File size: 6,358 Bytes
8efb4bd | 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 | import os
import shutil
import sys
import numpy as np
from typing import List, Optional
from math import cos, sin
import Bio
import Bio.PDB, Bio.SeqIO, Bio.SeqUtils
import Bio.PDB.Residue
def read_model_path(pdb_path: str):
if pdb_path.endswith(".cif"):
return Bio.PDB.MMCIFParser().get_structure("s_cif", pdb_path)
return Bio.PDB.PDBParser(QUIET=True).get_structure("s_pdb", pdb_path)
def _merge_models(model_path1: str, model_path2: str, output_path: str, output_cif: bool = False):
# print(f"merging {model_path1} and {model_path2} to {output_path}")
model_struct1 = read_model_path(model_path1)
model_struct2 = read_model_path(model_path2)
model_1 = next(iter(model_struct1))
model_2 = next(iter(model_struct2))
chains_1 = {i.get_id(): i for i in model_1.get_chains()}
chains_2 = {i.get_id(): i for i in model_2.get_chains()}
for chain in chains_2.values():
if chain.id in chains_1:
res_to_move = [i for i in chain.get_residues()]
chains_1[chain.id].child_list += res_to_move
chains_1[chain.id].child_list.sort(key=lambda x: x.id[1])
for res in res_to_move:
chain.detach_child(res.id)
res.detach_parent()
res.parent = chains_1[chain.id]
chains_1[chain.id].child_list += chain.child_list
else:
model_1.child_list.append(chain)
chain.parent = model_1
# save the new structure to output_pdb
if output_cif:
io = Bio.PDB.MMCIFIO()
else:
io = Bio.PDB.PDBIO()
io.set_structure(model_struct1)
io.save(output_path)
def _rotate_atom(coord, euler_rotation_tuple):
# based on ** gamb::Matrix3, gamb::RigidTrans **
x, y, z = euler_rotation_tuple
cx, cy, cz = cos(x), cos(y), cos(z)
sx, sy, sz = sin(x), sin(y), sin(z)
v0 = np.array([cz*cy, -sy*sx*cz - sz*cx, -sy*cx*cz + sz*sx])
v1 = np.array([sz*cy, -sy*sx*sz + cx*cz, -sy*cx*sz - sx*cz])
v2 = np.array([sy, cy*sx, cy*cx])
return np.array([
v0[0] * coord[0] + v0[1] * coord[1] + v0[2] * coord[2],
v1[0] * coord[0] + v1[1] * coord[1] + v1[2] * coord[2],
v2[0] * coord[0] + v2[1] * coord[1] + v2[2] * coord[2],
])
def apply_transform(pdb_path: str, output_path: str, transform_numbers: List[float]):
assert len(transform_numbers) == 6
pdb_parser = Bio.PDB.PDBParser(QUIET=True)
pdb_struct = pdb_parser.get_structure("original_pdb", pdb_path)
assert len(list(pdb_struct)) == 1, f"Too many models! {pdb_path}"
rotation_tuple, translation_tuple = transform_numbers[:3], transform_numbers[3:]
for atom in next(iter(pdb_struct)).get_atoms():
coord = atom.get_coord()
new_coord = _rotate_atom(coord, rotation_tuple)
new_coord += np.array(translation_tuple)
atom.set_coord(new_coord)
io = Bio.PDB.PDBIO()
io.set_structure(pdb_struct)
io.save(output_path)
def create_transformation_pdb(assembly_path: str, transforms_str: str, output_path: str, output_cif: bool = False):
# example: transforms_str = "0(-0.00760431 -1.00941 -2.38469 21.6924 -87.7727 -10.4274),1(0 0 0 0 0 0),
# 2(-2.96419 0.240678 -0.964002 65.6247 -63.7248 -42.0541)"
tmp_pdb_path = os.path.join(assembly_path, "tmp_comb_trans.pdb")
chains_path = os.path.join(assembly_path, "chain.list")
if not os.path.exists(chains_path):
chains_path = os.path.join(assembly_path, "chains.txt")
subunit_filenames = [i.split(" ")[0] for i in open(chains_path, "r").read().split("\n") if len(i) > 0]
if os.path.exists(output_path):
os.remove(output_path)
for transform_str in transforms_str.split(","):
chain_ind = int(transform_str.split("(")[0])
subunit_path = os.path.join(assembly_path, subunit_filenames[chain_ind])
transform_numbers_as_str = transform_str.split("(")[1][:-1]
transform_numbers = list(map(float, transform_numbers_as_str.split(" ")))
apply_transform(subunit_path, tmp_pdb_path, transform_numbers)
if os.path.exists(output_path):
_merge_models(output_path, tmp_pdb_path, output_path, output_cif=output_cif)
else:
if output_cif:
io = Bio.PDB.MMCIFIO()
io.set_structure(read_model_path(tmp_pdb_path))
io.save(output_path)
else:
shutil.copy(tmp_pdb_path, output_path)
if output_cif:
# fix _atom_site in cif
cif_lines = open(output_path, "r").read().split("\n")
cif_lines = [i + " " if i.startswith("_atom_site") else i for i in cif_lines]
open(output_path, "w").write("\n".join(cif_lines) + "\n")
os.remove(tmp_pdb_path)
def create_complexes(result_path: str, first_result: Optional[int] = None, last_result: Optional[int] = None,
output_folder: Optional[str] = None, output_cif: bool = False) \
-> List[str]:
output_folder = output_folder or os.path.dirname(result_path)
os.makedirs(output_folder, exist_ok=True)
assembly_path = os.path.dirname(result_path)
transforms_strs = [i[i.index("[") + 1:i.index("]")] for i in open(result_path, "r").read().split("\n") if i]
if first_result is None:
first_result = 0
if last_result is None or last_result > len(transforms_strs):
last_result = len(transforms_strs)
output_files = []
for i in range(first_result, last_result):
file_ext = ".cif" if output_cif else ".pdb"
output_path = os.path.join(output_folder,
os.path.basename(result_path).split(".")[0] + "_" + str(i) + file_ext)
create_transformation_pdb(assembly_path, transforms_strs[i], output_path=output_path, output_cif=output_cif)
output_files.append(output_path)
return output_files
if __name__ == '__main__':
if len(sys.argv) != 4:
raise Exception("Usage: <script> result_path first_result_num last_result_num")
_result_path = os.path.abspath(sys.argv[1])
_first_result = int(sys.argv[2]) - 1
_last_result = int(sys.argv[3])
create_complexes(_result_path, _first_result, _last_result)
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