Using Python CGI to create PV instances on the fly

[WCawdell]

I would like to use some Python code to write PV instances on the fly for my website. So far I have written the code to create a new .html file for a given PDB file, with the PV code. I believe it's all correct but unfortunately the PV window on the website is blank. I've attached the new HTML file function below:

def PV_Viewer_Page_Writer(title):
with open(f"pv_viewer_{title}.html", "w") as f:
f.write(''''''+"\n")
f.write(''''''+"\n")
f.write('''<title>Dengue Virus Methyl Transferase</title>'''+"\n")
f.write(''''''+"\n")
f.write(''''''+"\n")
f.write(''''''+"\n")
f.write('''

'''+"\n")
f.write(''''''+"\n")
f.write('''<script type='text/javascript' src='bio-pv.min.js'></script>'''+"\n")
f.write('''<script type='text/javascript'>'''+"\n")
f.write('''// override the default options with something less restrictive.'''+"\n")
f.write(''' var options = {'''+"\n")
f.write(''' width: 600,'''+"\n")
f.write(''' height: 600,'''+"\n")
f.write(''' antialias: true,'''+"\n")
f.write(''' quality : "high"'''+"\n")
f.write(''' };'''+"\n")
f.write('''// insert the viewer under the Dom element with id 'gl'.'''+"\n")
f.write(''' var viewer = pv.Viewer(document.getElementById('viewer'), options);'''+"\n")
f.write('''</script>'''+"\n")
f.write('''<script type='text/javascript'>'''+"\n")
f.write(''' function loadMethylTransferase() {'''+"\n")
f.write(''' // asynchronously load the PDB file for the dengue methyl transferase'''+"\n")
f.write(''' // from the server and display it in the viewer.'''+"\n")
f.write(''' pv.io.fetchPdb('4n14_pocket_H_with_data.pdb', function(structure) {'''+"\n")
f.write(''' // display the protein as cartoon, coloring the secondary structure'''+"\n")
f.write(''' // elements in a rainbow gradient.'''+"\n")
f.write(''' viewer.cartoon('protein', structure, { color : color.ssSuccession() });'''+"\n")
f.write(''' // there are two ligands in the structure, the co-factor S-adenosyl'''+"\n")
f.write(''' // homocysteine and the inhibitor ribavirin-5' triphosphate. They have'''+"\n")
f.write(''' // the three-letter codes SAH and RVP, respectively. Let's display them'''+"\n")
f.write(''' // with balls and sticks.'''+"\n")
f.write(''' var ligands = structure.select({ rnames : ['WR7'] });'''+"\n")
f.write(''' viewer.ballsAndSticks('ligands', ligands);'''+"\n")
f.write(''' viewer.centerOn(ligands);'''+"\n")
f.write(''' });'''+"\n")
f.write(''' }'''+"\n")
f.write(''' // load the methyl transferase once the DOM has finished loading. That's'''+"\n")
f.write(''' // the earliest point the WebGL context is available.'''+"\n")
f.write(''' document.addEventListener('DOMContentLoaded', loadMethylTransferase);'''+"\n")
f.write(''' </script>'''+"\n")

[mizuchi3]

The code will work, you simply need an element in the page with id='viewer'.

Also note that browsers will not load this directly from your PC with a file browser for security reasons, you would need to run at least a simple python -m http.server and view the page via http://localhost:8000

[WCawdell]

Thank you very much for your reply.

I currently use this line of code to embed the PV instance into an inline frame of my page:

print('<iframe src="pv_viewer_220_alt_pose_3.html" height="600" width="600" name="menu" title="menu"></iframe>')

Do I need to use a div with id='viewer' inside the iframe? Or do I need to ditch the iframes entirely? I used iframes before I properly understood divs and I could get rid of them if they're causing an issue.

Cheers!