Spaces:
Running
Running
| """ | |
| foldingdiff implements a diffusion model for generating protein structures. Inspired by the biological folding process, | |
| we perform diffusion on the angles between amino acid residues rather than the absolute 3D coordinates of each residue. | |
| By effectively treating each residue as its own reference frame, we shift the equivariance constraints into the | |
| representation space itself; this allows us to use a vanilla transformer model as our model. Here, we provide a simple | |
| online interface for generating single backbones with a given length, starting from a given random seed. | |
| Tips for generating proteins: | |
| * The maximum sequence sequence length this model has been trained on is 128 residues. The shorter a sequence is, the more likely it will be "designable" (see our preprint). | |
| * FoldingDiff does *not* generate the amino acid sequence for its structures, it simply fills the structure with Glycine residues; use a tool like ESM-IF1 to generate amino acids corresponding to generated structure. | |
| See our preprint at https://arxiv.org/abs/2209.15611 and our full codebase at https://github.com/microsoft/foldingdiff | |
| """ | |
| import os | |
| import gradio as gr | |
| import torch | |
| from foldingdiff import sampling | |
| from foldingdiff import angles_and_coords as ac | |
| def read_mol(molpath: str) -> str: | |
| with open(molpath, "r") as fp: | |
| lines = fp.readlines() | |
| mol = "" | |
| for l in lines: | |
| mol += l | |
| return mol | |
| def molecule(input_pdb: str) -> str: | |
| """Get the string to view the given pdb in 3dmol.js""" | |
| 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: "black" }; | |
| let viewer = $3Dmol.createViewer(element, config); | |
| viewer.addModel(pdb, "pdb"); | |
| viewer.getModel(0).setStyle({}, { stick: { 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 sample_at_length(l:int, seed:int): | |
| """ | |
| Sample a single structure at the given length | |
| """ | |
| torch.manual_seed(seed) | |
| l = int(l) | |
| # Sample the angles | |
| s = sampling.sample_simple("wukevin/foldingdiff_cath", n=1, sweep_lengths=(l, l+1))[0] | |
| # Create a PDB file after building out the structure in 3D coordinates | |
| outdir = os.path.join(os.getcwd(), "output") | |
| os.makedirs(outdir, exist_ok=True) | |
| pdb_file = ac.create_new_chain_nerf(os.path.join(outdir, "generated.pdb"), s) | |
| return molecule(pdb_file), pdb_file | |
| interface = gr.Interface( | |
| fn=sample_at_length, | |
| title="foldingdiff - protein backbone structure generation with diffusion models", | |
| description=__doc__, | |
| inputs=[ | |
| gr.Number(value=85, label="Protein backbone length to generate", show_label=True, precision=0), | |
| gr.Number(value=123, label="Random seed", show_label=True, precision=0), | |
| ], | |
| outputs=[ | |
| gr.HTML(), | |
| gr.File(label="Generated structure in PDB format (cartesian coordinates)"), | |
| # gr.Dataframe(label="Generated angles defining structure", max_rows=8), | |
| ], | |
| ) | |
| interface.launch() |