Spaces:
Running
Running
Add a molecule viewer
Browse files
app.py
CHANGED
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@@ -5,6 +5,66 @@ import torch
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from foldingdiff import sampling
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from foldingdiff import angles_and_coords as ac
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def sample_at_length(l:int, seed:int):
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"""
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Sample a single structure at the given length
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@@ -16,7 +76,7 @@ def sample_at_length(l:int, seed:int):
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outdir = os.path.join(os.getcwd(), "output")
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os.makedirs(outdir, exist_ok=True)
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pdb_file = ac.create_new_chain_nerf(os.path.join(outdir, "generated.pdb"), s)
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return s, pdb_file
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interface = gr.Interface(
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fn=sample_at_length,
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@@ -25,8 +85,9 @@ interface = gr.Interface(
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gr.Number(value=42, label="Random seed", show_label=True, precision=0),
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],
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outputs=[
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gr.
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gr.File(label="Generated structure in PDB format (cartesian coordinates)"),
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],
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)
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interface.launch()
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from foldingdiff import sampling
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from foldingdiff import angles_and_coords as ac
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def read_mol(molpath: str) -> str:
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with open(molpath, "r") as fp:
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lines = fp.readlines()
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mol = ""
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for l in lines:
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mol += l
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return mol
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def molecule(input_pdb: str) -> str:
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"""Get the string to view the given pdb in 3dmol.js"""
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mol = read_mol(input_pdb)
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x = (
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"""<!DOCTYPE html>
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<html>
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<head>
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<meta http-equiv="content-type" content="text/html; charset=UTF-8" />
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<style>
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body{
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font-family:sans-serif
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}
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.mol-container {
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width: 100%;
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height: 600px;
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position: relative;
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}
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.mol-container select{
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background-image:None;
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}
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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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let pdb = `"""
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+ mol
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+ """`
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$(document).ready(function () {
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let element = $("#container");
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let config = { backgroundColor: "black" };
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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({}, { stick: { colorscheme:"whiteCarbon" } });
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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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})
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</script>
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</body></html>"""
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)
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return f"""<iframe style="width: 100%; height: 600px" 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 sample_at_length(l:int, seed:int):
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"""
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Sample a single structure at the given length
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outdir = os.path.join(os.getcwd(), "output")
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os.makedirs(outdir, exist_ok=True)
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pdb_file = ac.create_new_chain_nerf(os.path.join(outdir, "generated.pdb"), s)
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return molecule(s), pdb_file, s
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interface = gr.Interface(
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fn=sample_at_length,
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gr.Number(value=42, label="Random seed", show_label=True, precision=0),
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],
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outputs=[
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gr.HTML(),
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gr.File(label="Generated structure in PDB format (cartesian coordinates)"),
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gr.Dataframe(label="Generated angles defining structure", max_rows=8),
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],
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)
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interface.launch()
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