Hugging Face's logo

Spaces:
osanseviero
/
esmfold
Paused

App Files Community
6
esmfold
File size: 4,870 Bytes 
19b831b
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
d61d9e2
 
 
 
 
 
 
19b831b
fe78de5
 
99bd894
bfccab3
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
19b831b
 
9960f8b
 
d61d9e2
19b831b
 
 
9960f8b
19b831b
 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
 
import gradio as gr
import os
import requests


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://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(sequence):
    headers = {
        'Content-Type': 'application/x-www-form-urlencoded',
    }

    response = requests.post('https://api.esmatlas.com/foldSequence/v1/pdb/', headers=headers, data=sequence)
    name = sequence[:3] + sequence[-3:] 
    pdb_filename = "test.pdb"
    pdb_string = response.content.decode('utf-8')
    with open(pdb_filename, "w") as out:
      out.write(pdb_string)

    return molecule(pdb_filename)


demo = gr.Blocks()

examples = [
    ["Plastic degradation protein", "MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ"],
    ["Antifreeze protein", "QCTGGADCTSCTGACTGCGNCPNAVTCTNSQHCVKANTCTGSTDCNTAQTCTNSKDCFEANTCTDSTNCYKATACTNSSGCPGH"],
    ["AI Generated protein", "MSGMKKLYEYTVTTLDEFLEKLKEFILNTSKDKIYKLTITNPKLIKDIGKAIAKAAEIADVDPKEIEEMIKAVEENELTKLVITIEQTDDKYVIKVELENEDGLVHSFEIYFKNKEEMEKFLELLEKLISKLSGS"],
    ["7-bladed propeller fold", "VKLAGNSSLCPINGWAVYSKDNSIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPHRTLMSCPVGEAPSPYNSRFESVAWSASACHDGTSWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFKMEKGKVVKSVELDAPNYHYEECSCYPNAGEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGAYGVKGFSFKYGNGVWIGRTKSTNSRSGFEMIWDPNGWTETDSSFSVKQDIVAITDWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKESTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTIDK"]
]

with demo:
    gr.Markdown("# ESM-2 Protein Folding demo")
    gr.Markdown("You can input a single protein sequence and you get the predicted protein structure")
    gr.HTML("""<div style="text-align: center; max-width: 700px; margin: 0 auto;">
              <div
              style="
                  display: inline-flex;
                  align-items: center;
                  gap: 0.8rem;
                  font-size: 1.75rem;
              "
              >
              <h1 style="font-weight: 900; margin-bottom: 7px; margin-top: 5px;">
                   ESM-2 Protein Folding demo
              </h1>
              </div>
              <p style="margin-bottom: 10px; font-size: 94%">
                  You can input a single protein sequence and you get the predicted protein structure
              </p>
          </div>""")
    with gr.Row():
        with gr.Box():
            name = gr.Textbox(label="Protein example", value=examples[1][0])
            inp = gr.Textbox(label="Protein sequence", lines=3, value=examples[1][1])
            gr.Examples(examples, [name, inp])
            btn = gr.Button("Predict structure")
    mol = gr.HTML()
    btn.click(fn=update, inputs=inp, outputs=mol)
    gr.Markdown("[ESM](https://esmatlas.com/about) by Meta using the API. You can also use Hugging Face `transformers` as shown [here](https://github.com/huggingface/notebooks/blob/main/examples/protein_folding.ipynb), which is supported since [v4.24](https://github.com/huggingface/transformers/releases/tag/v4.24.0).")
demo.launch()