import math import os import csv import random import torch from torch.utils import data import numpy as np from dateutil import parser import contigs from util import * from kinematics import * import pandas as pd import sys import torch.nn as nn from icecream import ic def write_pdb(filename, seq, atoms, Bfacts=None, prefix=None, chains=None): L = len(seq) ctr = 1 seq = seq.long() with open(filename, 'w+') as f: for i,s in enumerate(seq): if chains is None: chain='A' else: chain=chains[i] if (len(atoms.shape)==2): f.write ("%-6s%5s %4s %3s %s%4d %8.3f%8.3f%8.3f%6.2f%6.2f\n"%( "ATOM", ctr, " CA ", util.num2aa[s], chain, i+1, atoms[i,0], atoms[i,1], atoms[i,2], 1.0, Bfacts[i] ) ) ctr += 1 elif atoms.shape[1]==3: for j,atm_j in enumerate((" N "," CA "," C ")): f.write ("%-6s%5s %4s %3s %s%4d %8.3f%8.3f%8.3f%6.2f%6.2f\n"%( "ATOM", ctr, atm_j, num2aa[s], chain, i+1, atoms[i,j,0], atoms[i,j,1], atoms[i,j,2], 1.0, Bfacts[i] ) ) ctr += 1 else: atms = aa2long[s] for j,atm_j in enumerate(atms): if (atm_j is not None): f.write ("%-6s%5s %4s %3s %s%4d %8.3f%8.3f%8.3f%6.2f%6.2f\n"%( "ATOM", ctr, atm_j, num2aa[s], chain, i+1, atoms[i,j,0], atoms[i,j,1], atoms[i,j,2], 1.0, Bfacts[i] ) ) ctr += 1 def preprocess(xyz_t, t1d, DEVICE, masks_1d, ti_dev=None, ti_flip=None, ang_ref=None): B, _, L, _, _ = xyz_t.shape seq_tmp = t1d[...,:-1].argmax(dim=-1).reshape(-1,L).to(DEVICE, non_blocking=True) alpha, _, alpha_mask,_ = get_torsions(xyz_t.reshape(-1,L,27,3), seq_tmp, ti_dev, ti_flip, ang_ref) alpha_mask = torch.logical_and(alpha_mask, ~torch.isnan(alpha[...,0])) alpha[torch.isnan(alpha)] = 0.0 alpha = alpha.reshape(B,-1,L,10,2) alpha_mask = alpha_mask.reshape(B,-1,L,10,1) alpha_t = torch.cat((alpha, alpha_mask), dim=-1).reshape(B,-1,L,30) #t1d = torch.cat((t1d, chis.reshape(B,-1,L,30)), dim=-1) xyz_t = get_init_xyz(xyz_t) xyz_prev = xyz_t[:,0] state = t1d[:,0] alpha = alpha[:,0] t2d=xyz_to_t2d(xyz_t) return (t2d, alpha, alpha_mask, alpha_t, t1d, xyz_t, xyz_prev, state) def TemplFeaturizeFixbb(seq, conf_1d=None): """ Template 1D featurizer for fixed BB examples : Parameters: seq (torch.tensor, required): Integer sequence conf_1d (torch.tensor, optional): Precalcualted confidence tensor """ L = seq.shape[-1] t1d = torch.nn.functional.one_hot(seq, num_classes=21) # one hot sequence if conf_1d is None: conf = torch.ones_like(seq)[...,None] else: conf = conf_1d[:,None] t1d = torch.cat((t1d, conf), dim=-1) return t1d def MSAFeaturize_fixbb(msa, params): ''' Input: full msa information Output: Single sequence, with some percentage of amino acids mutated (but no resides 'masked') This is modified from autofold2, to remove mutations of the single sequence ''' N, L = msa.shape # raw MSA profile raw_profile = torch.nn.functional.one_hot(msa, num_classes=22) raw_profile = raw_profile.float().mean(dim=0) b_seq = list() b_msa_clust = list() b_msa_seed = list() b_msa_extra = list() b_mask_pos = list() for i_cycle in range(params['MAXCYCLE']): assert torch.max(msa) < 22 msa_onehot = torch.nn.functional.one_hot(msa[:1],num_classes=22) msa_fakeprofile_onehot = torch.nn.functional.one_hot(msa[:1],num_classes=26) #add the extra two indel planes, which will be set to zero msa_full_onehot = torch.cat((msa_onehot, msa_fakeprofile_onehot), dim=-1) #make fake msa_extra msa_extra_onehot = torch.nn.functional.one_hot(msa[:1],num_classes=25) #make fake msa_clust and mask_pos msa_clust = msa[:1] mask_pos = torch.full_like(msa_clust, 1).bool() b_seq.append(msa[0].clone()) b_msa_seed.append(msa_full_onehot[:1].clone()) #masked single sequence onehot (nb no mask so just single sequence onehot) b_msa_extra.append(msa_extra_onehot[:1].clone()) #masked single sequence onehot (nb no mask so just single sequence onehot) b_msa_clust.append(msa_clust[:1].clone()) #unmasked original single sequence b_mask_pos.append(mask_pos[:1].clone()) #mask positions in single sequence (all zeros) b_seq = torch.stack(b_seq) b_msa_clust = torch.stack(b_msa_clust) b_msa_seed = torch.stack(b_msa_seed) b_msa_extra = torch.stack(b_msa_extra) b_mask_pos = torch.stack(b_mask_pos) return b_seq, b_msa_clust, b_msa_seed, b_msa_extra, b_mask_pos def MSAFeaturize(msa, params): ''' Input: full msa information Output: Single sequence, with some percentage of amino acids mutated (but no resides 'masked') This is modified from autofold2, to remove mutations of the single sequence ''' N, L = msa.shape # raw MSA profile raw_profile = torch.nn.functional.one_hot(msa, num_classes=22) raw_profile = raw_profile.float().mean(dim=0) b_seq = list() b_msa_clust = list() b_msa_seed = list() b_msa_extra = list() b_mask_pos = list() for i_cycle in range(params['MAXCYCLE']): assert torch.max(msa) < 22 msa_onehot = torch.nn.functional.one_hot(msa,num_classes=22) msa_fakeprofile_onehot = torch.nn.functional.one_hot(msa,num_classes=26) #add the extra two indel planes, which will be set to zero msa_full_onehot = torch.cat((msa_onehot, msa_fakeprofile_onehot), dim=-1) #make fake msa_extra msa_extra_onehot = torch.nn.functional.one_hot(msa,num_classes=25) #make fake msa_clust and mask_pos msa_clust = msa mask_pos = torch.full_like(msa_clust, 1).bool() b_seq.append(msa[0].clone()) b_msa_seed.append(msa_full_onehot.clone()) #masked single sequence onehot (nb no mask so just single sequence onehot) b_msa_extra.append(msa_extra_onehot.clone()) #masked single sequence onehot (nb no mask so just single sequence onehot) b_msa_clust.append(msa_clust.clone()) #unmasked original single sequence b_mask_pos.append(mask_pos.clone()) #mask positions in single sequence (all zeros) b_seq = torch.stack(b_seq) b_msa_clust = torch.stack(b_msa_clust) b_msa_seed = torch.stack(b_msa_seed) b_msa_extra = torch.stack(b_msa_extra) b_mask_pos = torch.stack(b_mask_pos) return b_seq, b_msa_clust, b_msa_seed, b_msa_extra, b_mask_pos def mask_inputs(seq, msa_masked, msa_full, xyz_t, t1d, input_seq_mask=None, input_str_mask=None, input_t1dconf_mask=None, loss_seq_mask=None, loss_str_mask=None): """ Parameters: seq (torch.tensor, required): (B,I,L) integer sequence msa_masked (torch.tensor, required): (B,I,N_short,L,46) msa_full (torch,.tensor, required): (B,I,N_long,L,23) xyz_t (torch,tensor): (B,T,L,14,3) template crds BEFORE they go into get_init_xyz t1d (torch.tensor, required): (B,I,L,22) this is the t1d before tacking on the chi angles str_mask_1D (torch.tensor, required): Shape (L) rank 1 tensor where structure is masked at False positions seq_mask_1D (torch.tensor, required): Shape (L) rank 1 tensor where seq is masked at False positions """ ########### B,_,_ = seq.shape assert B == 1, 'batch sizes > 1 not supported' seq_mask = input_seq_mask[0] seq[:,:,~seq_mask] = 21 # mask token categorical value ### msa_masked ### ################## msa_masked[:,:,:,~seq_mask,:20] = 0 msa_masked[:,:,:,~seq_mask,20] = 0 msa_masked[:,:,:,~seq_mask,21] = 1 # set to the unkown char # index 44/45 is insertion/deletion # index 43 is the unknown token # index 42 is the masked token msa_masked[:,:,:,~seq_mask,22:42] = 0 msa_masked[:,:,:,~seq_mask,43] = 1 msa_masked[:,:,:,~seq_mask,42] = 0 # insertion/deletion stuff msa_masked[:,:,:,~seq_mask,44:] = 0 ### msa_full ### ################ msa_full[:,:,:,~seq_mask,:20] = 0 msa_full[:,:,:,~seq_mask,21] = 1 msa_full[:,:,:,~seq_mask,20] = 0 msa_full[:,:,:,~seq_mask,-1] = 0 #NOTE: double check this is insertions/deletions and 0 makes sense ### t1d ### ########### # NOTE: Not adjusting t1d last dim (confidence) from sequence mask t1d[:,:,~seq_mask,:20] = 0 t1d[:,:,~seq_mask,20] = 1 # unknown t1d[:,:,:,21] *= input_t1dconf_mask #JG added in here to make sure everything fits print('expanding t1d to 24 dims') t1d = torch.cat((t1d, torch.zeros((t1d.shape[0],t1d.shape[1],t1d.shape[2],2)).float()), -1).to(seq.device) xyz_t[:,:,~seq_mask,3:,:] = float('nan') # Structure masking str_mask = input_str_mask[0] xyz_t[:,:,~str_mask,:,:] = float('nan') return seq, msa_masked, msa_full, xyz_t, t1d ########################################################### #Functions for randomly translating/rotation input residues ########################################################### def get_translated_coords(args): ''' Parses args.res_translate ''' #get positions to translate res_translate = [] for res in args.res_translate.split(":"): temp_str = [] for i in res.split(','): temp_str.append(i) if temp_str[-1][0].isalpha() is True: temp_str.append(2.0) #set default distance for i in temp_str[:-1]: if '-' in i: start = int(i.split('-')[0][1:]) while start <= int(i.split('-')[1]): res_translate.append((i.split('-')[0][0] + str(start),float(temp_str[-1]))) start += 1 else: res_translate.append((i, float(temp_str[-1]))) start = 0 output = [] for i in res_translate: temp = (i[0], i[1], start) output.append(temp) start += 1 return output def get_tied_translated_coords(args, untied_translate=None): ''' Parses args.tie_translate ''' #pdb_idx = list(parsed_pdb['idx']) #xyz = parsed_pdb['xyz'] #get positions to translate res_translate = [] block = 0 for res in args.tie_translate.split(":"): temp_str = [] for i in res.split(','): temp_str.append(i) if temp_str[-1][0].isalpha() is True: temp_str.append(2.0) #set default distance for i in temp_str[:-1]: if '-' in i: start = int(i.split('-')[0][1:]) while start <= int(i.split('-')[1]): res_translate.append((i.split('-')[0][0] + str(start),float(temp_str[-1]), block)) start += 1 else: res_translate.append((i, float(temp_str[-1]), block)) block += 1 #sanity check if untied_translate != None: checker = [i[0] for i in res_translate] untied_check = [i[0] for i in untied_translate] for i in checker: if i in untied_check: print(f'WARNING: residue {i} is specified both in --res_translate and --tie_translate. Residue {i} will be ignored in --res_translate, and instead only moved in a tied block (--tie_translate)') final_output = res_translate for i in untied_translate: if i[0] not in checker: final_output.append((i[0],i[1],i[2] + block + 1)) else: final_output = res_translate return final_output def translate_coords(parsed_pdb, res_translate): ''' Takes parsed list in format [(chain_residue,distance,tieing_block)] and randomly translates residues accordingly. ''' pdb_idx = parsed_pdb['pdb_idx'] xyz = np.copy(parsed_pdb['xyz']) translated_coord_dict = {} #get number of blocks temp = [int(i[2]) for i in res_translate] blocks = np.max(temp) for block in range(blocks + 1): init_dist = 1.01 while init_dist > 1: #gives equal probability to any direction (as keeps going until init_dist is within unit circle) x = random.uniform(-1,1) y = random.uniform(-1,1) z = random.uniform(-1,1) init_dist = np.sqrt(x**2 + y**2 + z**2) x=x/init_dist y=y/init_dist z=z/init_dist translate_dist = random.uniform(0,1) #now choose distance (as proportion of maximum) that coordinates will be translated for res in res_translate: if res[2] == block: res_idx = pdb_idx.index((res[0][0],int(res[0][1:]))) original_coords = np.copy(xyz[res_idx,:,:]) for i in range(14): if parsed_pdb['mask'][res_idx, i]: xyz[res_idx,i,0] += np.float32(x * translate_dist * float(res[1])) xyz[res_idx,i,1] += np.float32(y * translate_dist * float(res[1])) xyz[res_idx,i,2] += np.float32(z * translate_dist * float(res[1])) translated_coords = xyz[res_idx,:,:] translated_coord_dict[res[0]] = (original_coords.tolist(), translated_coords.tolist()) return xyz[:,:,:], translated_coord_dict def parse_block_rotate(args): block_translate = [] block = 0 for res in args.block_rotate.split(":"): temp_str = [] for i in res.split(','): temp_str.append(i) if temp_str[-1][0].isalpha() is True: temp_str.append(10) #set default angle to 10 degrees for i in temp_str[:-1]: if '-' in i: start = int(i.split('-')[0][1:]) while start <= int(i.split('-')[1]): block_translate.append((i.split('-')[0][0] + str(start),float(temp_str[-1]), block)) start += 1 else: block_translate.append((i, float(temp_str[-1]), block)) block += 1 return block_translate def rotate_block(xyz, block_rotate,pdb_index): rotated_coord_dict = {} #get number of blocks temp = [int(i[2]) for i in block_rotate] blocks = np.max(temp) for block in range(blocks + 1): idxs = [pdb_index.index((i[0][0],int(i[0][1:]))) for i in block_rotate if i[2] == block] angle = [i[1] for i in block_rotate if i[2] == block][0] block_xyz = xyz[idxs,:,:] com = [float(torch.mean(block_xyz[:,:,i])) for i in range(3)] origin_xyz = np.copy(block_xyz) for i in range(np.shape(origin_xyz)[0]): for j in range(14): origin_xyz[i,j] = origin_xyz[i,j] - com rotated_xyz = rigid_rotate(origin_xyz,angle,angle,angle) recovered_xyz = np.copy(rotated_xyz) for i in range(np.shape(origin_xyz)[0]): for j in range(14): recovered_xyz[i,j] = rotated_xyz[i,j] + com recovered_xyz=torch.tensor(recovered_xyz) rotated_coord_dict[f'rotated_block_{block}_original'] = block_xyz rotated_coord_dict[f'rotated_block_{block}_rotated'] = recovered_xyz xyz_out = torch.clone(xyz) for i in range(len(idxs)): xyz_out[idxs[i]] = recovered_xyz[i] return xyz_out,rotated_coord_dict def rigid_rotate(xyz,a=180,b=180,c=180): #TODO fix this to make it truly uniform a=(a/180)*math.pi b=(b/180)*math.pi c=(c/180)*math.pi alpha = random.uniform(-a, a) beta = random.uniform(-b, b) gamma = random.uniform(-c, c) rotated = [] for i in range(np.shape(xyz)[0]): for j in range(14): try: x = xyz[i,j,0] y = xyz[i,j,1] z = xyz[i,j,2] x2 = x*math.cos(alpha) - y*math.sin(alpha) y2 = x*math.sin(alpha) + y*math.cos(alpha) x3 = x2*math.cos(beta) - z*math.sin(beta) z2 = x2*math.sin(beta) + z*math.cos(beta) y3 = y2*math.cos(gamma) - z2*math.sin(gamma) z3 = y2*math.sin(gamma) + z2*math.cos(gamma) rotated.append([x3,y3,z3]) except: rotated.append([float('nan'),float('nan'),float('nan')]) rotated=np.array(rotated) rotated=np.reshape(rotated, [np.shape(xyz)[0],14,3]) return rotated ######## from old pred_util.py def find_contigs(mask): """ Find contiguous regions in a mask that are True with no False in between Parameters: mask (torch.tensor or np.array, required): 1D boolean array Returns: contigs (list): List of tuples, each tuple containing the beginning and the """ assert len(mask.shape) == 1 # 1D tensor of bools contigs = [] found_contig = False for i,b in enumerate(mask): if b and not found_contig: # found the beginning of a contig contig = [i] found_contig = True elif b and found_contig: # currently have contig, continuing it pass elif not b and found_contig: # found the end, record previous index as end, reset indicator contig.append(i) found_contig = False contigs.append(tuple(contig)) else: # currently don't have a contig, and didn't find one pass # fence post bug - check if the very last entry was True and we didn't get to finish if b: contig.append(i+1) found_contig = False contigs.append(tuple(contig)) return contigs def reindex_chains(pdb_idx): """ Given a list of (chain, index) tuples, and the indices where chains break, create a reordered indexing Parameters: pdb_idx (list, required): List of tuples (chainID, index) breaks (list, required): List of indices where chains begin """ new_breaks, new_idx = [],[] current_chain = None chain_and_idx_to_torch = {} for i,T in enumerate(pdb_idx): chain, idx = T if chain != current_chain: new_breaks.append(i) current_chain = chain # create new space for chain id listings chain_and_idx_to_torch[chain] = {} # map original pdb (chain, idx) pair to index in tensor chain_and_idx_to_torch[chain][idx] = i # append tensor index to list new_idx.append(i) new_idx = np.array(new_idx) # now we have ordered list and know where the chainbreaks are in the new order num_additions = 0 for i in new_breaks[1:]: # skip the first trivial one new_idx[np.where(new_idx==(i+ num_additions*500))[0][0]:] += 500 num_additions += 1 return new_idx, chain_and_idx_to_torch,new_breaks[1:] class ObjectView(object): ''' Easy wrapper to access dictionary values with "dot" notiation instead ''' def __init__(self, d): self.__dict__ = d def split_templates(xyz_t, t1d, multi_templates,mappings,multi_tmpl_conf=None): templates = multi_templates.split(":") if multi_tmpl_conf is not None: multi_tmpl_conf = [float(i) for i in multi_tmpl_conf.split(",")] assert len(templates) == len(multi_tmpl_conf), "Number of templates must equal number of confidences specified in --multi_tmpl_conf flag" for idx, template in enumerate(templates): parts = template.split(",") template_mask = torch.zeros(xyz_t.shape[2]).bool() for part in parts: start = int(part.split("-")[0][1:]) end = int(part.split("-")[1]) + 1 chain = part[0] for i in range(start, end): try: ref_pos = mappings['complex_con_ref_pdb_idx'].index((chain, i)) hal_pos_0 = mappings['complex_con_hal_idx0'][ref_pos] except: ref_pos = mappings['con_ref_pdb_idx'].index((chain, i)) hal_pos_0 = mappings['con_hal_idx0'][ref_pos] template_mask[hal_pos_0] = True xyz_t_temp = torch.clone(xyz_t) xyz_t_temp[:,:,~template_mask,:,:] = float('nan') t1d_temp = torch.clone(t1d) t1d_temp[:,:,~template_mask,:20] =0 t1d_temp[:,:,~template_mask,20] = 1 if multi_tmpl_conf is not None: t1d_temp[:,:,template_mask,21] = multi_tmpl_conf[idx] if idx != 0: xyz_t_out = torch.cat((xyz_t_out, xyz_t_temp),dim=1) t1d_out = torch.cat((t1d_out, t1d_temp),dim=1) else: xyz_t_out = xyz_t_temp t1d_out = t1d_temp return xyz_t_out, t1d_out class ContigMap(): ''' New class for doing mapping. Supports multichain or multiple crops from a single receptor chain. Also supports indexing jump (+200) or not, based on contig input. Default chain outputs are inpainted chains as A (and B, C etc if multiple chains), and all fragments of receptor chain on the next one (generally B) Output chains can be specified. Sequence must be the same number of elements as in contig string ''' def __init__(self, parsed_pdb, contigs=None, inpaint_seq=None, inpaint_str=None, length=None, ref_idx=None, hal_idx=None, idx_rf=None, inpaint_seq_tensor=None, inpaint_str_tensor=None, topo=False): #sanity checks if contigs is None and ref_idx is None: sys.exit("Must either specify a contig string or precise mapping") if idx_rf is not None or hal_idx is not None or ref_idx is not None: if idx_rf is None or hal_idx is None or ref_idx is None: sys.exit("If you're specifying specific contig mappings, the reference and output positions must be specified, AND the indexing for RoseTTAFold (idx_rf)") self.chain_order='ABCDEFGHIJKLMNOPQRSTUVWXYZ' if length is not None: if '-' not in length: self.length = [int(length),int(length)+1] else: self.length = [int(length.split("-")[0]),int(length.split("-")[1])+1] else: self.length = None self.ref_idx = ref_idx self.hal_idx=hal_idx self.idx_rf=idx_rf self.inpaint_seq = ','.join(inpaint_seq).split(",") if inpaint_seq is not None else None self.inpaint_str = ','.join(inpaint_str).split(",") if inpaint_str is not None else None self.inpaint_seq_tensor=inpaint_seq_tensor self.inpaint_str_tensor=inpaint_str_tensor self.parsed_pdb = parsed_pdb self.topo=topo if ref_idx is None: #using default contig generation, which outputs in rosetta-like format self.contigs=contigs self.sampled_mask,self.contig_length,self.n_inpaint_chains = self.get_sampled_mask() self.receptor_chain = self.chain_order[self.n_inpaint_chains] self.receptor, self.receptor_hal, self.receptor_rf, self.inpaint, self.inpaint_hal, self.inpaint_rf= self.expand_sampled_mask() self.ref = self.inpaint + self.receptor self.hal = self.inpaint_hal + self.receptor_hal self.rf = self.inpaint_rf + self.receptor_rf else: #specifying precise mappings self.ref=ref_idx self.hal=hal_idx self.rf = rf_idx self.mask_1d = [False if i == ('_','_') else True for i in self.ref] #take care of sequence and structure masking if self.inpaint_seq_tensor is None: if self.inpaint_seq is not None: self.inpaint_seq = self.get_inpaint_seq_str(self.inpaint_seq) else: self.inpaint_seq = np.array([True if i != ('_','_') else False for i in self.ref]) else: self.inpaint_seq = self.inpaint_seq_tensor if self.inpaint_str_tensor is None: if self.inpaint_str is not None: self.inpaint_str = self.get_inpaint_seq_str(self.inpaint_str) else: self.inpaint_str = np.array([True if i != ('_','_') else False for i in self.ref]) else: self.inpaint_str = self.inpaint_str_tensor #get 0-indexed input/output (for trb file) self.ref_idx0,self.hal_idx0, self.ref_idx0_inpaint, self.hal_idx0_inpaint, self.ref_idx0_receptor, self.hal_idx0_receptor=self.get_idx0() def get_sampled_mask(self): ''' Function to get a sampled mask from a contig. ''' length_compatible=False count = 0 while length_compatible is False: inpaint_chains=0 contig_list = self.contigs sampled_mask = [] sampled_mask_length = 0 #allow receptor chain to be last in contig string if all([i[0].isalpha() for i in contig_list[-1].split(",")]): contig_list[-1] = f'{contig_list[-1]},0' for con in contig_list: if ((all([i[0].isalpha() for i in con.split(",")[:-1]]) and con.split(",")[-1] == '0')) or self.topo is True: #receptor chain sampled_mask.append(con) else: inpaint_chains += 1 #chain to be inpainted. These are the only chains that count towards the length of the contig subcons = con.split(",") subcon_out = [] for subcon in subcons: if subcon[0].isalpha(): subcon_out.append(subcon) if '-' in subcon: sampled_mask_length += (int(subcon.split("-")[1])-int(subcon.split("-")[0][1:])+1) else: sampled_mask_length += 1 else: if '-' in subcon: length_inpaint=random.randint(int(subcon.split("-")[0]),int(subcon.split("-")[1])) subcon_out.append(f'{length_inpaint}-{length_inpaint}') sampled_mask_length += length_inpaint elif subcon == '0': subcon_out.append('0') else: length_inpaint=int(subcon) subcon_out.append(f'{length_inpaint}-{length_inpaint}') sampled_mask_length += int(subcon) sampled_mask.append(','.join(subcon_out)) #check length is compatible if self.length is not None: if sampled_mask_length >= self.length[0] and sampled_mask_length < self.length[1]: length_compatible = True else: length_compatible = True count+=1 if count == 100000: #contig string incompatible with this length sys.exit("Contig string incompatible with --length range") return sampled_mask, sampled_mask_length, inpaint_chains def expand_sampled_mask(self): chain_order='ABCDEFGHIJKLMNOPQRSTUVWXYZ' receptor = [] inpaint = [] receptor_hal = [] inpaint_hal = [] receptor_idx = 1 inpaint_idx = 1 inpaint_chain_idx=-1 receptor_chain_break=[] inpaint_chain_break = [] for con in self.sampled_mask: if (all([i[0].isalpha() for i in con.split(",")[:-1]]) and con.split(",")[-1] == '0') or self.topo is True: #receptor chain subcons = con.split(",")[:-1] assert all([i[0] == subcons[0][0] for i in subcons]), "If specifying fragmented receptor in a single block of the contig string, they MUST derive from the same chain" assert all(int(subcons[i].split("-")[0][1:]) < int(subcons[i+1].split("-")[0][1:]) for i in range(len(subcons)-1)), "If specifying multiple fragments from the same chain, pdb indices must be in ascending order!" for idx, subcon in enumerate(subcons): ref_to_add = [(subcon[0], i) for i in np.arange(int(subcon.split("-")[0][1:]),int(subcon.split("-")[1])+1)] receptor.extend(ref_to_add) receptor_hal.extend([(self.receptor_chain,i) for i in np.arange(receptor_idx, receptor_idx+len(ref_to_add))]) receptor_idx += len(ref_to_add) if idx != len(subcons)-1: idx_jump = int(subcons[idx+1].split("-")[0][1:]) - int(subcon.split("-")[1]) -1 receptor_chain_break.append((receptor_idx-1,idx_jump)) #actual chain break in pdb chain else: receptor_chain_break.append((receptor_idx-1,200)) #200 aa chain break else: inpaint_chain_idx += 1 for subcon in con.split(","): if subcon[0].isalpha(): ref_to_add=[(subcon[0], i) for i in np.arange(int(subcon.split("-")[0][1:]),int(subcon.split("-")[1])+1)] inpaint.extend(ref_to_add) inpaint_hal.extend([(chain_order[inpaint_chain_idx], i) for i in np.arange(inpaint_idx,inpaint_idx+len(ref_to_add))]) inpaint_idx += len(ref_to_add) else: inpaint.extend([('_','_')] * int(subcon.split("-")[0])) inpaint_hal.extend([(chain_order[inpaint_chain_idx], i) for i in np.arange(inpaint_idx,inpaint_idx+int(subcon.split("-")[0]))]) inpaint_idx += int(subcon.split("-")[0]) inpaint_chain_break.append((inpaint_idx-1,200)) if self.topo is True or inpaint_hal == []: receptor_hal = [(i[0], i[1]) for i in receptor_hal] else: receptor_hal = [(i[0], i[1] + inpaint_hal[-1][1]) for i in receptor_hal] #rosetta-like numbering #get rf indexes, with chain breaks inpaint_rf = np.arange(0,len(inpaint)) receptor_rf = np.arange(len(inpaint)+200,len(inpaint)+len(receptor)+200) for ch_break in inpaint_chain_break[:-1]: receptor_rf[:] += 200 inpaint_rf[ch_break[0]:] += ch_break[1] for ch_break in receptor_chain_break[:-1]: receptor_rf[ch_break[0]:] += ch_break[1] return receptor, receptor_hal, receptor_rf.tolist(), inpaint, inpaint_hal, inpaint_rf.tolist() def get_inpaint_seq_str(self, inpaint_s): ''' function to generate inpaint_str or inpaint_seq masks specific to this contig ''' s_mask = np.copy(self.mask_1d) inpaint_s_list = [] for i in inpaint_s: if '-' in i: inpaint_s_list.extend([(i[0],p) for p in range(int(i.split("-")[0][1:]), int(i.split("-")[1])+1)]) else: inpaint_s_list.append((i[0],int(i[1:]))) for res in inpaint_s_list: if res in self.ref: s_mask[self.ref.index(res)] = False #mask this residue return np.array(s_mask) def get_idx0(self): ref_idx0=[] hal_idx0=[] ref_idx0_inpaint=[] hal_idx0_inpaint=[] ref_idx0_receptor=[] hal_idx0_receptor=[] for idx, val in enumerate(self.ref): if val != ('_','_'): assert val in self.parsed_pdb['pdb_idx'],f"{val} is not in pdb file!" hal_idx0.append(idx) ref_idx0.append(self.parsed_pdb['pdb_idx'].index(val)) for idx, val in enumerate(self.inpaint): if val != ('_','_'): hal_idx0_inpaint.append(idx) ref_idx0_inpaint.append(self.parsed_pdb['pdb_idx'].index(val)) for idx, val in enumerate(self.receptor): if val != ('_','_'): hal_idx0_receptor.append(idx) ref_idx0_receptor.append(self.parsed_pdb['pdb_idx'].index(val)) return ref_idx0, hal_idx0, ref_idx0_inpaint, hal_idx0_inpaint, ref_idx0_receptor, hal_idx0_receptor def get_mappings(rm): mappings = {} mappings['con_ref_pdb_idx'] = [i for i in rm.inpaint if i != ('_','_')] mappings['con_hal_pdb_idx'] = [rm.inpaint_hal[i] for i in range(len(rm.inpaint_hal)) if rm.inpaint[i] != ("_","_")] mappings['con_ref_idx0'] = rm.ref_idx0_inpaint mappings['con_hal_idx0'] = rm.hal_idx0_inpaint if rm.inpaint != rm.ref: mappings['complex_con_ref_pdb_idx'] = [i for i in rm.ref if i != ("_","_")] mappings['complex_con_hal_pdb_idx'] = [rm.hal[i] for i in range(len(rm.hal)) if rm.ref[i] != ("_","_")] mappings['receptor_con_ref_pdb_idx'] = [i for i in rm.receptor if i != ("_","_")] mappings['receptor_con_hal_pdb_idx'] = [rm.receptor_hal[i] for i in range(len(rm.receptor_hal)) if rm.receptor[i] != ("_","_")] mappings['complex_con_ref_idx0'] = rm.ref_idx0 mappings['complex_con_hal_idx0'] = rm.hal_idx0 mappings['receptor_con_ref_idx0'] = rm.ref_idx0_receptor mappings['receptor_con_hal_idx0'] = rm.hal_idx0_receptor mappings['inpaint_str'] = rm.inpaint_str mappings['inpaint_seq'] = rm.inpaint_seq mappings['sampled_mask'] = rm.sampled_mask mappings['mask_1d'] = rm.mask_1d return mappings def lddt_unbin(pred_lddt): nbin = pred_lddt.shape[1] bin_step = 1.0 / nbin lddt_bins = torch.linspace(bin_step, 1.0, nbin, dtype=pred_lddt.dtype, device=pred_lddt.device) pred_lddt = nn.Softmax(dim=1)(pred_lddt) return torch.sum(lddt_bins[None,:,None]*pred_lddt, dim=1)