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import gradio as gr
import os
def get_pdb(pdb_code="", filepath=""):
if pdb_code is None or pdb_code == "":
try:
return 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):
mol = read_mol(input_pdb)
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 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({}, { cartoon: { colorscheme:"whiteCarbon" } });
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>"""
def update(inp, file):
pdb_path = get_pdb(inp, file)
return molecule(pdb_path)
demo = gr.Blocks()
with demo:
gr.Markdown("# PDB viewer using 3Dmol.js")
gr.Markdown("""If using please cite:
> 3Dmol.js: molecular visualization with WebGL, Nicholas Rego, David Koes , Bioinformatics, Volume 31, Issue 8, April 2015, Pages 1322–1324, https://doi.org/10.1093/bioinformatics/btu829""")
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], outputs=mol)
demo.launch()
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