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simonduerr commited on
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30f2e61
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1 Parent(s): 3c00078

Update app.py

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Files changed (1) hide show
  1. app.py +63 -27
app.py CHANGED
@@ -8,32 +8,37 @@ from gradio_moleculeview import moleculeview
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  import cellscape
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- def predict(input_mol, style, contour_level, view_str, chains):
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- # write view to file
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- with open("view_matrix", "w") as f:
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- f.write(json.loads(view_str))
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-
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- chain_str = ""
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- chain_dict = json.loads(chains)
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- # sort keys in dict and add colors to chain_str
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- for chain in sorted(chain_dict.keys()):
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- chain_str += f" '{chain_dict[chain]}'"
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- if style == "Goodsell3D":
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- os.system(f"cellscape cartoon --pdb {input_mol.name} --outline residue --color_by chain --depth_shading --depth_lines --colors {chain_str} --depth flat --back_outline --view view_matrix --save outline_all.svg")
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- elif style == "Contour":
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- os.system(f"cellscape cartoon --pdb {input_mol.name} --outline chain --color_by chain --depth_contour_interval {contour_level} --colors {chain_str} --depth contours --back_outline --view view_matrix --save outline_all.svg")
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- else:
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- os.system(f"cellscape cartoon --pdb {input_mol.name} --outline chain --colors {chain_str} --depth flat --back_outline --view view_matrix --save outline_all.svg")
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-
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- #read content of file
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- print(os.stat("outline_all.svg").st_size / (1024 * 1024))
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- os.system("inkscape outline_all.svg --actions='select-all;path-simplify;export-plain-svg' --export-filename pdb_opt.svg")
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- print(os.stat("outline_all.svg").st_size / (1024 * 1024))
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-
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- html_output = """
 
 
 
 
 
 
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- <button id="copySvgBtn" style="padding:4px;border:1px solid gray;margin:3px">Copy SVG to Clipboard</button>
 
 
 
 
 
 
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  <button id="copyPngBtn" style="padding:4px;border:1px solid gray;margin:3px">Copy PNG to Clipboard</button>
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  <!-- Buttons for Download -->
@@ -127,10 +132,41 @@ document.getElementById('copyPngBtn').addEventListener('click', copyPngToClipboa
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  document.getElementById('downloadSvgBtn').addEventListener('click', downloadSvg);
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  document.getElementById('downloadPngBtn').addEventListener('click', downloadPng);
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  </script>
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- """
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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- with open("pdb_opt.svg", "r") as f:
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- return f.read().replace("<svg", "<svg id='svgElement'")+html_output, "pdb_opt.svg"
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  import cellscape
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+ def html_output(input_file):
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+ with open(input_file, "r") as f:
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+ svg = f.read().replace("<svg", "<svg id='svgElement'")
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+
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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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+ </head>
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+ <body>
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+
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+ """
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+ + svg
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+ + """
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+ <button id="copySvgBtn" style="padding:4px;border:1px solid gray;margin:3px">Copy SVG to Clipboard</button>
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  <button id="copyPngBtn" style="padding:4px;border:1px solid gray;margin:3px">Copy PNG to Clipboard</button>
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  <!-- Buttons for Download -->
 
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  document.getElementById('downloadSvgBtn').addEventListener('click', downloadSvg);
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  document.getElementById('downloadPngBtn').addEventListener('click', downloadPng);
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  </script>
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+
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+ </body></html>"""
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+ )
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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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+
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+ def predict(input_mol, style, contour_level, view_str, chains):
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+ # write view to file
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+ with open("view_matrix", "w") as f:
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+ f.write(json.loads(view_str))
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+
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+ chain_str = ""
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+ chain_dict = json.loads(chains)
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+
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+ # sort keys in dict and add colors to chain_str
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+ for chain in sorted(chain_dict.keys()):
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+ chain_str += f" '{chain_dict[chain]}'"
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+ if style == "Goodsell3D":
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+ os.system(f"cellscape cartoon --pdb {input_mol.name} --outline residue --color_by chain --depth_shading --depth_lines --colors {chain_str} --depth flat --back_outline --view view_matrix --save outline_all.svg")
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+ elif style == "Contour":
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+ os.system(f"cellscape cartoon --pdb {input_mol.name} --outline chain --color_by chain --depth_contour_interval {contour_level} --colors {chain_str} --depth contours --back_outline --view view_matrix --save outline_all.svg")
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+ else:
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+ os.system(f"cellscape cartoon --pdb {input_mol.name} --outline chain --colors {chain_str} --depth flat --back_outline --view view_matrix --save outline_all.svg")
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+
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+ #read content of file
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+ print(os.stat("outline_all.svg").st_size / (1024 * 1024))
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+ os.system("inkscape outline_all.svg --actions='select-all;path-simplify;export-plain-svg' --export-filename pdb_opt.svg")
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+ print(os.stat("outline_all.svg").st_size / (1024 * 1024))
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+
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+ return html_output("outline_all.svg"), "pdb_opt.svg"
 
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