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Runtime error
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import gradio as gr
from shutil import copyfile
import gradio as gr
import os
def get_pdb(pdb_code="", filepath=""):
if pdb_code is None or pdb_code == "":
try:
#move file to home folder to have it accessible from the web
copyfile(filepath.name, os.path.join(os.getcwd(), os.path.basename(filepath.name)))
return os.path.join(os.getcwd(), os.path.basename(filepath.name))
except AttributeError as e:
return None
else:
os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb")
return f"{pdb_code}.pdb"
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, public_link):
print(input_pdb)
print(public_link+'/file='+os.path.basename(input_pdb))
link = public_link+"/file="+os.path.basename(input_pdb)
x ="""<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
<title>PDBe Molstar - Helper functions</title>
<!-- Molstar CSS & JS -->
<link rel="stylesheet" type="text/css" href="https://www.ebi.ac.uk/pdbe/pdb-component-library/css/pdbe-molstar-light-3.1.0.css">
<script type="text/javascript" src="https://www.ebi.ac.uk/pdbe/pdb-component-library/js/pdbe-molstar-plugin-3.1.0.js"></script>
<style>
* {
margin: 0;
padding: 0;
box-sizing: border-box;
}
.msp-plugin ::-webkit-scrollbar-thumb {
background-color: #474748 !important;
}
.viewerSection {
margin: 120px 0 0 0px;
}
#myViewer{
float:left;
width:100%;
height: 600px;
position:relative;
}
</style>
</head>
<body>
<div class="viewerSection">
<!-- Molstar container -->
<div id="myViewer"></div>
</div>
<script>
//Create plugin instance
var viewerInstance = new PDBeMolstarPlugin();
//Set options (Checkout available options list in the documentation)
var options = {
customData: {
url: \""""+link+"""\",
format: "pdb"
},
alphafoldView: true,
bgColor: {r:255, g:255, b:255},
//hideCanvasControls: ["selection", "animation", "controlToggle", "controlInfo"]
}
//Get element from HTML/Template to place the viewer
var viewerContainer = document.getElementById("myViewer");
//Call render method to display the 3D view
viewerInstance.render(viewerContainer, options);
</script>
</body>
</html>"""
return f"""<iframe style="width: 100%; height: 720px" 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>"""
def update(inp, file, public_link):
pdb_path = get_pdb(inp, file)
return molecule(pdb_path, public_link)
demo = gr.Blocks()
with demo:
gr.Markdown("# PDB viewer using Mol*")
gr.Markdown("""If using please cite
> David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; 10.1093/nar/gkab31.""")
public_link = gr.Variable(value="https://simonduerr-molstar-gradio.hf.space")
with gr.Row():
with gr.Box():
inp = gr.Textbox(
placeholder="PDB Code or upload file below", label="Input structure"
)
file = gr.File(file_count="single")
gr.Examples(["2CBA", "6VXX"], inp)
btn = gr.Button("View structure")
mol = gr.HTML()
btn.click(fn=update, inputs=[inp, file, public_link], outputs=mol)
_, _, pl = demo.launch() # use public link with share=True locally |