import argparse import os.path def main(args): import json, time, os, sys, glob import shutil import warnings import numpy as np import torch from torch import optim from torch.utils.data import DataLoader from torch.utils.data.dataset import random_split, Subset import copy import torch.nn as nn import torch.nn.functional as F import random import os.path import subprocess from protein_mpnn_utils import loss_nll, loss_smoothed, gather_edges, gather_nodes, gather_nodes_t, cat_neighbors_nodes, _scores, _S_to_seq, tied_featurize, parse_PDB, parse_fasta from protein_mpnn_utils import StructureDataset, StructureDatasetPDB, ProteinMPNN if args.seed: seed=args.seed else: seed=int(np.random.randint(0, high=999, size=1, dtype=int)[0]) torch.manual_seed(seed) random.seed(seed) np.random.seed(seed) hidden_dim = 128 num_layers = 3 if args.path_to_model_weights: model_folder_path = args.path_to_model_weights if model_folder_path[-1] != '/': model_folder_path = model_folder_path + '/' else: file_path = os.path.realpath(__file__) k = file_path.rfind("/") if args.ca_only: print("Using CA-ProteinMPNN!") model_folder_path = file_path[:k] + '/ca_model_weights/' if args.use_soluble_model: print("WARNING: CA-SolubleMPNN is not available yet") sys.exit() else: if args.use_soluble_model: print("Using ProteinMPNN trained on soluble proteins only!") model_folder_path = file_path[:k] + '/soluble_model_weights/' else: model_folder_path = file_path[:k] + '/vanilla_model_weights/' checkpoint_path = model_folder_path + f'{args.model_name}.pt' folder_for_outputs = args.out_folder NUM_BATCHES = args.num_seq_per_target//args.batch_size BATCH_COPIES = args.batch_size temperatures = [float(item) for item in args.sampling_temp.split()] omit_AAs_list = args.omit_AAs alphabet = 'ACDEFGHIKLMNPQRSTVWYX' alphabet_dict = dict(zip(alphabet, range(21))) print_all = args.suppress_print == 0 omit_AAs_np = np.array([AA in omit_AAs_list for AA in alphabet]).astype(np.float32) device = torch.device("cuda:0" if (torch.cuda.is_available()) else "cpu") if os.path.isfile(args.chain_id_jsonl): with open(args.chain_id_jsonl, 'r') as json_file: json_list = list(json_file) for json_str in json_list: chain_id_dict = json.loads(json_str) else: chain_id_dict = None if print_all: print(40*'-') print('chain_id_jsonl is NOT loaded') if os.path.isfile(args.fixed_positions_jsonl): with open(args.fixed_positions_jsonl, 'r') as json_file: json_list = list(json_file) for json_str in json_list: fixed_positions_dict = json.loads(json_str) else: if print_all: print(40*'-') print('fixed_positions_jsonl is NOT loaded') fixed_positions_dict = None if os.path.isfile(args.pssm_jsonl): with open(args.pssm_jsonl, 'r') as json_file: json_list = list(json_file) pssm_dict = {} for json_str in json_list: pssm_dict.update(json.loads(json_str)) else: if print_all: print(40*'-') print('pssm_jsonl is NOT loaded') pssm_dict = None if os.path.isfile(args.omit_AA_jsonl): with open(args.omit_AA_jsonl, 'r') as json_file: json_list = list(json_file) for json_str in json_list: omit_AA_dict = json.loads(json_str) else: if print_all: print(40*'-') print('omit_AA_jsonl is NOT loaded') omit_AA_dict = None if os.path.isfile(args.bias_AA_jsonl): with open(args.bias_AA_jsonl, 'r') as json_file: json_list = list(json_file) for json_str in json_list: bias_AA_dict = json.loads(json_str) else: if print_all: print(40*'-') print('bias_AA_jsonl is NOT loaded') bias_AA_dict = None if os.path.isfile(args.tied_positions_jsonl): with open(args.tied_positions_jsonl, 'r') as json_file: json_list = list(json_file) for json_str in json_list: tied_positions_dict = json.loads(json_str) else: if print_all: print(40*'-') print('tied_positions_jsonl is NOT loaded') tied_positions_dict = None if os.path.isfile(args.bias_by_res_jsonl): with open(args.bias_by_res_jsonl, 'r') as json_file: json_list = list(json_file) for json_str in json_list: bias_by_res_dict = json.loads(json_str) if print_all: print('bias by residue dictionary is loaded') else: if print_all: print(40*'-') print('bias by residue dictionary is not loaded, or not provided') bias_by_res_dict = None if print_all: print(40*'-') bias_AAs_np = np.zeros(len(alphabet)) if bias_AA_dict: for n, AA in enumerate(alphabet): if AA in list(bias_AA_dict.keys()): bias_AAs_np[n] = bias_AA_dict[AA] if args.pdb_path: pdb_dict_list = parse_PDB(args.pdb_path, ca_only=args.ca_only) dataset_valid = StructureDatasetPDB(pdb_dict_list, truncate=None, max_length=args.max_length) all_chain_list = [item[-1:] for item in list(pdb_dict_list[0]) if item[:9]=='seq_chain'] #['A','B', 'C',...] if args.pdb_path_chains: designed_chain_list = [str(item) for item in args.pdb_path_chains.split()] else: designed_chain_list = all_chain_list fixed_chain_list = [letter for letter in all_chain_list if letter not in designed_chain_list] chain_id_dict = {} chain_id_dict[pdb_dict_list[0]['name']]= (designed_chain_list, fixed_chain_list) else: dataset_valid = StructureDataset(args.jsonl_path, truncate=None, max_length=args.max_length, verbose=print_all) checkpoint = torch.load(checkpoint_path, map_location=device) noise_level_print = checkpoint['noise_level'] model = ProteinMPNN(ca_only=args.ca_only, num_letters=21, node_features=hidden_dim, edge_features=hidden_dim, hidden_dim=hidden_dim, num_encoder_layers=num_layers, num_decoder_layers=num_layers, augment_eps=args.backbone_noise, k_neighbors=checkpoint['num_edges']) model.to(device) model.load_state_dict(checkpoint['model_state_dict']) model.eval() if print_all: print(40*'-') print('Number of edges:', checkpoint['num_edges']) print(f'Training noise level: {noise_level_print}A') # Build paths for experiment base_folder = folder_for_outputs if base_folder[-1] != '/': base_folder = base_folder + '/' if not os.path.exists(base_folder): os.makedirs(base_folder) if not os.path.exists(base_folder + 'seqs'): os.makedirs(base_folder + 'seqs') if args.save_score: if not os.path.exists(base_folder + 'scores'): os.makedirs(base_folder + 'scores') if args.score_only: if not os.path.exists(base_folder + 'score_only'): os.makedirs(base_folder + 'score_only') if args.conditional_probs_only: if not os.path.exists(base_folder + 'conditional_probs_only'): os.makedirs(base_folder + 'conditional_probs_only') if args.unconditional_probs_only: if not os.path.exists(base_folder + 'unconditional_probs_only'): os.makedirs(base_folder + 'unconditional_probs_only') if args.save_probs: if not os.path.exists(base_folder + 'probs'): os.makedirs(base_folder + 'probs') # Timing start_time = time.time() total_residues = 0 protein_list = [] total_step = 0 # Validation epoch with torch.no_grad(): test_sum, test_weights = 0., 0. for ix, protein in enumerate(dataset_valid): score_list = [] global_score_list = [] all_probs_list = [] all_log_probs_list = [] S_sample_list = [] batch_clones = [copy.deepcopy(protein) for i in range(BATCH_COPIES)] X, S, mask, lengths, chain_M, chain_encoding_all, chain_list_list, visible_list_list, masked_list_list, masked_chain_length_list_list, chain_M_pos, omit_AA_mask, residue_idx, dihedral_mask, tied_pos_list_of_lists_list, pssm_coef, pssm_bias, pssm_log_odds_all, bias_by_res_all, tied_beta = tied_featurize(batch_clones, device, chain_id_dict, fixed_positions_dict, omit_AA_dict, tied_positions_dict, pssm_dict, bias_by_res_dict, ca_only=args.ca_only) pssm_log_odds_mask = (pssm_log_odds_all > args.pssm_threshold).float() #1.0 for true, 0.0 for false name_ = batch_clones[0]['name'] if args.score_only: loop_c = 0 if args.path_to_fasta: fasta_names, fasta_seqs = parse_fasta(args.path_to_fasta, omit=["/"]) loop_c = len(fasta_seqs) for fc in range(1+loop_c): if fc == 0: structure_sequence_score_file = base_folder + '/score_only/' + batch_clones[0]['name'] + f'_pdb' else: structure_sequence_score_file = base_folder + '/score_only/' + batch_clones[0]['name'] + f'_fasta_{fc}' native_score_list = [] global_native_score_list = [] if fc > 0: input_seq_length = len(fasta_seqs[fc-1]) S_input = torch.tensor([alphabet_dict[AA] for AA in fasta_seqs[fc-1]], device=device)[None,:].repeat(X.shape[0], 1) S[:,:input_seq_length] = S_input #assumes that S and S_input are alphabetically sorted for masked_chains for j in range(NUM_BATCHES): randn_1 = torch.randn(chain_M.shape, device=X.device) log_probs = model(X, S, mask, chain_M*chain_M_pos, residue_idx, chain_encoding_all, randn_1) mask_for_loss = mask*chain_M*chain_M_pos scores = _scores(S, log_probs, mask_for_loss) native_score = scores.cpu().data.numpy() native_score_list.append(native_score) global_scores = _scores(S, log_probs, mask) global_native_score = global_scores.cpu().data.numpy() global_native_score_list.append(global_native_score) native_score = np.concatenate(native_score_list, 0) global_native_score = np.concatenate(global_native_score_list, 0) ns_mean = native_score.mean() ns_mean_print = np.format_float_positional(np.float32(ns_mean), unique=False, precision=4) ns_std = native_score.std() ns_std_print = np.format_float_positional(np.float32(ns_std), unique=False, precision=4) global_ns_mean = global_native_score.mean() global_ns_mean_print = np.format_float_positional(np.float32(global_ns_mean), unique=False, precision=4) global_ns_std = global_native_score.std() global_ns_std_print = np.format_float_positional(np.float32(global_ns_std), unique=False, precision=4) ns_sample_size = native_score.shape[0] seq_str = _S_to_seq(S[0,], chain_M[0,]) np.savez(structure_sequence_score_file, score=native_score, global_score=global_native_score, S=S[0,].cpu().numpy(), seq_str=seq_str) if print_all: if fc == 0: print(f'Score for {name_} from PDB, mean: {ns_mean_print}, std: {ns_std_print}, sample size: {ns_sample_size}, global score, mean: {global_ns_mean_print}, std: {global_ns_std_print}, sample size: {ns_sample_size}') else: print(f'Score for {name_}_{fc} from FASTA, mean: {ns_mean_print}, std: {ns_std_print}, sample size: {ns_sample_size}, global score, mean: {global_ns_mean_print}, std: {global_ns_std_print}, sample size: {ns_sample_size}') elif args.conditional_probs_only: if print_all: print(f'Calculating conditional probabilities for {name_}') conditional_probs_only_file = base_folder + '/conditional_probs_only/' + batch_clones[0]['name'] log_conditional_probs_list = [] for j in range(NUM_BATCHES): randn_1 = torch.randn(chain_M.shape, device=X.device) log_conditional_probs = model.conditional_probs(X, S, mask, chain_M*chain_M_pos, residue_idx, chain_encoding_all, randn_1, args.conditional_probs_only_backbone) log_conditional_probs_list.append(log_conditional_probs.cpu().numpy()) concat_log_p = np.concatenate(log_conditional_probs_list, 0) #[B, L, 21] mask_out = (chain_M*chain_M_pos*mask)[0,].cpu().numpy() np.savez(conditional_probs_only_file, log_p=concat_log_p, S=S[0,].cpu().numpy(), mask=mask[0,].cpu().numpy(), design_mask=mask_out) elif args.unconditional_probs_only: if print_all: print(f'Calculating sequence unconditional probabilities for {name_}') unconditional_probs_only_file = base_folder + '/unconditional_probs_only/' + batch_clones[0]['name'] log_unconditional_probs_list = [] for j in range(NUM_BATCHES): log_unconditional_probs = model.unconditional_probs(X, mask, residue_idx, chain_encoding_all) log_unconditional_probs_list.append(log_unconditional_probs.cpu().numpy()) concat_log_p = np.concatenate(log_unconditional_probs_list, 0) #[B, L, 21] mask_out = (chain_M*chain_M_pos*mask)[0,].cpu().numpy() np.savez(unconditional_probs_only_file, log_p=concat_log_p, S=S[0,].cpu().numpy(), mask=mask[0,].cpu().numpy(), design_mask=mask_out) else: randn_1 = torch.randn(chain_M.shape, device=X.device) log_probs = model(X, S, mask, chain_M*chain_M_pos, residue_idx, chain_encoding_all, randn_1) mask_for_loss = mask*chain_M*chain_M_pos scores = _scores(S, log_probs, mask_for_loss) #score only the redesigned part native_score = scores.cpu().data.numpy() global_scores = _scores(S, log_probs, mask) #score the whole structure-sequence global_native_score = global_scores.cpu().data.numpy() # Generate some sequences ali_file = base_folder + '/seqs/' + batch_clones[0]['name'] + '.fa' score_file = base_folder + '/scores/' + batch_clones[0]['name'] + '.npz' probs_file = base_folder + '/probs/' + batch_clones[0]['name'] + '.npz' if print_all: print(f'Generating sequences for: {name_}') t0 = time.time() with open(ali_file, 'w') as f: for temp in temperatures: for j in range(NUM_BATCHES): randn_2 = torch.randn(chain_M.shape, device=X.device) if tied_positions_dict == None: sample_dict = model.sample(X, randn_2, S, chain_M, chain_encoding_all, residue_idx, mask=mask, temperature=temp, omit_AAs_np=omit_AAs_np, bias_AAs_np=bias_AAs_np, chain_M_pos=chain_M_pos, omit_AA_mask=omit_AA_mask, pssm_coef=pssm_coef, pssm_bias=pssm_bias, pssm_multi=args.pssm_multi, pssm_log_odds_flag=bool(args.pssm_log_odds_flag), pssm_log_odds_mask=pssm_log_odds_mask, pssm_bias_flag=bool(args.pssm_bias_flag), bias_by_res=bias_by_res_all) S_sample = sample_dict["S"] else: sample_dict = model.tied_sample(X, randn_2, S, chain_M, chain_encoding_all, residue_idx, mask=mask, temperature=temp, omit_AAs_np=omit_AAs_np, bias_AAs_np=bias_AAs_np, chain_M_pos=chain_M_pos, omit_AA_mask=omit_AA_mask, pssm_coef=pssm_coef, pssm_bias=pssm_bias, pssm_multi=args.pssm_multi, pssm_log_odds_flag=bool(args.pssm_log_odds_flag), pssm_log_odds_mask=pssm_log_odds_mask, pssm_bias_flag=bool(args.pssm_bias_flag), tied_pos=tied_pos_list_of_lists_list[0], tied_beta=tied_beta, bias_by_res=bias_by_res_all) # Compute scores S_sample = sample_dict["S"] log_probs = model(X, S_sample, mask, chain_M*chain_M_pos, residue_idx, chain_encoding_all, randn_2, use_input_decoding_order=True, decoding_order=sample_dict["decoding_order"]) mask_for_loss = mask*chain_M*chain_M_pos scores = _scores(S_sample, log_probs, mask_for_loss) scores = scores.cpu().data.numpy() global_scores = _scores(S_sample, log_probs, mask) #score the whole structure-sequence global_scores = global_scores.cpu().data.numpy() all_probs_list.append(sample_dict["probs"].cpu().data.numpy()) all_log_probs_list.append(log_probs.cpu().data.numpy()) S_sample_list.append(S_sample.cpu().data.numpy()) for b_ix in range(BATCH_COPIES): masked_chain_length_list = masked_chain_length_list_list[b_ix] masked_list = masked_list_list[b_ix] seq_recovery_rate = torch.sum(torch.sum(torch.nn.functional.one_hot(S[b_ix], 21)*torch.nn.functional.one_hot(S_sample[b_ix], 21),axis=-1)*mask_for_loss[b_ix])/torch.sum(mask_for_loss[b_ix]) seq = _S_to_seq(S_sample[b_ix], chain_M[b_ix]) score = scores[b_ix] score_list.append(score) global_score = global_scores[b_ix] global_score_list.append(global_score) native_seq = _S_to_seq(S[b_ix], chain_M[b_ix]) if b_ix == 0 and j==0 and temp==temperatures[0]: start = 0 end = 0 list_of_AAs = [] for mask_l in masked_chain_length_list: end += mask_l list_of_AAs.append(native_seq[start:end]) start = end native_seq = "".join(list(np.array(list_of_AAs)[np.argsort(masked_list)])) l0 = 0 for mc_length in list(np.array(masked_chain_length_list)[np.argsort(masked_list)])[:-1]: l0 += mc_length native_seq = native_seq[:l0] + '/' + native_seq[l0:] l0 += 1 sorted_masked_chain_letters = np.argsort(masked_list_list[0]) print_masked_chains = [masked_list_list[0][i] for i in sorted_masked_chain_letters] sorted_visible_chain_letters = np.argsort(visible_list_list[0]) print_visible_chains = [visible_list_list[0][i] for i in sorted_visible_chain_letters] native_score_print = np.format_float_positional(np.float32(native_score.mean()), unique=False, precision=4) global_native_score_print = np.format_float_positional(np.float32(global_native_score.mean()), unique=False, precision=4) script_dir = os.path.dirname(os.path.realpath(__file__)) try: commit_str = subprocess.check_output(f'git --git-dir {script_dir}/.git rev-parse HEAD', shell=True, stderr=subprocess.DEVNULL).decode().strip() except subprocess.CalledProcessError: commit_str = 'unknown' if args.ca_only: print_model_name = 'CA_model_name' else: print_model_name = 'model_name' f.write('>{}, score={}, global_score={}, fixed_chains={}, designed_chains={}, {}={}, git_hash={}, seed={}\n{}\n'.format(name_, native_score_print, global_native_score_print, print_visible_chains, print_masked_chains, print_model_name, args.model_name, commit_str, seed, native_seq)) #write the native sequence start = 0 end = 0 list_of_AAs = [] for mask_l in masked_chain_length_list: end += mask_l list_of_AAs.append(seq[start:end]) start = end seq = "".join(list(np.array(list_of_AAs)[np.argsort(masked_list)])) l0 = 0 for mc_length in list(np.array(masked_chain_length_list)[np.argsort(masked_list)])[:-1]: l0 += mc_length seq = seq[:l0] + '/' + seq[l0:] l0 += 1 score_print = np.format_float_positional(np.float32(score), unique=False, precision=4) global_score_print = np.format_float_positional(np.float32(global_score), unique=False, precision=4) seq_rec_print = np.format_float_positional(np.float32(seq_recovery_rate.detach().cpu().numpy()), unique=False, precision=4) sample_number = j*BATCH_COPIES+b_ix+1 f.write('>T={}, sample={}, score={}, global_score={}, seq_recovery={}\n{}\n'.format(temp,sample_number,score_print,global_score_print,seq_rec_print,seq)) #write generated sequence if args.save_score: np.savez(score_file, score=np.array(score_list, np.float32), global_score=np.array(global_score_list, np.float32)) if args.save_probs: all_probs_concat = np.concatenate(all_probs_list) all_log_probs_concat = np.concatenate(all_log_probs_list) S_sample_concat = np.concatenate(S_sample_list) np.savez(probs_file, probs=np.array(all_probs_concat, np.float32), log_probs=np.array(all_log_probs_concat, np.float32), S=np.array(S_sample_concat, np.int32), mask=mask_for_loss.cpu().data.numpy(), chain_order=chain_list_list) t1 = time.time() dt = round(float(t1-t0), 4) num_seqs = len(temperatures)*NUM_BATCHES*BATCH_COPIES total_length = X.shape[1] if print_all: print(f'{num_seqs} sequences of length {total_length} generated in {dt} seconds') if __name__ == "__main__": argparser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) argparser.add_argument("--suppress_print", type=int, default=0, help="0 for False, 1 for True") argparser.add_argument("--ca_only", action="store_true", default=False, help="Parse CA-only structures and use CA-only models (default: false)") argparser.add_argument("--path_to_model_weights", type=str, default="", help="Path to model weights folder;") argparser.add_argument("--model_name", type=str, default="v_48_020", help="ProteinMPNN model name: v_48_002, v_48_010, v_48_020, v_48_030; v_48_010=version with 48 edges 0.10A noise") argparser.add_argument("--use_soluble_model", action="store_true", default=False, help="Flag to load ProteinMPNN weights trained on soluble proteins only.") argparser.add_argument("--seed", type=int, default=0, help="If set to 0 then a random seed will be picked;") argparser.add_argument("--save_score", type=int, default=0, help="0 for False, 1 for True; save score=-log_prob to npy files") argparser.add_argument("--save_probs", type=int, default=0, help="0 for False, 1 for True; save MPNN predicted probabilites per position") argparser.add_argument("--score_only", type=int, default=0, help="0 for False, 1 for True; score input backbone-sequence pairs") argparser.add_argument("--path_to_fasta", type=str, default="", help="score provided input sequence in a fasta format; e.g. GGGGGG/PPPPS/WWW for chains A, B, C sorted alphabetically and separated by /") argparser.add_argument("--conditional_probs_only", type=int, default=0, help="0 for False, 1 for True; output conditional probabilities p(s_i given the rest of the sequence and backbone)") argparser.add_argument("--conditional_probs_only_backbone", type=int, default=0, help="0 for False, 1 for True; if true output conditional probabilities p(s_i given backbone)") argparser.add_argument("--unconditional_probs_only", type=int, default=0, help="0 for False, 1 for True; output unconditional probabilities p(s_i given backbone) in one forward pass") argparser.add_argument("--backbone_noise", type=float, default=0.00, help="Standard deviation of Gaussian noise to add to backbone atoms") argparser.add_argument("--num_seq_per_target", type=int, default=1, help="Number of sequences to generate per target") argparser.add_argument("--batch_size", type=int, default=1, help="Batch size; can set higher for titan, quadro GPUs, reduce this if running out of GPU memory") argparser.add_argument("--max_length", type=int, default=200000, help="Max sequence length") argparser.add_argument("--sampling_temp", type=str, default="0.1", help="A string of temperatures, 0.2 0.25 0.5. Sampling temperature for amino acids. Suggested values 0.1, 0.15, 0.2, 0.25, 0.3. Higher values will lead to more diversity.") argparser.add_argument("--out_folder", type=str, help="Path to a folder to output sequences, e.g. /home/out/") argparser.add_argument("--pdb_path", type=str, default='', help="Path to a single PDB to be designed") argparser.add_argument("--pdb_path_chains", type=str, default='', help="Define which chains need to be designed for a single PDB ") argparser.add_argument("--jsonl_path", type=str, help="Path to a folder with parsed pdb into jsonl") argparser.add_argument("--chain_id_jsonl",type=str, default='', help="Path to a dictionary specifying which chains need to be designed and which ones are fixed, if not specied all chains will be designed.") argparser.add_argument("--fixed_positions_jsonl", type=str, default='', help="Path to a dictionary with fixed positions") argparser.add_argument("--omit_AAs", type=list, default='X', help="Specify which amino acids should be omitted in the generated sequence, e.g. 'AC' would omit alanine and cystine.") argparser.add_argument("--bias_AA_jsonl", type=str, default='', help="Path to a dictionary which specifies AA composion bias if neededi, e.g. {A: -1.1, F: 0.7} would make A less likely and F more likely.") argparser.add_argument("--bias_by_res_jsonl", default='', help="Path to dictionary with per position bias.") argparser.add_argument("--omit_AA_jsonl", type=str, default='', help="Path to a dictionary which specifies which amino acids need to be omited from design at specific chain indices") argparser.add_argument("--pssm_jsonl", type=str, default='', help="Path to a dictionary with pssm") argparser.add_argument("--pssm_multi", type=float, default=0.0, help="A value between [0.0, 1.0], 0.0 means do not use pssm, 1.0 ignore MPNN predictions") argparser.add_argument("--pssm_threshold", type=float, default=0.0, help="A value between -inf + inf to restric per position AAs") argparser.add_argument("--pssm_log_odds_flag", type=int, default=0, help="0 for False, 1 for True") argparser.add_argument("--pssm_bias_flag", type=int, default=0, help="0 for False, 1 for True") argparser.add_argument("--tied_positions_jsonl", type=str, default='', help="Path to a dictionary with tied positions") args = argparser.parse_args() main(args)