viewer_description = """
PDB viewer using 3Dmol.js
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
See also:
https://huggingface.co/blog/spaces_3dmoljs
https://huggingface.co/spaces/simonduerr/3dmol.js/blob/main/app.py
"""
def gen_3dmol_vis(pdb_text: str, sdf_text: str):
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 = `""" + pdb_text + """`
let sdf = `""" + sdf_text + """`
$(document).ready(function () {
let element = $("#container");
let config = { backgroundColor: "white" };
let viewer = $3Dmol.createViewer(element, config);
viewer.addModel(pdb, "pdb", { format: "pdb" });
pdb_model = viewer.getModel(0);
// Cartoon view for protein
// First argument is a selector
pdb_model.setStyle({}, {cartoon: {color: "spectrum", opacity: 0.8}});
viewer.addModel(sdf, "sdf", {format: "sdf"});
sdf_model = viewer.getModel(1);
// Stick view for SDF
sdf_model.setStyle({}, {stick: {color: "red", radius: 0.2, opacity: 0.8}});
viewer.zoomTo();
viewer.render();
// viewer.zoom(0.8, 2000);
})
</script>
</body></html>"""
)
return f"""<iframe style="width: 100%; height: 600px" name="result" 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>"""