ok, here my input pdb, example_short.pdb :
ATOM 1 N MET A 1 14.067 31.664 -1.639 1.00 80.87 N
ATOM 2 HN1 MET A 1 14.250 31.259 -0.699 1.00 0.00 H
ATOM 3 HN2 MET A 1 14.891 32.220 -1.945 1.00 0.00 H
ATOM 4 HN3 MET A 1 13.229 32.279 -1.596 1.00 0.00 H
ATOM 5 CA MET A 1 13.824 30.564 -2.612 1.00 79.17 C
ATOM 6 HA MET A 1 14.702 29.921 -2.671 1.00 0.00 H
ATOM 7 C MET A 1 13.556 31.158 -3.989 1.00 78.52 C
ATOM 8 O MET A 1 13.301 32.365 -4.085 1.00 79.40 O
ATOM 9 CB MET A 1 12.634 29.724 -2.148 1.00 83.38 C
ATOM 10 HB1 MET A 1 12.600 29.755 -1.059 1.00 0.00 H
ATOM 11 HB2 MET A 1 11.725 30.170 -2.552 1.00 0.00 H
ATOM 12 CG MET A 1 12.680 28.264 -2.580 1.00 85.71 C
ATOM 13 HG1 MET A 1 12.066 28.145 -3.473 1.00 0.00 H
ATOM 14 HG2 MET A 1 12.274 27.650 -1.776 1.00 0.00 H
ATOM 15 SD MET A 1 14.354 27.697 -2.951 1.00100.24 S
ATOM 16 CE MET A 1 15.137 27.675 -1.338 1.00 97.10 C
ATOM 17 HE1 MET A 1 15.118 28.678 -0.913 1.00 0.00 H
ATOM 18 HE2 MET A 1 14.597 26.991 -0.683 1.00 0.00 H
ATOM 19 HE3 MET A 1 16.170 27.342 -1.441 1.00 0.00 H
ATOM 20 N GLU A 2 13.604 30.306 -5.018 1.00 75.32 N
ATOM 21 H GLU A 2 13.628 29.291 -4.794 1.00 0.00 H
ATOM 22 CA GLU A 2 13.626 30.684 -6.444 1.00 72.66 C
ATOM 23 HA GLU A 2 13.508 29.732 -6.961 1.00 0.00 H
ATOM 24 C GLU A 2 14.903 31.384 -6.843 1.00 65.44 C
ATOM 25 O GLU A 2 15.489 31.127 -7.892 1.00 67.46 O
ATOM 26 CB GLU A 2 12.516 31.672 -6.810 1.00 72.71 C
ATOM 27 HB1 GLU A 2 12.094 32.068 -5.886 1.00 0.00 H
ATOM 28 HB2 GLU A 2 12.960 32.486 -7.383 1.00 0.00 H
ATOM 29 CG GLU A 2 11.397 31.081 -7.622 1.00 77.72 C
ATOM 30 HG1 GLU A 2 10.901 31.877 -8.178 1.00 0.00 H
ATOM 31 HG2 GLU A 2 11.809 30.354 -8.321 1.00 0.00 H
ATOM 32 CD GLU A 2 10.385 30.393 -6.731 1.00 79.89 C
ATOM 33 OE1 GLU A 2 9.171 30.574 -6.987 1.00 82.69 O
ATOM 34 OE2 GLU A 2 10.824 29.702 -5.779 1.00 72.73 O
ATOM 35 N ASN A 3 15.194 32.399 -6.043 1.00 60.12 N
ATOM 36 H ASN A 3 14.712 32.444 -5.123 1.00 0.00 H
ATOM 37 CA ASN A 3 16.140 33.452 -6.363 1.00 56.21 C
ATOM 38 HA ASN A 3 16.072 33.715 -7.419 1.00 0.00 H
ATOM 39 C ASN A 3 17.548 32.968 -6.047 1.00 50.40 C
ATOM 40 O ASN A 3 18.513 33.666 -6.331 1.00 50.95 O
ATOM 41 CB ASN A 3 15.821 34.667 -5.493 1.00 57.10 C
ATOM 42 HB1 ASN A 3 15.913 34.381 -4.445 1.00 0.00 H
ATOM 43 HB2 ASN A 3 16.538 35.457 -5.717 1.00 0.00 H
ATOM 44 CG ASN A 3 14.425 35.196 -5.732 1.00 62.07 C
ATOM 45 OD1 ASN A 3 14.220 36.001 -6.641 1.00 69.12 O
ATOM 46 ND2 ASN A 3 13.464 34.748 -4.923 1.00 57.21 N
ATOM 47 1HD2 ASN A 3 12.486 35.079 -5.045 1.00 0.00 H
ATOM 48 2HD2 ASN A 3 13.693 34.068 -4.170 1.00 0.00 H
ATOM 49 N PHE A 4 17.643 31.764 -5.492 1.00 47.14 N
ATOM 50 H PHE A 4 16.781 31.193 -5.378 1.00 0.00 H
ATOM 51 CA PHE A 4 18.914 31.219 -5.038 1.00 46.77 C
ATOM 52 HA PHE A 4 19.696 31.915 -5.340 1.00 0.00 H
ATOM 53 C PHE A 4 19.239 29.888 -5.695 1.00 48.73 C
ATOM 54 O PHE A 4 18.490 28.919 -5.594 1.00 49.50 O
ATOM 55 CB PHE A 4 18.922 31.095 -3.507 1.00 42.32 C
ATOM 56 HB1 PHE A 4 18.091 30.456 -3.207 1.00 0.00 H
ATOM 57 HB2 PHE A 4 19.862 30.635 -3.201 1.00 0.00 H
ATOM 58 CG PHE A 4 18.787 32.415 -2.806 1.00 39.42 C
ATOM 59 CD1 PHE A 4 17.545 32.878 -2.408 1.00 40.76 C
ATOM 60 HD1 PHE A 4 16.673 32.232 -2.509 1.00 0.00 H
ATOM 61 CD2 PHE A 4 19.881 33.258 -2.648 1.00 35.13 C
ATOM 62 HD2 PHE A 4 20.857 32.941 -3.015 1.00 0.00 H
ATOM 63 CE1 PHE A 4 17.397 34.138 -1.889 1.00 36.49 C
ATOM 64 HE1 PHE A 4 16.400 34.520 -1.669 1.00 0.00 H
ATOM 65 CE2 PHE A 4 19.757 34.474 -2.043 1.00 32.88 C
ATOM 66 HE2 PHE A 4 20.640 35.090 -1.873 1.00 0.00 H
ATOM 67 CZ PHE A 4 18.507 34.929 -1.643 1.00 43.95 C
ATOM 68 HZ PHE A 4 18.401 35.892 -1.144 1.00 0.00 H
END
here my code :
from Bio import PDB
from Bio.PDB import PICIO, PDBIO
from typing import TypedDict, Dict, Tuple
parser = PDB.PDBParser(PERMISSIVE=1, QUIET=1)
structure: PDB.Structure.Structure = parser.get_structure("prova", "example_short.pdb")
structure.atom_to_internal_coordinates()
chain: PDB.Chain.Chain = list(structure.get_chains())[0]
ic_chain: PDB.internal_coords.IC_Chain = chain.internal_coord
d: Dict[Tuple[PDB.internal_coords.AtomKey,
PDB.internal_coords.AtomKey,
PDB.internal_coords.AtomKey,
PDB.internal_coords.AtomKey],
PDB.internal_coords.Dihedron] = ic_chain.dihedra
cnt = 1
for key in d:
if key[0].akl[3] == 'N':
if key[1].akl[3] == 'CA':
if key[2].akl[3] == 'C':
if key[3].akl[3] == 'N':
print ('\n',cnt,' : ', [x.akl[3] for x in key], d[key].angle)
d[key].angle += 45
cnt += 1
cnt = 1
for key in d:
if key[0].akl[3] == 'N':
if key[1].akl[3] == 'CA':
if key[2].akl[3] == 'C':
if key[3].akl[3] == 'N':
print ('\n',cnt,' : ', [x.akl[3] for x in key], d[key].angle)
cnt += 1
structure.internal_to_atom_coordinates(verbose = True)
io = PDBIO()
io.set_structure(structure)
io.save('atom_coord.pdb', preserve_atom_numbering=True)
here an image of the original vs new quadripeptid (cartoon repr, just backbone) :
original is rainbowed one (blue to red), magenta is the new one
saved as atom_coord.pdb
I believe I changed φ (Phi) adding 45° since
Now, a φ angle is N-CA-C-N