File size: 14,536 Bytes
1fdc49a | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 | import time
import sys
import io
from typing import Union, List
import requests
import warnings
from os.path import splitext, basename
from Bio import PDB
from Bio.PDB import PDBParser, PDBIO
from Bio.SeqUtils import seq1
from Bio import SeqIO
from bisect import bisect_left, bisect_right
import torch
import numpy as np
from igfold.utils.coordinates import place_fourth_atom
from igfold.utils.fasta import get_fasta_chain_seq
from igfold.utils.general import _aa_1_3_dict, exists
def renumber_pdb(old_pdb, renum_pdb=None):
if not exists(renum_pdb):
renum_pdb = old_pdb
success = False
time.sleep(5)
for i in range(10):
try:
with open(old_pdb, 'rb') as f:
response = requests.post(
'http://www.bioinf.org.uk/abs/abnum/abnumpdb.cgi',
params={
"plain": "1",
"output": "-HL",
"scheme": "-c"
},
files={"pdb": f},
)
success = response.status_code == 200 and not ("<html>"
in response.text)
if success:
break
else:
time.sleep((i + 1) * 5)
except requests.exceptions.ConnectionError:
time.sleep(60)
# if success:
if success:
new_pdb_data = response.text
with open(renum_pdb, "w") as f:
f.write(new_pdb_data)
else:
print(
"Failed to renumber PDB. This is likely due to a connection error or a timeout with the AbNum server."
)
def count_pdb_chains(pdb_file):
parser = PDBParser()
with warnings.catch_warnings(record=True):
structure = parser.get_structure("_", pdb_file)
l = len(list(structure.get_chains()))
return l
def reorder_pdb_chains(pdb_file, chain_order):
"""Reorder the chains in a PDB file and update residue numbers"""
parser = PDBParser()
with warnings.catch_warnings(record=True):
structure = parser.get_structure("_", pdb_file)
chains = list(structure.get_chains())
if len(chains) != len(chain_order):
raise ValueError(
f"Number of chains in PDB file ({len(chains)}) does not match number of chains in chain order ({len(chain_order)})"
)
chain_order = [c.upper() for c in chain_order]
sorted_chains = sorted(chains, key=lambda c: chain_order.index(c.id))
new_structure = PDB.Structure.Structure("_")
new_model = PDB.Model.Model(0)
new_structure.add(new_model)
atom_num = 1
for chain in sorted_chains:
new_chain = PDB.Chain.Chain(chain.id)
new_model.add(new_chain)
for residue in chain.get_residues():
new_residue = PDB.Residue.Residue(
residue.id,
residue.resname,
residue.segid,
)
new_chain.add(new_residue)
for atom in residue:
new_atom = PDB.Atom.Atom(
atom.name,
atom.coord,
atom.occupancy,
atom.bfactor,
atom.altloc,
atom.fullname,
atom_num,
atom.element,
)
new_residue.add(new_atom)
atom_num += 1
io = PDBIO()
io.set_structure(new_structure)
io.save(pdb_file)
def get_atom_coord(residue, atom_type):
if exists(residue) and atom_type in residue:
return residue[atom_type].get_coord()
else:
return [0, 0, 0]
def get_cb_or_ca_coord(residue):
if not exists(residue):
return [0, 0, 0]
if 'CB' in residue:
return residue['CB'].get_coord()
elif 'CA' in residue:
return residue['CA'].get_coord()
else:
return [0, 0, 0]
def get_continuous_ranges(residues):
""" Returns ranges of residues which are continuously connected (peptide bond length 1.2-1.45 Å) """
dists = []
for res_i in range(len(residues) - 1):
dists.append(
np.linalg.norm(
np.array(get_atom_coord(residues[res_i], "C")) -
np.array(get_atom_coord(residues[res_i + 1], "N"))))
ranges = []
start_i = 0
for d_i, d in enumerate(dists):
if d > 1.45 or d < 1.2:
ranges.append((start_i, d_i + 1))
start_i = d_i + 1
if d_i == len(dists) - 1:
ranges.append((start_i, None))
return ranges
def place_missing_cb_o(atom_coords):
cb_coords = place_fourth_atom(
atom_coords['C'],
atom_coords['N'],
atom_coords['CA'],
torch.tensor(1.522),
torch.tensor(1.927),
torch.tensor(-2.143),
)
o_coords = place_fourth_atom(
torch.roll(atom_coords['N'], shifts=-1, dims=0),
atom_coords['CA'],
atom_coords['C'],
torch.tensor(1.231),
torch.tensor(2.108),
torch.tensor(-3.142),
)
bb_mask = get_atom_coords_mask(atom_coords['N']) & get_atom_coords_mask(
atom_coords['CA']) & get_atom_coords_mask(atom_coords['C'])
missing_cb = (get_atom_coords_mask(atom_coords['CB']) & bb_mask) == 0
atom_coords['CB'][missing_cb] = cb_coords[missing_cb]
bb_mask = get_atom_coords_mask(
torch.roll(
atom_coords['N'],
shifts=-1,
dims=0,
)) & get_atom_coords_mask(atom_coords['CA']) & get_atom_coords_mask(
atom_coords['C'])
missing_o = (get_atom_coords_mask(atom_coords['O']) & bb_mask) == 0
atom_coords['O'][missing_o] = o_coords[missing_o]
def get_atom_coords(pdb_file, fasta_file=None):
p = PDBParser()
file_name = splitext(basename(pdb_file))[0]
structure = p.get_structure(
file_name,
pdb_file,
)
if fasta_file:
residues = []
for chain in structure.get_chains():
pdb_seq = get_pdb_chain_seq(
pdb_file,
chain.id,
)
chain_dict = {"A": "H", "B": "L", "H": "H", "L": "L"}
fasta_seq = get_fasta_chain_seq(
fasta_file,
chain_dict[chain.id],
)
chain_residues = list(chain.get_residues())
continuous_ranges = get_continuous_ranges(chain_residues)
fasta_residues = [None for _ in range(len(fasta_seq))]
fasta_r = (0, 0)
for pdb_r in continuous_ranges:
fasta_r_start = fasta_seq[fasta_r[1]:].index(
pdb_seq[pdb_r[0]:pdb_r[1]]) + fasta_r[1]
fasta_r_end = (len(pdb_seq) if pdb_r[1] == None else
pdb_r[1]) - pdb_r[0] + fasta_r_start
fasta_r = (fasta_r_start, fasta_r_end)
fasta_residues[fasta_r[0]:fasta_r[1]] = chain_residues[
pdb_r[0]:pdb_r[1]]
residues += fasta_residues
else:
residues = list(structure.get_residues())
n_coords = torch.tensor([get_atom_coord(r, 'N') for r in residues])
ca_coords = torch.tensor([get_atom_coord(r, 'CA') for r in residues])
c_coords = torch.tensor([get_atom_coord(r, 'C') for r in residues])
cb_coords = torch.tensor([get_atom_coord(r, 'CB') for r in residues])
cb_ca_coords = torch.tensor([get_cb_or_ca_coord(r) for r in residues])
o_coords = torch.tensor([get_atom_coord(r, 'O') for r in residues])
atom_coords = {}
atom_coords['N'] = n_coords
atom_coords['CA'] = ca_coords
atom_coords['C'] = c_coords
atom_coords['CB'] = cb_coords
atom_coords['CBCA'] = cb_ca_coords
atom_coords['O'] = o_coords
place_missing_cb_o(atom_coords)
return atom_coords
def get_atom_coords_mask(coords):
mask = torch.ByteTensor([1 if sum(_) != 0 else 0 for _ in coords])
mask = mask & (1 - torch.any(torch.isnan(coords), dim=1).byte())
return mask
def get_atom_coords_mask_for_dict(atom_coords):
atom_coords_masks = {}
for atom, coords in atom_coords.items():
atom_coords_masks[atom] = get_atom_coords_mask(coords)
return atom_coords_masks
def pdb2fasta(pdb_file, num_chains=None):
"""Converts a PDB file to a fasta formatted string using its ATOM data"""
pdb_id = basename(pdb_file).split('.')[0]
parser = PDBParser()
structure = parser.get_structure(
pdb_id,
pdb_file,
)
real_num_chains = len([0 for _ in structure.get_chains()])
if num_chains is not None and num_chains != real_num_chains:
print('WARNING: Skipping {}. Expected {} chains, got {}'.format(
pdb_file, num_chains, real_num_chains))
return ''
fasta = ''
for chain in structure.get_chains():
id_ = chain.id
seq = seq1(''.join([residue.resname for residue in chain]))
fasta += '>{}:{}\t{}\n'.format(pdb_id, id_, len(seq))
max_line_length = 80
for i in range(0, len(seq), max_line_length):
fasta += f'{seq[i:i + max_line_length]}\n'
return fasta
def get_pdb_chain_seq(
pdb_file,
chain_id,
):
p = PDBParser()
file_name = splitext(basename(pdb_file))[0]
structure = p.get_structure(
file_name,
pdb_file,
)
pdb_seq = None
for chain in structure.get_chains():
if chain.id == chain_id:
pdb_seq = "".join(
[seq1(r.get_resname()) for r in chain.get_residues()])
return pdb_seq
def cdr_indices(
chothia_pdb_file,
cdr,
offset_heavy=True,
):
"""Gets the index of a given CDR loop"""
cdr_chothia_range_dict = {
"h1": (26, 32),
"h2": (52, 56),
"h3": (95, 102),
"l1": (24, 34),
"l2": (50, 56),
"l3": (89, 97)
}
cdr = str.lower(cdr)
assert cdr in cdr_chothia_range_dict.keys()
chothia_range = cdr_chothia_range_dict[cdr]
chain_id = cdr[0].upper()
parser = PDBParser()
pdb_id = basename(chothia_pdb_file).split('.')[0]
structure = parser.get_structure(
pdb_id,
chothia_pdb_file,
)
cdr_chain_structure = None
for chain in structure.get_chains():
if chain.id == chain_id:
cdr_chain_structure = chain
break
if cdr_chain_structure is None:
print("PDB must have a chain with chain id \"[PBD ID]:{}\"".format(
chain_id))
sys.exit(-1)
residue_id_nums = [res.get_id()[1] for res in cdr_chain_structure]
# Binary search to find the start and end of the CDR loop
cdr_start = bisect_left(
residue_id_nums,
chothia_range[0],
)
cdr_end = bisect_right(
residue_id_nums,
chothia_range[1],
) - 1
if len(get_pdb_chain_seq(
chothia_pdb_file,
chain_id=chain_id,
)) != len(residue_id_nums):
print('ERROR in PDB file ' + chothia_pdb_file)
print('residue id len', len(residue_id_nums))
if chain_id == "L" and offset_heavy:
heavy_seq_len = get_pdb_chain_seq(
chothia_pdb_file,
chain_id="H",
)
cdr_start += len(heavy_seq_len)
cdr_end += len(heavy_seq_len)
return cdr_start, cdr_end
def get_cdr_range_dict(
chothia_pdb_file,
heavy_only=False,
light_only=False,
offset_heavy=True,
):
cdr_names = ["h1", "h2", "h3", "l1", "l2", "l3"]
if heavy_only:
cdr_names = cdr_names[:3]
if light_only:
cdr_names = cdr_names[3:]
cdr_range_dict = {
cdr: cdr_indices(
chothia_pdb_file,
cdr,
offset_heavy=offset_heavy,
)
for cdr in cdr_names
}
return cdr_range_dict
def h3_indices(chothia_pdb_file):
"""Gets the index of the CDR H3 loop"""
return cdr_indices(chothia_pdb_file, cdr="h3")
def get_chain_numbering(
pdb_file,
chain_id,
):
seq = []
parser = PDBParser()
structure = parser.get_structure("_", pdb_file)
for chain in structure.get_chains():
if chain.id == chain_id:
for r in chain.get_residues():
res_num = str(r._id[1]) + r._id[2]
res_num = res_num.replace(" ", "")
seq.append(res_num)
return seq
def save_PDB(
out_pdb: str,
coords: torch.Tensor,
seq: str,
chains: List[str] = None,
error: torch.Tensor = None,
delim: Union[int, List[int]] = None,
atoms=['N', 'CA', 'C', 'O', 'CB'],
write_pdb=True,
) -> None:
"""
Write set of N, CA, C, O, CB coords to PDB file
"""
if not exists(chains):
chains = ["H", "L"]
if type(delim) == type(None):
delim = -1
elif type(delim) == int:
delim = [delim]
if not exists(error):
error = torch.zeros(len(seq))
pdb_string = ""
k = 0
for r, residue in enumerate(coords):
AA = _aa_1_3_dict[seq[r]]
for a, atom in enumerate(residue):
chain_num = np.where(np.array(delim) - r > 0)[0][0]
chain_id = chains[chain_num]
if AA == "GLY" and atoms[a] == "CB": continue
x, y, z = atom
pdb_string += "ATOM %5d %-2s %3s %s%4d %8.3f%8.3f%8.3f %4.2f %4.2f %s \n" % (
k + 1, atoms[a], AA, chain_id, r + 1, x, y, z, 1, error[r], atoms[a][0])
k += 1
if r + 1 == delim[chain_num]:
pdb_string += "TER %5d %3s %s%4d\n" % (
k + 1, AA, chain_id, r + 1)
k += 1
pdb_string += "END\n"
if write_pdb:
with open(out_pdb, "w") as f:
f.write(pdb_string)
return pdb_string
def write_pdb_bfactor(
in_pdb_file,
out_pdb_file,
bfactor,
b_chain=None,
):
parser = PDBParser()
with warnings.catch_warnings(record=True):
structure = parser.get_structure(
"_",
in_pdb_file,
)
i = 0
for chain in structure.get_chains():
if exists(b_chain) and chain._id != b_chain:
continue
for r in chain.get_residues():
[a.set_bfactor(bfactor[i]) for a in r.get_atoms()]
i += 1
io = PDBIO()
io.set_structure(structure)
io.save(out_pdb_file)
def clean_pdb(pdb_file):
with open(pdb_file, "r") as f:
lines = f.readlines()
with open(pdb_file, "w") as f:
for l in lines:
if "ATOM" in l:
f.write(l) |