Hugging Face's logo

Spaces:
osanseviero
/
esmfold
Paused

App Files Community
6
esmfold
File size: 4,719 Bytes 
19b831b
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
d61d9e2
 
 
 
 
 
 
19b831b
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
 
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.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()