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| from transformers import AutoTokenizer, EsmForProteinFolding | |
| from transformers.models.esm.openfold_utils.protein import to_pdb, Protein as OFProtein | |
| from transformers.models.esm.openfold_utils.feats import atom14_to_atom37 | |
| from Bio import SeqIO | |
| import gradio as gr | |
| import spaces | |
| from gradio_molecule3d import Molecule3D | |
| reps = [ | |
| { | |
| "model": 0, | |
| "chain": "", | |
| "resname": "", | |
| "style": "stick", | |
| "color": "whiteCarbon", | |
| "residue_range": "", | |
| "around": 0, | |
| "byres": False, | |
| "visible": False | |
| } | |
| ] | |
| 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://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 = `""" | |
| + 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 convert_outputs_to_pdb(outputs): | |
| final_atom_positions = atom14_to_atom37(outputs["positions"][-1], outputs) | |
| outputs = {k: v.to("cpu").numpy() for k, v in outputs.items()} | |
| final_atom_positions = final_atom_positions.cpu().numpy() | |
| final_atom_mask = outputs["atom37_atom_exists"] | |
| pdbs = [] | |
| for i in range(outputs["aatype"].shape[0]): | |
| aa = outputs["aatype"][i] | |
| pred_pos = final_atom_positions[i] | |
| mask = final_atom_mask[i] | |
| resid = outputs["residue_index"][i] + 1 | |
| pred = OFProtein( | |
| aatype=aa, | |
| atom_positions=pred_pos, | |
| atom_mask=mask, | |
| residue_index=resid, | |
| b_factors=outputs["plddt"][i], | |
| chain_index=outputs["chain_index"][i] if "chain_index" in outputs else None, | |
| ) | |
| pdbs.append(to_pdb(pred)) | |
| return pdbs | |
| tokenizer = AutoTokenizer.from_pretrained("facebook/esmfold_v1") | |
| model = EsmForProteinFolding.from_pretrained("facebook/esmfold_v1", low_cpu_mem_usage=True) | |
| model = model.cuda() | |
| model.esm = model.esm.half() | |
| import torch | |
| torch.backends.cuda.matmul.allow_tf32 = True | |
| model.trunk.set_chunk_size(64) | |
| def fold_protein(test_protein): | |
| tokenized_input = tokenizer([test_protein], return_tensors="pt", add_special_tokens=False)['input_ids'] | |
| tokenized_input = tokenized_input.cuda() | |
| with torch.no_grad(): | |
| output = model(tokenized_input) | |
| pdb = convert_outputs_to_pdb(output) | |
| with open("output_structure.pdb", "w") as f: | |
| f.write("".join(pdb)) | |
| html = molecule("output_structure.pdb") | |
| return html, "output_structure.pdb" | |
| def fold_protein_wpdb(test_protein, pdb_path): | |
| tokenized_input = tokenizer([test_protein], return_tensors="pt", add_special_tokens=False)['input_ids'] | |
| tokenized_input = tokenized_input.cuda() | |
| with torch.no_grad(): | |
| output = model(tokenized_input) | |
| pdb = convert_outputs_to_pdb(output) | |
| with open(pdb_path, "w") as f: | |
| f.write("".join(pdb)) | |
| html = molecule(pdb_path) | |
| return html | |
| def load_protein_sequences(fasta_file): | |
| protein_sequences = {} | |
| for record in SeqIO.parse(fasta_file, "fasta"): | |
| protein_sequences[record.id] = str(record.seq) | |
| return protein_sequences | |
| def show_split(inputfile): | |
| seqs = load_protein_sequences(inputfile) | |
| htmls = [] | |
| pdb_paths = [] | |
| for seq in seqs: | |
| pdb_path = f'{seq.replace(" ", "_").replace(",","")}.pdb' | |
| pdb_paths.append(pdb_path) | |
| html = fold_protein_wpdb(seqs[seq], pdb_path) | |
| x = f"""<h3>>{seq}</h3> | |
| <br> | |
| """ | |
| htmls.append(x+html) | |
| final = "\n<br>\n".join(htmls) | |
| realhtml = "<div>\n"+final+"\n</div>" | |
| return realhtml, pdb_paths | |
| iface = gr.Interface( | |
| title="SingleProteinviz", | |
| fn=fold_protein, | |
| inputs=gr.Textbox( | |
| label="Protein Sequence", | |
| info="Find sequences examples below, and complete examples with images at: https://github.com/AstraBert/proteinviz/tree/main/examples.md; if you input a sequence, you're gonna get the static image and the 3D model to explore and play with", | |
| lines=5, | |
| value=f"Paste or write amino-acidic sequence here", | |
| ), | |
| outputs=[gr.HTML(label="Protein 3D model"), Molecule3D(label="Molecular 3D model", reps=reps)], | |
| examples=[ | |
| "MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH", | |
| "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS", | |
| "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG", | |
| ] | |
| ) | |
| demo1 = gr.Interface( | |
| title="BulkProteinviz", | |
| fn=show_split, | |
| inputs=gr.File( | |
| label="FASTA File With Protein Sequences", | |
| ), | |
| outputs= [gr.HTML(label="Protein 3D models"), Molecule3D(label="Molecular 3D models", reps=reps, file_count="multiple")], | |
| examples = ["proteins.fasta"] | |
| ) | |
| demo = gr.TabbedInterface([iface, demo1], ["Single Protein Structure Prediction", "Bulk Protein Structure Prediction"], title="""<h1 align='center'>Proteinviz</h1> | |
| <br> | |
| <h2 align='center'>Support this space with a ⭐ on <a href='https://github.com/AstraBert/proteinviz'>GitHub</a></h2>""") | |
| demo.launch() |