import argparse import shutil import gradio as gr import numpy as np import os import torch import subprocess import output from rdkit import Chem from src import const from src.datasets import ( get_dataloader, collate_with_fragment_edges, collate_with_fragment_without_pocket_edges, parse_molecule, MOADDataset ) from src.lightning import DDPM from src.linker_size_lightning import SizeClassifier from src.generation import generate_linkers, try_to_convert_to_sdf, get_pocket from zipfile import ZipFile MIN_N_STEPS = 100 MAX_N_STEPS = 500 MAX_BATCH_SIZE = 20 MODELS_METADATA = { 'geom_difflinker': { 'link': 'https://zenodo.org/record/7121300/files/geom_difflinker.ckpt?download=1', 'path': 'models/geom_difflinker.ckpt', }, 'geom_difflinker_given_anchors': { 'link': 'https://zenodo.org/record/7775568/files/geom_difflinker_given_anchors.ckpt?download=1', 'path': 'models/geom_difflinker_given_anchors.ckpt', }, 'pockets_difflinker': { 'link': 'https://zenodo.org/record/7775568/files/pockets_difflinker_full_no_anchors.ckpt?download=1', 'path': 'models/pockets_difflinker.ckpt', }, 'pockets_difflinker_given_anchors': { 'link': 'https://zenodo.org/record/7775568/files/pockets_difflinker_full.ckpt?download=1', 'path': 'models/pockets_difflinker_given_anchors.ckpt', }, } parser = argparse.ArgumentParser() parser.add_argument('--ip', type=str, default=None) args = parser.parse_args() device = torch.device("cuda" if torch.cuda.is_available() else "cpu") print(f'Device: {device}') os.makedirs("results", exist_ok=True) os.makedirs("models", exist_ok=True) size_gnn_path = 'models/geom_size_gnn.ckpt' if not os.path.exists(size_gnn_path): print('Downloading SizeGNN model...') link = 'https://zenodo.org/record/7121300/files/geom_size_gnn.ckpt?download=1' subprocess.run(f'wget {link} -O {size_gnn_path}', shell=True) size_nn = SizeClassifier.load_from_checkpoint('models/geom_size_gnn.ckpt', map_location=device).eval().to(device) print('Loaded SizeGNN model') diffusion_models = {} for model_name, metadata in MODELS_METADATA.items(): link = metadata['link'] diffusion_path = metadata['path'] if not os.path.exists(diffusion_path): print(f'Downloading {model_name}...') subprocess.run(f'wget {link} -O {diffusion_path}', shell=True) diffusion_models[model_name] = DDPM.load_from_checkpoint(diffusion_path, map_location=device).eval().to(device) print(f'Loaded model {model_name}') print(os.curdir) print(os.path.abspath(os.curdir)) print(os.listdir(os.curdir)) def read_molecule_content(path): with open(path, "r") as f: return "".join(f.readlines()) def read_molecule(path): if path.endswith('.pdb'): return Chem.MolFromPDBFile(path, sanitize=False, removeHs=True) elif path.endswith('.mol'): return Chem.MolFromMolFile(path, sanitize=False, removeHs=True) elif path.endswith('.mol2'): return Chem.MolFromMol2File(path, sanitize=False, removeHs=True) elif path.endswith('.sdf'): return Chem.SDMolSupplier(path, sanitize=False, removeHs=True)[0] raise Exception('Unknown file extension') def read_molecule_file(in_file, allowed_extentions): if isinstance(in_file, str): path = in_file else: path = in_file.name extension = path.split('.')[-1] if extension not in allowed_extentions: msg = output.INVALID_FORMAT_MSG.format(extension=extension) return None, None, msg try: mol = read_molecule(path) except Exception as e: e = str(e).replace('\'', '') msg = output.ERROR_FORMAT_MSG.format(message=e) return None, None, msg if extension == 'pdb': content = Chem.MolToPDBBlock(mol) elif extension in ['mol', 'mol2', 'sdf']: content = Chem.MolToMolBlock(mol, kekulize=False) extension = 'mol' else: raise NotImplementedError return content, extension, None def show_input(in_fragments, in_protein): vis = '' if in_fragments is not None and in_protein is None: vis = show_fragments(in_fragments) elif in_fragments is None and in_protein is not None: vis = show_target(in_protein) elif in_fragments is not None and in_protein is not None: vis = show_fragments_and_target(in_fragments, in_protein) return [vis, gr.Dropdown.update(choices=[], value=None, visible=False), None] def show_fragments(in_fragments): molecule, extension, html = read_molecule_file(in_fragments, allowed_extentions=['sdf', 'pdb', 'mol', 'mol2']) if molecule is not None: html = output.FRAGMENTS_RENDERING_TEMPLATE.format(molecule=molecule, fmt=extension) return output.IFRAME_TEMPLATE.format(html=html) def show_target(in_protein): molecule, extension, html = read_molecule_file(in_protein, allowed_extentions=['pdb']) if molecule is not None: html = output.TARGET_RENDERING_TEMPLATE.format(molecule=molecule, fmt=extension) return output.IFRAME_TEMPLATE.format(html=html) def show_fragments_and_target(in_fragments, in_protein): fragments_molecule, fragments_extension, msg = read_molecule_file(in_fragments, ['sdf', 'pdb', 'mol', 'mol2']) if fragments_molecule is None: return output.IFRAME_TEMPLATE.format(html=msg) target_molecule, target_extension, msg = read_molecule_file(in_protein, allowed_extentions=['pdb']) if fragments_molecule is None: return output.IFRAME_TEMPLATE.format(html=msg) html = output.FRAGMENTS_AND_TARGET_RENDERING_TEMPLATE.format( molecule=fragments_molecule, fmt=fragments_extension, target=target_molecule, target_fmt=target_extension, ) return output.IFRAME_TEMPLATE.format(html=html) def clear_fragments_input(in_protein): vis = '' if in_protein is not None: vis = show_target(in_protein) return [None, vis, gr.Dropdown.update(choices=[], value=None, visible=False), None] def clear_protein_input(in_fragments): vis = '' if in_fragments is not None: vis = show_fragments(in_fragments) return [None, vis, gr.Dropdown.update(choices=[], value=None, visible=False), None] def click_on_example(example): fragment_fname, target_fname = example fragment_path = f'examples/{fragment_fname}' if fragment_fname != '' else None target_path = f'examples/{target_fname}' if target_fname != '' else None return [fragment_path, target_path] + show_input(fragment_path, target_path) def draw_sample(sample_path, out_files, num_samples): with_protein = (len(out_files) == num_samples + 3) in_file = out_files[1] in_sdf = in_file if isinstance(in_file, str) else in_file.name input_fragments_content = read_molecule_content(in_sdf) fragments_fmt = in_sdf.split('.')[-1] offset = 2 input_target_content = None target_fmt = None if with_protein: offset += 1 in_pdb = out_files[2] if isinstance(out_files[2], str) else out_files[2].name input_target_content = read_molecule_content(in_pdb) target_fmt = in_pdb.split('.')[-1] out_sdf = sample_path if isinstance(sample_path, str) else sample_path.name generated_molecule_content = read_molecule_content(out_sdf) molecule_fmt = out_sdf.split('.')[-1] if with_protein: html = output.SAMPLES_WITH_TARGET_RENDERING_TEMPLATE.format( fragments=input_fragments_content, fragments_fmt=fragments_fmt, molecule=generated_molecule_content, molecule_fmt=molecule_fmt, target=input_target_content, target_fmt=target_fmt, ) else: html = output.SAMPLES_RENDERING_TEMPLATE.format( fragments=input_fragments_content, fragments_fmt=fragments_fmt, molecule=generated_molecule_content, molecule_fmt=molecule_fmt, ) return output.IFRAME_TEMPLATE.format(html=html) def compress(output_fnames, name): archive_path = f'results/all_files_{name}.zip' with ZipFile(archive_path, 'w') as archive: for fname in output_fnames: archive.write(fname) return archive_path def generate(in_fragments, in_protein, n_steps, n_atoms, num_samples, selected_atoms): if in_fragments is None: return [None, None, None, None] if in_protein is None: return generate_without_pocket(in_fragments, n_steps, n_atoms, num_samples, selected_atoms) else: return generate_with_pocket(in_fragments, in_protein, n_steps, n_atoms, num_samples, selected_atoms) def generate_without_pocket(input_file, n_steps, n_atoms, num_samples, selected_atoms): # Parsing selected atoms (javascript output) selected_atoms = selected_atoms.strip() if selected_atoms == '': selected_atoms = [] else: selected_atoms = list(map(int, selected_atoms.split(','))) # Selecting model if len(selected_atoms) == 0: selected_model_name = 'geom_difflinker' else: selected_model_name = 'geom_difflinker_given_anchors' print(f'Start generating with model {selected_model_name}, selected_atoms:', selected_atoms) ddpm = diffusion_models[selected_model_name] path = input_file.name extension = path.split('.')[-1] if extension not in ['sdf', 'pdb', 'mol', 'mol2']: msg = output.INVALID_FORMAT_MSG.format(extension=extension) return [output.IFRAME_TEMPLATE.format(html=msg), None, None, None] try: molecule = read_molecule(path) try: molecule = Chem.RemoveAllHs(molecule) except: pass name = '.'.join(path.split('/')[-1].split('.')[:-1]) inp_sdf = f'results/input_{name}.sdf' except Exception as e: e = str(e).replace('\'', '') error = f'Could not read the molecule: {e}' msg = output.ERROR_FORMAT_MSG.format(message=error) return [output.IFRAME_TEMPLATE.format(html=msg), None, None, None] if molecule.GetNumAtoms() > 100: error = f'Too large molecule: upper limit is 100 heavy atoms' msg = output.ERROR_FORMAT_MSG.format(message=error) return [output.IFRAME_TEMPLATE.format(html=msg), None, None, None] with Chem.SDWriter(inp_sdf) as w: w.SetKekulize(False) w.write(molecule) positions, one_hot, charges = parse_molecule(molecule, is_geom=True) anchors = np.zeros_like(charges) anchors[selected_atoms] = 1 fragment_mask = np.ones_like(charges) linker_mask = np.zeros_like(charges) print('Read and parsed molecule') dataset = [{ 'uuid': '0', 'name': '0', 'positions': torch.tensor(positions, dtype=const.TORCH_FLOAT, device=device), 'one_hot': torch.tensor(one_hot, dtype=const.TORCH_FLOAT, device=device), 'charges': torch.tensor(charges, dtype=const.TORCH_FLOAT, device=device), 'anchors': torch.tensor(anchors, dtype=const.TORCH_FLOAT, device=device), 'fragment_mask': torch.tensor(fragment_mask, dtype=const.TORCH_FLOAT, device=device), 'linker_mask': torch.tensor(linker_mask, dtype=const.TORCH_FLOAT, device=device), 'num_atoms': len(positions), }] * num_samples dataloader = get_dataloader(dataset, batch_size=num_samples, collate_fn=collate_with_fragment_edges) print('Created dataloader') ddpm.edm.T = n_steps if n_atoms == 0: def sample_fn(_data): out, _ = size_nn.forward(_data, return_loss=False) probabilities = torch.softmax(out, dim=1) distribution = torch.distributions.Categorical(probs=probabilities) samples = distribution.sample() sizes = [] for label in samples.detach().cpu().numpy(): sizes.append(size_nn.linker_id2size[label]) sizes = torch.tensor(sizes, device=samples.device, dtype=torch.long) return sizes else: def sample_fn(_data): return torch.ones(_data['positions'].shape[0], device=device, dtype=torch.long) * n_atoms for data in dataloader: try: generate_linkers(ddpm=ddpm, data=data, sample_fn=sample_fn, name=name, with_pocket=False) except Exception as e: e = str(e).replace('\'', '') error = f'Caught exception while generating linkers: {e}' msg = output.ERROR_FORMAT_MSG.format(message=error) return [output.IFRAME_TEMPLATE.format(html=msg), None, None, None] out_files = try_to_convert_to_sdf(name, num_samples) out_files = [inp_sdf] + out_files out_files = [compress(out_files, name=name)] + out_files choice = out_files[2] return [ draw_sample(choice, out_files, num_samples), out_files, gr.Dropdown.update( choices=out_files[2:], value=choice, visible=True, ), None ] def generate_with_pocket(in_fragments, in_protein, n_steps, n_atoms, num_samples, selected_atoms): # Parsing selected atoms (javascript output) selected_atoms = selected_atoms.strip() if selected_atoms == '': selected_atoms = [] else: selected_atoms = list(map(int, selected_atoms.split(','))) # Selecting model if len(selected_atoms) == 0: selected_model_name = 'pockets_difflinker' else: selected_model_name = 'pockets_difflinker_given_anchors' print(f'Start generating with model {selected_model_name}, selected_atoms:', selected_atoms) ddpm = diffusion_models[selected_model_name] fragments_path = in_fragments.name fragments_extension = fragments_path.split('.')[-1] if fragments_extension not in ['sdf', 'pdb', 'mol', 'mol2']: msg = output.INVALID_FORMAT_MSG.format(extension=fragments_extension) return [output.IFRAME_TEMPLATE.format(html=msg), None, None, None] protein_path = in_protein.name protein_extension = protein_path.split('.')[-1] if protein_extension not in ['pdb']: msg = output.INVALID_FORMAT_MSG.format(extension=protein_extension) return [output.IFRAME_TEMPLATE.format(html=msg), None, None, None] try: fragments_mol = read_molecule(fragments_path) name = '.'.join(fragments_path.split('/')[-1].split('.')[:-1]) except Exception as e: e = str(e).replace('\'', '') error = f'Could not read the molecule: {e}' msg = output.ERROR_FORMAT_MSG.format(message=error) return [output.IFRAME_TEMPLATE.format(html=msg), None, None, None] if fragments_mol.GetNumAtoms() > 100: error = f'Too large molecule: upper limit is 100 heavy atoms' msg = output.ERROR_FORMAT_MSG.format(message=error) return [output.IFRAME_TEMPLATE.format(html=msg), None, None, None] inp_sdf = f'results/input_{name}.sdf' with Chem.SDWriter(inp_sdf) as w: w.SetKekulize(False) w.write(fragments_mol) inp_pdb = f'results/target_{name}.pdb' shutil.copy(protein_path, inp_pdb) frag_pos, frag_one_hot, frag_charges = parse_molecule(fragments_mol, is_geom=True) pocket_pos, pocket_one_hot, pocket_charges = get_pocket(fragments_mol, protein_path) print(f'Detected pocket with {len(pocket_pos)} atoms') positions = np.concatenate([frag_pos, pocket_pos], axis=0) one_hot = np.concatenate([frag_one_hot, pocket_one_hot], axis=0) charges = np.concatenate([frag_charges, pocket_charges], axis=0) anchors = np.zeros_like(charges) anchors[selected_atoms] = 1 fragment_only_mask = np.concatenate([ np.ones_like(frag_charges), np.zeros_like(pocket_charges), ]) pocket_mask = np.concatenate([ np.zeros_like(frag_charges), np.ones_like(pocket_charges), ]) linker_mask = np.concatenate([ np.zeros_like(frag_charges), np.zeros_like(pocket_charges), ]) fragment_mask = np.concatenate([ np.ones_like(frag_charges), np.ones_like(pocket_charges), ]) print('Read and parsed molecule') dataset = [{ 'uuid': '0', 'name': '0', 'positions': torch.tensor(positions, dtype=const.TORCH_FLOAT, device=device), 'one_hot': torch.tensor(one_hot, dtype=const.TORCH_FLOAT, device=device), 'charges': torch.tensor(charges, dtype=const.TORCH_FLOAT, device=device), 'anchors': torch.tensor(anchors, dtype=const.TORCH_FLOAT, device=device), 'fragment_only_mask': torch.tensor(fragment_only_mask, dtype=const.TORCH_FLOAT, device=device), 'pocket_mask': torch.tensor(pocket_mask, dtype=const.TORCH_FLOAT, device=device), 'fragment_mask': torch.tensor(fragment_mask, dtype=const.TORCH_FLOAT, device=device), 'linker_mask': torch.tensor(linker_mask, dtype=const.TORCH_FLOAT, device=device), 'num_atoms': len(positions), }] * num_samples dataset = MOADDataset(data=dataset) ddpm.val_dataset = dataset batch_size = min(num_samples, MAX_BATCH_SIZE) dataloader = get_dataloader(dataset, batch_size=batch_size, collate_fn=collate_with_fragment_without_pocket_edges) print('Created dataloader') ddpm.edm.T = n_steps if n_atoms == 0: def sample_fn(_data): out, _ = size_nn.forward(_data, return_loss=False) probabilities = torch.softmax(out, dim=1) distribution = torch.distributions.Categorical(probs=probabilities) samples = distribution.sample() sizes = [] for label in samples.detach().cpu().numpy(): sizes.append(size_nn.linker_id2size[label]) sizes = torch.tensor(sizes, device=samples.device, dtype=torch.long) return sizes else: def sample_fn(_data): return torch.ones(_data['positions'].shape[0], device=device, dtype=torch.long) * n_atoms for batch_i, data in enumerate(dataloader): try: offset_idx = batch_i * batch_size generate_linkers( ddpm=ddpm, data=data, sample_fn=sample_fn, name=name, with_pocket=True, offset_idx=offset_idx, ) except Exception as e: e = str(e).replace('\'', '') error = f'Caught exception while generating linkers: {e}' msg = output.ERROR_FORMAT_MSG.format(message=error) return [output.IFRAME_TEMPLATE.format(html=msg), None, None, None] out_files = try_to_convert_to_sdf(name, num_samples) out_files = [inp_sdf, inp_pdb] + out_files out_files = [compress(out_files, name=name)] + out_files choice = out_files[3] return [ draw_sample(choice, out_files, num_samples), out_files, gr.Dropdown.update( choices=out_files[3:], value=choice, visible=True, ), None ] demo = gr.Blocks() with demo: gr.Markdown('# DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design') gr.Markdown( 'Given a set of disconnected fragments in 3D, ' 'DiffLinker places missing atoms in between and designs a molecule incorporating all the initial fragments. ' 'Our method can link an arbitrary number of fragments, requires no information on the attachment atoms ' 'and linker size, and can be conditioned on the protein pockets.' ) gr.Markdown( '[**[Paper]**](https://arxiv.org/abs/2210.05274) ' '[**[Code]**](https://github.com/igashov/DiffLinker)' ) with gr.Box(): with gr.Row(): with gr.Column(): gr.Markdown('## Input') gr.Markdown('Upload the file with 3D-coordinates of the input fragments in .pdb, .mol2 or .sdf format:') input_fragments_file = gr.File(file_count='single', label='Input Fragments') gr.Markdown('Upload the file of the target protein in .pdb format (optionally):') input_protein_file = gr.File(file_count='single', label='Target Protein (Optional)') n_steps = gr.Slider( minimum=MIN_N_STEPS, maximum=MAX_N_STEPS, label="Number of Denoising Steps", step=10 ) n_atoms = gr.Slider( minimum=0, maximum=20, value=5, label="Linker Size: DiffLinker will predict it if set to 0", step=1 ) n_samples = gr.Slider(minimum=5, maximum=50, label="Number of Samples", step=5) examples = gr.Dataset( components=[gr.File(visible=False), gr.File(visible=False)], samples=[ ['examples/example_1.sdf', ''], ['examples/example_2.sdf', ''], ['examples/3hz1_fragments.sdf', 'examples/3hz1_protein.pdb'], ['examples/5ou2_fragments.sdf', 'examples/5ou2_protein.pdb'], ], type='values', headers=['Input Fragments', 'Target Protein'], ) button = gr.Button('Generate Linker!') gr.Markdown('') gr.Markdown('## Output Files') gr.Markdown('Download files with the generated molecules here:') output_files = gr.File(file_count='multiple', label='Output Files', interactive=False) hidden = gr.Textbox(visible=False) with gr.Column(): gr.Markdown('## Visualization') gr.Markdown('**Hint:** click on atoms to select anchor points (optionally)') samples = gr.Dropdown( choices=[], value=None, type='value', multiselect=False, visible=False, interactive=True, label='Samples' ) visualization = gr.HTML() input_fragments_file.change( fn=show_input, inputs=[input_fragments_file, input_protein_file], outputs=[visualization, samples, hidden], ) input_protein_file.change( fn=show_input, inputs=[input_fragments_file, input_protein_file], outputs=[visualization, samples, hidden], ) input_fragments_file.clear( fn=clear_fragments_input, inputs=[input_protein_file], outputs=[input_fragments_file, visualization, samples, hidden], ) input_protein_file.clear( fn=clear_protein_input, inputs=[input_fragments_file], outputs=[input_protein_file, visualization, samples, hidden], ) examples.click( fn=click_on_example, inputs=[examples], outputs=[input_fragments_file, input_protein_file, visualization, samples, hidden] ) button.click( fn=generate, inputs=[input_fragments_file, input_protein_file, n_steps, n_atoms, n_samples, hidden], outputs=[visualization, output_files, samples, hidden], _js=output.RETURN_SELECTION_JS, ) samples.select( fn=draw_sample, inputs=[samples, output_files, n_samples], outputs=[visualization], ) demo.load(_js=output.STARTUP_JS) demo.launch(server_name=args.ip)