用 Biopython 替换 PDB 原子名称
问题描述 投票：0回答：1
我有一个包含蛋白质和一个配体的 pdb。我不喜欢配体的氢的命名方式（1H2，2H2，1H3，2H3，...），我想要 H1，H2，H3，H4，...
我编写了以下脚本，问题是似乎无法分配新的原子ID。 Atom.id 反映了更改，但输出 pdb 结构中不存在此更改，该结构保留旧名称。
from Bio.PDB import PDBParser, PDBIO
io = PDBIO()
target_pdb_path = 'mypdb.pdb'
pdb = PDBParser(QUIET=True).get_structure('target', target_pdb_path)[0]
hydrogens = []
for atom in pdb.get_atoms():
if atom.parent.id[0].startswith('H_'):
# The atom is an hydrogen and is an HETATM record
if 'H' in atom.name:
hydrogens.append(atom)
# Rename hydrogens of the ligand
for h_num, h in enumerate(hydrogens, 1):
# this is working, but the change is not present in the output pdb structure
h.id = f'H{h_num} '
io.set_structure(pdb)
io.save('test.pdb')
看看分配 h.id 不会改变 full_id。我也尝试替换整个 full_id 元组，但这也不起作用。 不幸的是，似乎没有方法可以像 Atom.set_bfactor()、Atom.set_coord() 等其他功能一样更改 id。
In [233]: h.full_id # still the old id 3H18
Out[233]: ('target', 0, 'X', ('H_EOD', 401, ' '), ('3H18', ' '))
In [234]: h.id # my new id
Out[234]: 'H29 '
有人有解决办法吗？非常感谢！
1个回答
0
投票
投票
好的我的尝试，需要创建我的输入并更改输出：将原子名称
H1 ... H15X1 .. X15small_pdb_h_gtp_no-connect_numb.pdbCOMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 3.1.1
ATOM 1 N VAL A 6 20.799 29.221 8.701 1.00 0.00 N
ATOM 2 CA VAL A 6 20.474 28.731 7.364 1.00 0.00 C
ATOM 3 C VAL A 6 21.733 28.489 6.533 1.00 0.00 C
ATOM 4 O VAL A 6 22.566 29.380 6.440 1.00 0.00 O
ATOM 5 CB VAL A 6 19.553 29.779 6.711 1.00 0.00 C
ATOM 6 CG1 VAL A 6 19.327 29.527 5.222 1.00 0.00 C
ATOM 7 CG2 VAL A 6 18.217 29.772 7.421 1.00 0.00 C
ATOM 8 N VAL A 7 21.974 27.342 5.919 1.00 0.00 N
ATOM 9 CA VAL A 7 23.122 27.169 5.031 1.00 0.00 C
ATOM 10 C VAL A 7 22.555 27.122 3.620 1.00 0.00 C
ATOM 11 O VAL A 7 21.609 26.378 3.344 1.00 0.00 O
ATOM 12 CB VAL A 7 23.896 25.869 5.351 1.00 0.00 C
ATOM 13 CG1 VAL A 7 25.132 25.702 4.504 1.00 0.00 C
ATOM 14 CG2 VAL A 7 24.334 25.857 6.792 1.00 0.00 C
ATOM 15 N VAL A 8 23.076 27.936 2.718 1.00 0.00 N
ATOM 16 CA VAL A 8 22.670 27.904 1.328 1.00 0.00 C
ATOM 17 C VAL A 8 23.672 27.034 0.554 1.00 0.00 C
ATOM 18 O VAL A 8 24.852 27.397 0.465 1.00 0.00 O
ATOM 19 CB VAL A 8 22.621 29.343 0.825 1.00 0.00 C
ATOM 20 CG1 VAL A 8 22.080 29.353 -0.590 1.00 0.00 C
ATOM 21 CG2 VAL A 8 21.725 30.215 1.697 1.00 0.00 C
ATOM 22 N LEU A 9 23.250 25.888 0.004 1.00 0.00 N
ATOM 23 CA LEU A 9 24.132 24.905 -0.620 1.00 0.00 C
ATOM 24 C LEU A 9 23.960 24.767 -2.131 1.00 0.00 C
ATOM 25 O LEU A 9 22.841 24.930 -2.621 1.00 0.00 O
ATOM 26 CB LEU A 9 23.843 23.559 -0.010 1.00 0.00 C
ATOM 27 CG LEU A 9 24.288 23.347 1.414 1.00 0.00 C
ATOM 28 CD1 LEU A 9 23.675 22.070 1.962 1.00 0.00 C
ATOM 29 CD2 LEU A 9 25.809 23.357 1.478 1.00 0.00 C
ATOM 30 N GLY A 10 24.997 24.458 -2.908 1.00 0.00 N
ATOM 31 CA GLY A 10 24.827 24.183 -4.325 1.00 0.00 C
ATOM 32 C GLY A 10 26.134 24.261 -5.102 1.00 0.00 C
ATOM 33 O GLY A 10 27.188 24.556 -4.534 1.00 0.00 O
ATOM 34 N SER A 11 26.094 24.027 -6.416 1.00 0.00 N
ATOM 35 CA SER A 11 27.280 24.074 -7.267 1.00 0.00 C
ATOM 36 C SER A 11 27.618 25.490 -7.674 1.00 0.00 C
ATOM 37 O SER A 11 26.824 26.425 -7.519 1.00 0.00 O
ATOM 38 CB SER A 11 27.073 23.274 -8.536 1.00 0.00 C
ATOM 39 OG SER A 11 26.744 21.934 -8.227 1.00 0.00 O
ATOM 40 N GLY A 12 28.805 25.674 -8.235 1.00 0.00 N
ATOM 41 CA GLY A 12 29.215 26.993 -8.714 1.00 0.00 C
ATOM 42 C GLY A 12 28.280 27.618 -9.752 1.00 0.00 C
ATOM 43 O GLY A 12 27.692 26.945 -10.605 1.00 0.00 O
ATOM 44 N GLY A 13 28.091 28.929 -9.645 1.00 0.00 N
ATOM 45 CA GLY A 13 27.363 29.714 -10.618 1.00 0.00 C
ATOM 46 C GLY A 13 25.862 29.638 -10.485 1.00 0.00 C
ATOM 47 O GLY A 13 25.218 30.556 -10.943 1.00 0.00 O
ATOM 48 N VAL A 14 25.245 28.666 -9.827 1.00 0.00 N
ATOM 49 CA VAL A 14 23.798 28.557 -9.709 1.00 0.00 C
ATOM 50 C VAL A 14 23.042 29.783 -9.203 1.00 0.00 C
ATOM 51 O VAL A 14 21.827 29.901 -9.354 1.00 0.00 O
ATOM 52 CB VAL A 14 23.452 27.347 -8.833 1.00 0.00 C
ATOM 53 CG1 VAL A 14 24.080 26.099 -9.412 1.00 0.00 C
ATOM 54 CG2 VAL A 14 23.860 27.539 -7.373 1.00 0.00 C
ATOM 55 N GLY A 15 23.716 30.722 -8.558 1.00 0.00 N
ATOM 56 CA GLY A 15 23.016 31.867 -8.019 1.00 0.00 C
ATOM 57 C GLY A 15 22.880 31.944 -6.498 1.00 0.00 C
ATOM 58 O GLY A 15 22.118 32.782 -6.042 1.00 0.00 O
ATOM 59 N LYS A 16 23.638 31.182 -5.686 1.00 0.00 N
ATOM 60 CA LYS A 16 23.597 31.199 -4.210 1.00 0.00 C
ATOM 61 C LYS A 16 23.834 32.561 -3.602 1.00 0.00 C
ATOM 62 O LYS A 16 23.068 33.033 -2.760 1.00 0.00 O
ATOM 63 CB LYS A 16 24.593 30.232 -3.570 1.00 0.00 C
ATOM 64 CG LYS A 16 24.311 28.785 -3.934 1.00 0.00 C
ATOM 65 CD LYS A 16 25.192 27.838 -3.179 1.00 0.00 C
ATOM 66 CE LYS A 16 26.652 28.055 -3.425 1.00 0.00 C
ATOM 67 NZ LYS A 16 26.949 27.601 -4.751 1.00 0.00 N1+
ATOM 68 N SER A 17 24.877 33.238 -4.071 1.00 0.00 N
ATOM 69 CA SER A 17 25.190 34.560 -3.573 1.00 0.00 C
ATOM 70 C SER A 17 24.268 35.615 -4.118 1.00 0.00 C
ATOM 71 O SER A 17 24.071 36.602 -3.432 1.00 0.00 O
ATOM 72 CB SER A 17 26.604 34.908 -3.927 1.00 0.00 C
ATOM 73 OG SER A 17 27.409 33.729 -3.728 1.00 0.00 O
ATOM 74 N ALA A 18 23.680 35.451 -5.313 1.00 0.00 N
ATOM 75 CA ALA A 18 22.810 36.455 -5.871 1.00 0.00 C
ATOM 76 C ALA A 18 21.496 36.379 -5.125 1.00 0.00 C
ATOM 77 O ALA A 18 20.955 37.417 -4.776 1.00 0.00 O
ATOM 78 CB ALA A 18 22.613 36.235 -7.354 1.00 0.00 C
ATOM 79 N LEU A 19 20.989 35.191 -4.814 1.00 0.00 N
ATOM 80 CA LEU A 19 19.844 35.014 -3.938 1.00 0.00 C
ATOM 81 C LEU A 19 20.085 35.556 -2.524 1.00 0.00 C
ATOM 82 O LEU A 19 19.305 36.384 -2.066 1.00 0.00 O
ATOM 83 CB LEU A 19 19.470 33.531 -3.907 1.00 0.00 C
ATOM 84 CG LEU A 19 18.824 32.928 -5.141 1.00 0.00 C
ATOM 85 CD1 LEU A 19 18.781 31.438 -5.031 1.00 0.00 C
ATOM 86 CD2 LEU A 19 17.401 33.437 -5.328 1.00 0.00 C
ATOM 87 N THR A 20 21.156 35.175 -1.820 1.00 0.00 N
ATOM 88 CA THR A 20 21.471 35.686 -0.501 1.00 0.00 C
ATOM 89 C THR A 20 21.646 37.203 -0.512 1.00 0.00 C
ATOM 90 O THR A 20 20.988 37.911 0.261 1.00 0.00 O
ATOM 91 CB THR A 20 22.726 34.996 0.064 1.00 0.00 C
ATOM 92 CG2 THR A 20 23.091 35.495 1.437 1.00 0.00 C
ATOM 93 OG1 THR A 20 22.462 33.599 0.110 1.00 0.00 O
ATOM 94 N VAL A 21 22.471 37.750 -1.410 1.00 0.00 N
ATOM 95 CA VAL A 21 22.686 39.189 -1.491 1.00 0.00 C
ATOM 96 C VAL A 21 21.419 39.954 -1.866 1.00 0.00 C
ATOM 97 O VAL A 21 21.240 41.085 -1.417 1.00 0.00 O
ATOM 98 CB VAL A 21 23.871 39.505 -2.398 1.00 0.00 C
ATOM 99 CG1 VAL A 21 24.142 40.980 -2.468 1.00 0.00 C
ATOM 100 CG2 VAL A 21 25.140 38.840 -1.868 1.00 0.00 C
ATOM 101 N GLN A 22 20.472 39.394 -2.613 1.00 0.00 N
ATOM 102 CA GLN A 22 19.197 40.059 -2.841 1.00 0.00 C
ATOM 103 C GLN A 22 18.364 40.109 -1.555 1.00 0.00 C
ATOM 104 O GLN A 22 17.817 41.169 -1.258 1.00 0.00 O
ATOM 105 CB GLN A 22 18.451 39.349 -3.987 1.00 0.00 C
ATOM 106 CG GLN A 22 17.112 39.921 -4.504 1.00 0.00 C
ATOM 107 CD GLN A 22 17.229 41.246 -5.220 1.00 0.00 C
ATOM 108 NE2 GLN A 22 18.028 41.314 -6.268 1.00 0.00 N
ATOM 109 OE1 GLN A 22 16.583 42.229 -4.878 1.00 0.00 O
ATOM 110 N PHE A 23 18.259 39.026 -0.754 1.00 0.00 N
ATOM 111 CA PHE A 23 17.568 39.052 0.531 1.00 0.00 C
ATOM 112 C PHE A 23 18.183 40.098 1.444 1.00 0.00 C
ATOM 113 O PHE A 23 17.500 40.989 1.922 1.00 0.00 O
ATOM 114 CB PHE A 23 17.614 37.706 1.233 1.00 0.00 C
ATOM 115 CG PHE A 23 16.806 37.646 2.525 1.00 0.00 C
ATOM 116 CD1 PHE A 23 15.460 37.952 2.534 1.00 0.00 C
ATOM 117 CD2 PHE A 23 17.420 37.237 3.694 1.00 0.00 C
ATOM 118 CE1 PHE A 23 14.729 37.821 3.695 1.00 0.00 C
ATOM 119 CE2 PHE A 23 16.685 37.107 4.854 1.00 0.00 C
ATOM 120 CZ PHE A 23 15.341 37.392 4.850 1.00 0.00 C
HETATM 121 PA GTP A 180 26.277 33.726 -8.045 1.00 0.00 P
HETATM 122 PB GTP A 180 27.017 31.171 -6.766 1.00 0.00 P
HETATM 123 PG GTP A 180 29.710 30.132 -5.989 1.00 0.00 P
HETATM 124 C5' GTP A 180 26.615 33.475 -10.679 1.00 0.00 C
HETATM 125 O5' GTP A 180 25.804 33.834 -9.555 1.00 0.00 O
HETATM 126 C4' GTP A 180 26.219 34.288 -11.894 1.00 0.00 C
HETATM 127 O4' GTP A 180 24.826 34.017 -12.143 1.00 0.00 O
HETATM 128 C3' GTP A 180 26.372 35.802 -11.724 1.00 0.00 C
HETATM 129 O3' GTP A 180 26.880 36.347 -12.936 1.00 0.00 O
HETATM 130 C2' GTP A 180 24.932 36.243 -11.481 1.00 0.00 C
HETATM 131 O2' GTP A 180 24.719 37.581 -11.901 1.00 0.00 O
HETATM 132 C1' GTP A 180 24.069 35.240 -12.240 1.00 0.00 C
HETATM 133 N1 GTP A 180 19.000 35.036 -13.013 1.00 0.00 N
HETATM 134 O1A GTP A 180 25.089 33.867 -7.187 1.00 0.00 O1-
HETATM 135 O1B GTP A 180 26.072 30.050 -6.958 1.00 0.00 O1-
HETATM 136 O1G GTP A 180 29.197 28.937 -5.265 1.00 0.00 O
HETATM 137 C2 GTP A 180 20.022 35.339 -13.903 1.00 0.00 C
HETATM 138 N2 GTP A 180 19.627 35.619 -15.147 1.00 0.00 N
HETATM 139 O2A GTP A 180 27.427 34.635 -7.843 1.00 0.00 O
HETATM 140 O2B GTP A 180 26.960 31.913 -5.483 1.00 0.00 O
HETATM 141 O2G GTP A 180 30.881 29.816 -6.827 1.00 0.00 O1-
HETATM 142 N3 GTP A 180 21.301 35.367 -13.569 1.00 0.00 N
HETATM 143 O3A GTP A 180 26.807 32.212 -7.961 1.00 0.00 O
HETATM 144 O3B GTP A 180 28.517 30.631 -6.995 1.00 0.00 O
HETATM 145 O3G GTP A 180 30.013 31.278 -5.117 1.00 0.00 O
HETATM 146 C4 GTP A 180 21.489 35.054 -12.257 1.00 0.00 C
HETATM 147 C5 GTP A 180 20.554 34.737 -11.307 1.00 0.00 C
HETATM 148 C6 GTP A 180 19.183 34.712 -11.659 1.00 0.00 C
HETATM 149 O6 GTP A 180 18.205 34.448 -10.957 1.00 0.00 O
HETATM 150 N7 GTP A 180 21.168 34.483 -10.079 1.00 0.00 N
HETATM 151 C8 GTP A 180 22.443 34.655 -10.325 1.00 0.00 C
HETATM 152 N9 GTP A 180 22.724 35.005 -11.630 1.00 0.00 N
HETATM 286 H1 GTP A 180 27.642 33.664 -10.448 1.00 0.00 H
HETATM 287 H2 GTP A 180 26.472 32.436 -10.894 1.00 0.00 H
HETATM 288 H3 GTP A 180 26.872 34.003 -12.692 1.00 0.00 H
HETATM 289 H4 GTP A 180 27.038 36.109 -10.945 1.00 0.00 H
HETATM 290 H5 GTP A 180 26.303 36.091 -13.672 1.00 0.00 H
HETATM 291 H6 GTP A 180 24.683 36.247 -10.440 1.00 0.00 H
HETATM 292 H7 GTP A 180 24.926 37.660 -12.845 1.00 0.00 H
HETATM 293 H8 GTP A 180 23.874 35.594 -13.231 1.00 0.00 H
HETATM 294 H9 GTP A 180 18.670 35.593 -15.377 1.00 0.00 H
HETATM 295 H10 GTP A 180 20.293 35.851 -15.834 1.00 0.00 H
HETATM 296 H11 GTP A 180 27.124 35.555 -7.891 1.00 0.00 H
HETATM 297 H12 GTP A 180 26.059 32.241 -5.339 1.00 0.00 H
HETATM 298 H13 GTP A 180 22.030 35.588 -14.193 1.00 0.00 H
HETATM 299 H14 GTP A 180 30.718 31.035 -4.497 1.00 0.00 H
HETATM 300 H15 GTP A 180 23.174 34.539 -9.606 1.00 0.00 H
使用代码：
from Bio.PDB import PDBParser, PDBIO
from Bio.PDB.Atom import Atom
io = PDBIO()
target_pdb_path = 'small_pdb_h_gtp_no-connect_numb.pdb'
pdb = PDBParser(QUIET=True).get_structure('target', target_pdb_path)[0]
hydrogens = []
for atom in pdb.get_atoms():
if atom.parent.id[0].startswith('H_'):
print(atom.parent.id , atom.name)
# The atom is an hydrogen and is an HETATM record
if 'H' in atom.name:
print('ok')
hydrogens.append(atom)
print('\n\nhydrogens : \n ', hydrogens)
# Rename hydrogens of the ligand
for h_num, h in enumerate(hydrogens, 1):
# this is working, but the change is not present in the output pdb structure
print(h.id, h.full_id , type(h))
par = h.parent
par.detach_child(h.id)
print(par ,' ... ', h.parent)
"""
https://biopython.org/docs/latest/api/Bio.PDB.Atom.html?highlight=atom#module-Bio.PDB.Atom
Bio.PDB.Atom module
Atom class, used in Structure objects
class Bio.PDB.Atom.Atom(name, coord, bfactor, occupancy, altloc, fullname, serial_number, element=None, pqr_charge=None, radius=None)
__init__(name, coord, bfactor, occupancy, altloc, fullname, serial_number, element=None, pqr_charge=None, radius=None)
"""
h_new = Atom(f'X{h_num}' , h.get_coord() , h.get_bfactor() , h.get_occupancy() , h.get_altloc() , f'X{h_num}' ,
h.get_serial_number() , 'H' , h.get_charge() , h.get_radius())
par.add(h_new)
print(h_new.id ,h_new.name , h_new.full_id)
print(h_new.id ,h_new.name , h_new.full_id[4][0])
print(par , h_new.parent , '\n\n')
io.set_structure(pdb)
io.save('test.pdb', preserve_atom_numbering = False)
我得到输出：
('H_GTP', 180, ' ') PA
('H_GTP', 180, ' ') PB
('H_GTP', 180, ' ') PG
('H_GTP', 180, ' ') C5'
('H_GTP', 180, ' ') O5'
('H_GTP', 180, ' ') C4'
('H_GTP', 180, ' ') O4'
('H_GTP', 180, ' ') C3'
('H_GTP', 180, ' ') O3'
('H_GTP', 180, ' ') C2'
('H_GTP', 180, ' ') O2'
('H_GTP', 180, ' ') C1'
('H_GTP', 180, ' ') N1
('H_GTP', 180, ' ') O1A
('H_GTP', 180, ' ') O1B
('H_GTP', 180, ' ') O1G
('H_GTP', 180, ' ') C2
('H_GTP', 180, ' ') N2
('H_GTP', 180, ' ') O2A
('H_GTP', 180, ' ') O2B
('H_GTP', 180, ' ') O2G
('H_GTP', 180, ' ') N3
('H_GTP', 180, ' ') O3A
('H_GTP', 180, ' ') O3B
('H_GTP', 180, ' ') O3G
('H_GTP', 180, ' ') C4
('H_GTP', 180, ' ') C5
('H_GTP', 180, ' ') C6
('H_GTP', 180, ' ') O6
('H_GTP', 180, ' ') N7
('H_GTP', 180, ' ') C8
('H_GTP', 180, ' ') N9
('H_GTP', 180, ' ') H1
ok
('H_GTP', 180, ' ') H2
ok
('H_GTP', 180, ' ') H3
ok
('H_GTP', 180, ' ') H4
ok
('H_GTP', 180, ' ') H5
ok
('H_GTP', 180, ' ') H6
ok
('H_GTP', 180, ' ') H7
ok
('H_GTP', 180, ' ') H8
ok
('H_GTP', 180, ' ') H9
ok
('H_GTP', 180, ' ') H10
ok
('H_GTP', 180, ' ') H11
ok
('H_GTP', 180, ' ') H12
ok
('H_GTP', 180, ' ') H13
ok
('H_GTP', 180, ' ') H14
ok
('H_GTP', 180, ' ') H15
ok
hydrogens :
[<Atom H1>, <Atom H2>, <Atom H3>, <Atom H4>, <Atom H5>, <Atom H6>, <Atom H7>, <Atom H8>, <Atom H9>, <Atom H10>, <Atom H11>, <Atom H12>, <Atom H13>, <Atom H14>, <Atom H15>]
H1 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H1', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X1 X1 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X1', ' '))
X1 X1 X1
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H2 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H2', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X2 X2 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X2', ' '))
X2 X2 X2
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H3 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H3', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X3 X3 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X3', ' '))
X3 X3 X3
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H4 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H4', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X4 X4 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X4', ' '))
X4 X4 X4
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H5 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H5', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X5 X5 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X5', ' '))
X5 X5 X5
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H6 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H6', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X6 X6 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X6', ' '))
X6 X6 X6
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H7 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H7', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X7 X7 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X7', ' '))
X7 X7 X7
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H8 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H8', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X8 X8 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X8', ' '))
X8 X8 X8
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H9 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H9', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X9 X9 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X9', ' '))
X9 X9 X9
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H10 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H10', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X10 X10 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X10', ' '))
X10 X10 X10
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H11 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H11', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X11 X11 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X11', ' '))
X11 X11 X11
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H12 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H12', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X12 X12 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X12', ' '))
X12 X12 X12
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H13 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H13', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X13 X13 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X13', ' '))
X13 X13 X13
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H14 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H14', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X14 X14 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X14', ' '))
X14 X14 X14
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
H15 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H15', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= > ... None
X15 X15 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X15', ' '))
X15 X15 X15
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= >
带文件
test.pdbATOM 1 N VAL A 6 20.799 29.221 8.701 1.00 0.00 N
ATOM 2 CA VAL A 6 20.474 28.731 7.364 1.00 0.00 C
....
....
ATOM 119 CE2 PHE A 23 16.685 37.107 4.854 1.00 0.00 C
ATOM 120 CZ PHE A 23 15.341 37.392 4.850 1.00 0.00 C
HETATM 121 PA GTP A 180 26.277 33.726 -8.045 1.00 0.00 P
HETATM 122 PB GTP A 180 27.017 31.171 -6.766 1.00 0.00 P
HETATM 123 PG GTP A 180 29.710 30.132 -5.989 1.00 0.00 P
HETATM 124 C5' GTP A 180 26.615 33.475 -10.679 1.00 0.00 C
HETATM 125 O5' GTP A 180 25.804 33.834 -9.555 1.00 0.00 O
HETATM 126 C4' GTP A 180 26.219 34.288 -11.894 1.00 0.00 C
HETATM 127 O4' GTP A 180 24.826 34.017 -12.143 1.00 0.00 O
HETATM 128 C3' GTP A 180 26.372 35.802 -11.724 1.00 0.00 C
HETATM 129 O3' GTP A 180 26.880 36.347 -12.936 1.00 0.00 O
HETATM 130 C2' GTP A 180 24.932 36.243 -11.481 1.00 0.00 C
HETATM 131 O2' GTP A 180 24.719 37.581 -11.901 1.00 0.00 O
HETATM 132 C1' GTP A 180 24.069 35.240 -12.240 1.00 0.00 C
HETATM 133 N1 GTP A 180 19.000 35.036 -13.013 1.00 0.00 N
HETATM 134 O1A GTP A 180 25.089 33.867 -7.187 1.00 0.00 O
HETATM 135 O1B GTP A 180 26.072 30.050 -6.958 1.00 0.00 O
HETATM 136 O1G GTP A 180 29.197 28.937 -5.265 1.00 0.00 O
HETATM 137 C2 GTP A 180 20.022 35.339 -13.903 1.00 0.00 C
HETATM 138 N2 GTP A 180 19.627 35.619 -15.147 1.00 0.00 N
HETATM 139 O2A GTP A 180 27.427 34.635 -7.843 1.00 0.00 O
HETATM 140 O2B GTP A 180 26.960 31.913 -5.483 1.00 0.00 O
HETATM 141 O2G GTP A 180 30.881 29.816 -6.827 1.00 0.00 O
HETATM 142 N3 GTP A 180 21.301 35.367 -13.569 1.00 0.00 N
HETATM 143 O3A GTP A 180 26.807 32.212 -7.961 1.00 0.00 O
HETATM 144 O3B GTP A 180 28.517 30.631 -6.995 1.00 0.00 O
HETATM 145 O3G GTP A 180 30.013 31.278 -5.117 1.00 0.00 O
HETATM 146 C4 GTP A 180 21.489 35.054 -12.257 1.00 0.00 C
HETATM 147 C5 GTP A 180 20.554 34.737 -11.307 1.00 0.00 C
HETATM 148 C6 GTP A 180 19.183 34.712 -11.659 1.00 0.00 C
HETATM 149 O6 GTP A 180 18.205 34.448 -10.957 1.00 0.00 O
HETATM 150 N7 GTP A 180 21.168 34.483 -10.079 1.00 0.00 N
HETATM 151 C8 GTP A 180 22.443 34.655 -10.325 1.00 0.00 C
HETATM 152 N9 GTP A 180 22.724 35.005 -11.630 1.00 0.00 N
HETATM 153 X1 GTP A 180 27.642 33.664 -10.448 1.00 0.00 H
HETATM 154 X2 GTP A 180 26.472 32.436 -10.894 1.00 0.00 H
HETATM 155 X3 GTP A 180 26.872 34.003 -12.692 1.00 0.00 H
HETATM 156 X4 GTP A 180 27.038 36.109 -10.945 1.00 0.00 H
HETATM 157 X5 GTP A 180 26.303 36.091 -13.672 1.00 0.00 H
HETATM 158 X6 GTP A 180 24.683 36.247 -10.440 1.00 0.00 H
HETATM 159 X7 GTP A 180 24.926 37.660 -12.845 1.00 0.00 H
HETATM 160 X8 GTP A 180 23.874 35.594 -13.231 1.00 0.00 H
HETATM 161 X9 GTP A 180 18.670 35.593 -15.377 1.00 0.00 H
HETATM 162 X10 GTP A 180 20.293 35.851 -15.834 1.00 0.00 H
HETATM 163 X11 GTP A 180 27.124 35.555 -7.891 1.00 0.00 H
HETATM 164 X12 GTP A 180 26.059 32.241 -5.339 1.00 0.00 H
HETATM 165 X13 GTP A 180 22.030 35.588 -14.193 1.00 0.00 H
HETATM 166 X14 GTP A 180 30.718 31.035 -4.497 1.00 0.00 H
HETATM 167 X15 GTP A 180 23.174 34.539 -9.606 1.00 0.00 H
TER 168 GTP A 180
END
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