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3dmol.js
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import gradio as gr

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: 700px;
    position: relative;
    }
    .mol-container select{
        background-image:None;
    }
    </style>
    <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: 800px; height: 800px" 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")
    inp = gr.Textbox(placeholder="PDB Code or upload file below", label="Input structure")
    file = gr.File(file_count="single")
    btn = gr.Button("View structure")
    mol = gr.HTML()
    btn.click(fn=update,inputs=[inp, file],outputs=mol]
    
 demo.launch()