red; display: inline-block;"></div>
-        <span style="margin-left: 3px;">Heavy chain</span><br>
-        <div style="width: 20px; height: 20px; background-color: blue; display: inline-block;"></div>
-        <span style="margin-left: 3px;">Light chain</span>
-        <div style="display: flex; justify-content: space-between; margin-top: 5px;">
-        <a href="data:application/octet-stream;base64,{base64_content}" download="structure.pdb">Download File</a>
-        </div>
-    </div>
-    """
 def validate(seq):
     alphabet = set('ACDEFGHIKLMNPQRSTVWY')
-    leftover = set(seq.upper()) - alphabet
-    return not leftover
 def clean_sequence(seq):
     return re.sub(r'\s+', '', seq)
 def pred_seq(h_seq, l_seq):
-    h_seq = clean_sequence(h_seq).upper()
-    l_seq = clean_sequence(l_seq).upper()
-    print("Logs","___"*10)
-    print(f"Heavy chain: {h_seq}")
-    print(f"Light chain: {l_seq}")
-    hostname = socket.gethostname()
-    ip_address = socket.gethostbyname(hostname)
-    print(f"Hostname: {hostname}")
-    print(f"IP Address: {ip_address}")
-    print("___"*10)
-    h_is_valid = validate(h_seq)
-    l_is_valid = validate(l_seq)
-    if h_is_valid and l_is_valid:
-        sequences = {
-            "H": h_seq,
-            "L": l_seq
-        }
-        f_name = ''.join([random.choice("ACDEFGHIKLMNPQRSTVWY") for _ in range(15)])
-        pred_pdb = f"{f_name}.pdb"
-        igfold = IgFoldRunner(num_models = 1)
-        igfold.fold(
-            pred_pdb,
-            sequences=sequences,
-            do_refine=False,
-            do_renum=False
-        )
-        html = molecule(pred_pdb, h_seq, l_seq)
-    else:
-        html = "<p>ERROR! Not valid sequence. Please use only standard amino acid letters (ACDEFGHIKLMNPQRSTVWY)</p>"
-    return html
-# Примеры последовательностей
 examples = [
-    [
-        "QVQLKESGPGLVAPSQSLSITCTVSGFSLSSYGVSWVRQPPGKGLEWLGVIWGDGSTNYHPNLMSRLSISKDISKSQVLFKLNSLQTDDTATYYCVTLDYWGQGTSVTVSS",
-        "DVVMTQTPLSLPVSLGDQASISCRSSQSLVHRNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGLYFCFQTTYVPNTFGGGTKLEIK"
-    ],
-    [
-        "EVQLLESGGGLVQPGGSLRLSCAASGFTFSLYWMGWVRQAPGKGLEWVSSISSSGGVTPYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLGELGWFDPWGQGTLVTVSS",
-        "DIQMTQSPSSLSASVGDRVTITCRASQGISSYLNWYQQKPGKAPKLLIYYASNLQNGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGTKVEIK"
-    ],
-    [
-        "EVQLVQSGPEVKKPGTSVKVSCKASGFTFMSSAVQWVRQARGQRLEWIGWIVIGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSISCNDGFDIWGQGTMVTVS",
-        "EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPITFGQGTKLEIK"
-    ]
 ]
 with gr.Blocks() as demo:
     gr.Markdown('# Antibody Structure Prediction')
-    gr.Markdown("## Examples")
     with gr.Row():
-        h_text = gr.Textbox(lines=5, label="Heavy chain",
-                           placeholder="Enter heavy chain sequence (e.g. QVQLKESGP...)")
-        l_text = gr.Textbox(lines=5, label="Light chain",
-                           placeholder="Enter light chain sequence (e.g. DVVMTQTPL...)")
-    # Создаем примеры с помощью gr.Examples
-    gr.Examples(
-        examples=examples,
-        inputs=[h_text, l_text],
-        label="Click on any example to paste it into the input fields",
-        fn=pred_seq,
-        outputs=gr.HTML()
-    )
-    btn = gr.Button(value="Submit")
     output_html = gr.HTML()
     btn.click(pred_seq, inputs=[h_text, l_text], outputs=output_html)
 if __name__ == "__main__":
-    demo.launch()

+import csv
+csv.field_size_limit(131072 * 10)
 import gradio as gr
 from igfold import IgFoldRunner
 import os
 import base64
 import socket
 import re
+from pathlib import Path
 def read_mol(molpath):
+    try:
+        with open(molpath, "r") as fp:
+            return fp.read()
+    except Exception as e:
+        print(f"Error reading PDB file: {e}")
+        return ""
 def molecule(input_pdb, h_seq, l_seq):
+    try:
+        mol = read_mol(input_pdb)
+        if not mol:
+            return "<p>Error: Failed to read PDB file</p>"
+        byte_content = mol.encode('utf-8')
+        base64_content = base64.b64encode(byte_content).decode('utf-8')
+        x = f"""<!DOCTYPE html><html><head>
+        <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+        <style>body{{font-family:sans-serif}}
+        .mol-container {{width: 100%; height: 600px; position: relative;}}
+        .mol-container select{{background-image:None;}}</style>
+        <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.3/jquery.min.js"></script>
+        <script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
+        </head><body><div id="container" class="mol-container"></div>
         <script>
+        $(document).ready(function () {{
+            let element = $("#container");
+            let config = {{ backgroundColor: "white" }};
+            let viewer = $3Dmol.createViewer(element, config);
+            viewer.addModel(`{mol}`, "pdb");
+            viewer.getModel(0).setStyle({{chain: "H"}}, {{cartoon:{{color:"red"}}}});
+            viewer.getModel(0).setStyle({{chain: "L"}}, {{cartoon:{{color:"blue"}}}});
+            viewer.addSurface($3Dmol.SurfaceType.VDW, {{opacity: 0.4, color: "lightblue"}});
+            viewer.zoomTo();
+            viewer.render();
+            viewer.zoom(0.8, 2000);
+        }})
+        </script></body></html>"""
+        return f"""<iframe style="width: 100%; height: 600px" srcdoc='{x}'></iframe>
+        <div style="position: absolute; top: 10px; right: 10px; background-color: white; padding: 10px; border: 1px solid black;">
+            <div style="width: 20px; height: 20px; background-color: red; display: inline-block;"></div>
+            <span>Heavy chain</span><br>
+            <div style="width: 20px; height: 20px; background-color: blue; display: inline-block;"></div>
+            <span>Light chain</span>
+            <div style="margin-top: 5px;">
+            <a href="data:application/octet-stream;base64,{base64_content}" download="structure.pdb">Download PDB</a>
+            </div>
+        </div>"""
+    except Exception as e:
+        print(f"Error in molecule visualization: {e}")
+        return f"<p>Error generating visualization: {str(e)}</p>"
 def validate(seq):
     alphabet = set('ACDEFGHIKLMNPQRSTVWY')
+    return not (set(seq.upper()) - alphabet)
 def clean_sequence(seq):
     return re.sub(r'\s+', '', seq)
 def pred_seq(h_seq, l_seq):
+    try:
+        h_seq = clean_sequence(h_seq).upper()
+        l_seq = clean_sequence(l_seq).upper()
+        if not (validate(h_seq) and validate(l_seq)):
+            return "<p>Error: Invalid amino acid characters detected</p>"
+        sequences = {"H": h_seq, "L": l_seq}
+        f_name = f"temp_{random.randint(0, 100000)}.pdb"
+        try:
+            igfold = IgFoldRunner(num_models=1)
+            igfold.fold(f_name, sequences=sequences, do_refine=False, do_renum=False)
+            if not os.path.exists(f_name):
+                return "<p>Error: Failed to generate PDB file</p>"
+            html = molecule(f_name, h_seq, l_seq)
+        finally:
+            if os.path.exists(f_name):
+                os.remove(f_name)
+        return html
+    except Exception as e:
+        print(f"Error in prediction: {e}")
+        return f"<p>Error: {str(e)}</p>"
 examples = [
+    ["QVQLKESGPGLVAPSQSLSITCTVSGFSLSSYGVSWVRQPPGKGLEWLGVIWGDGSTNYHPNLMSRLSISKDISKSQVLFKLNSLQTDDTATYYCVTLDYWGQGTSVTVSS",
+     "DVVMTQTPLSLPVSLGDQASISCRSSQSLVHRNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGLYFCFQTTYVPNTFGGGTKLEIK"],
+    ["EVQLLESGGGLVQPGGSLRLSCAASGFTFSLYWMGWVRQAPGKGLEWVSSISSSGGVTPYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLGELGWFDPWGQGTLVTVSS",
+     "DIQMTQSPSSLSASVGDRVTITCRASQGISSYLNWYQQKPGKAPKLLIYYASNLQNGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGTKVEIK"]
 ]
 with gr.Blocks() as demo:
     gr.Markdown('# Antibody Structure Prediction')
     with gr.Row():
+        h_text = gr.Textbox(lines=5, label="Heavy chain", placeholder="Enter heavy chain sequence...")
+        l_text = gr.Textbox(lines=5, label="Light chain", placeholder="Enter light chain sequence...")
+    gr.Examples(examples=examples, inputs=[h_text, l_text], label="Example sequences")
+    btn = gr.Button("Predict Structure")
     output_html = gr.HTML()
     btn.click(pred_seq, inputs=[h_text, l_text], outputs=output_html)
 if __name__ == "__main__":
+    demo.launch(show_error=True, server_name="0.0.0.0")