Spaces:
Paused
Paused
Added dropdown, colors, etc.
Browse files
app.py
CHANGED
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@@ -3,6 +3,9 @@ import os
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import requests
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def read_mol(molpath):
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with open(molpath, "r") as fp:
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lines = fp.readlines()
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@@ -13,7 +16,6 @@ def read_mol(molpath):
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def molecule(input_pdb):
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mol = read_mol(input_pdb)
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x = (
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@@ -27,7 +29,7 @@ def molecule(input_pdb):
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}
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.mol-container {
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width: 100%;
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height:
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position: relative;
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}
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.mol-container select{
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@@ -36,7 +38,7 @@ def molecule(input_pdb):
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</style>
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<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
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</head>
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<body>
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<div id="container" class="mol-container"></div>
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<script>
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@@ -49,7 +51,7 @@ def molecule(input_pdb):
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let config = { backgroundColor: "white" };
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let viewer = $3Dmol.createViewer(element, config);
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viewer.addModel(pdb, "pdb");
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viewer.getModel(0).setStyle({}, { cartoon: { colorscheme:"
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viewer.zoomTo();
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viewer.render();
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viewer.zoom(0.8, 2000);
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@@ -58,14 +60,14 @@ def molecule(input_pdb):
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</body></html>"""
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)
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return f"""<iframe style="width: 100%; height:
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display-capture; encrypted-media;" sandbox="allow-modals allow-forms
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allow-scripts allow-same-origin allow-popups
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allow-top-navigation-by-user-activation allow-downloads" allowfullscreen=""
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allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""
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def update(sequence):
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headers = {
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'Content-Type': 'application/x-www-form-urlencoded',
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}
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@@ -80,14 +82,22 @@ def update(sequence):
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return molecule(pdb_filename)
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demo = gr.Blocks()
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examples = [
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["Plastic degradation protein", "MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ"],
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["Antifreeze protein", "QCTGGADCTSCTGACTGCGNCPNAVTCTNSQHCVKANTCTGSTDCNTAQTCTNSKDCFEANTCTDSTNCYKATACTNSSGCPGH"],
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["AI Generated protein", "MSGMKKLYEYTVTTLDEFLEKLKEFILNTSKDKIYKLTITNPKLIKDIGKAIAKAAEIADVDPKEIEEMIKAVEENELTKLVITIEQTDDKYVIKVELENEDGLVHSFEIYFKNKEEMEKFLELLEKLISKLSGS"],
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["7-bladed propeller fold", "VKLAGNSSLCPINGWAVYSKDNSIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPHRTLMSCPVGEAPSPYNSRFESVAWSASACHDGTSWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFKMEKGKVVKSVELDAPNYHYEECSCYPNAGEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGAYGVKGFSFKYGNGVWIGRTKSTNSRSGFEMIWDPNGWTETDSSFSVKQDIVAITDWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKESTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTIDK"]
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]
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with demo:
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gr.HTML("""<div style="text-align: center; max-width: 700px; margin: 0 auto;">
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@@ -107,13 +117,13 @@ with demo:
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You can input a single protein sequence and you get the predicted protein structure
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</p>
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</div>""")
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with gr.Row():
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gr.Examples(examples, [name, inp])
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btn = gr.Button("Predict structure")
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mol = gr.HTML()
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btn.click(fn=update, inputs=inp, outputs=mol)
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demo.launch()
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import requests
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DEFAULT_SEQ = "MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ"
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def read_mol(molpath):
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with open(molpath, "r") as fp:
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lines = fp.readlines()
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def molecule(input_pdb):
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mol = read_mol(input_pdb)
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x = (
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}
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.mol-container {
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width: 100%;
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height: 380px;
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position: relative;
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}
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.mol-container select{
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</style>
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<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
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</head>
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<body style="overflow: hidden;">
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<div id="container" class="mol-container"></div>
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<script>
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let config = { backgroundColor: "white" };
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let viewer = $3Dmol.createViewer(element, config);
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viewer.addModel(pdb, "pdb");
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viewer.getModel(0).setStyle({}, { cartoon: { colorscheme: {"prop":"resi","gradient":"roygb", "min": 26, "max": 250} } });
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viewer.zoomTo();
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viewer.render();
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viewer.zoom(0.8, 2000);
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</body></html>"""
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)
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return f"""<iframe style="width: 100%; height: 380px" name="result" allow="midi; geolocation; microphone; camera;
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display-capture; encrypted-media;" sandbox="allow-modals allow-forms
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allow-scripts allow-same-origin allow-popups
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allow-top-navigation-by-user-activation allow-downloads" allowfullscreen=""
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allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""
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def update(sequence=DEFAULT_SEQ):
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headers = {
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'Content-Type': 'application/x-www-form-urlencoded',
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}
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return molecule(pdb_filename)
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def suggest(option):
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if option == "Plastic degradation protein":
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suggestion = "MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ"
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elif option == "Antifreeze protein":
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suggestion = "QCTGGADCTSCTGACTGCGNCPNAVTCTNSQHCVKANTCTGSTDCNTAQTCTNSKDCFEANTCTDSTNCYKATACTNSSGCPGH"
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elif option == "AI Generated protein":
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suggestion = "MSGMKKLYEYTVTTLDEFLEKLKEFILNTSKDKIYKLTITNPKLIKDIGKAIAKAAEIADVDPKEIEEMIKAVEENELTKLVITIEQTDDKYVIKVELENEDGLVHSFEIYFKNKEEMEKFLELLEKLISKLSGS"
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elif option == "7-bladed propeller fold":
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suggestion = "VKLAGNSSLCPINGWAVYSKDNSIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPHRTLMSCPVGEAPSPYNSRFESVAWSASACHDGTSWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFKMEKGKVVKSVELDAPNYHYEECSCYPNAGEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGAYGVKGFSFKYGNGVWIGRTKSTNSRSGFEMIWDPNGWTETDSSFSVKQDIVAITDWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKESTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTIDK"
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else:
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suggestion = ""
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return suggestion
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demo = gr.Blocks()
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with demo:
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gr.HTML("""<div style="text-align: center; max-width: 700px; margin: 0 auto;">
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You can input a single protein sequence and you get the predicted protein structure
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</p>
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</div>""")
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name = gr.Dropdown(label="Choose a Sample Protein", value="Plastic degradation protein", choices=["Antifreeze protein", "Plastic degradation protein", "AI Generated protein", "7-bladed propeller fold", "custom"])
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with gr.Row():
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inp = gr.Textbox(label="Protein sequence", lines=3, value=DEFAULT_SEQ, placeholder="Write your protein sequence here...")
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btn = gr.Button("🔬 Predict Structure ").style(full_width=False)
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mol = gr.HTML(update)
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btn.click(fn=update, inputs=inp, outputs=mol)
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name.change(fn=suggest, inputs=name, outputs=inp)
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name.change(fn=lambda :"", inputs=None, outputs=mol)
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gr.Markdown("A demo of [ESM](https://esmatlas.com/about) by Meta using the API. You can also use ESM in Hugging Face `transformers` as shown [here](https://github.com/huggingface/notebooks/blob/main/examples/protein_folding.ipynb), which is supported since [v4.24](https://github.com/huggingface/transformers/releases/tag/v4.24.0).")
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demo.launch()
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