How do I translate an atom using Biopython? The transform method is throwing error
I am trying to transform the coordinates of atom but when I am using random vector; I am getting this error -
rotation = rotmat(pi, Vector(np.random.rand(3,1)))
File "/home/sanu/.local/lib/python3.8/site-packages/Bio/PDB/vectors.py", line 204, in rotmat
rot = numpy.dot(refmat(q, -p), refmat(p, -p))
File "/home/sanu/.local/lib/python3.8/site-packages/Bio/PDB/vectors.py", line 167, in refmat
q = q.normalized()
AttributeError: 'float' object has no attribute 'normalized'
for model in simulation_pdb:
for chain in model:
if chain.get_id() == "Y":
for residue in chain:
for atom in residue:
#translation = np.random.rand(3,1)
#rotation = rotmat(pi, Vector(np.random.rand(3,1)))
translation = array((np.random.rand(3,1)), 'f')
rotation = rotmat(np.pi, array(np.random.rand(3,1)))
atom.transform(rotation, translation)
print(atom, atom.get_vector())
In case of the above code (as it is, no random vector), I am getting this error -
rotation = rotmat(np.pi, array(np.random.rand(3,1)))
File "/home/sanu/.local/lib/python3.8/site-packages/Bio/PDB/vectors.py", line 204, in rotmat
rot = numpy.dot(refmat(q, -p), refmat(p, -p))
File "/home/sanu/.local/lib/python3.8/site-packages/Bio/PDB/vectors.py", line 166, in refmat
p = p.normalized()
AttributeError: 'numpy.ndarray' object has no attribute 'normalized'
What am I doing wrong here? Seems like the transform function is expecting some other datatype; which I don't know.
Edit1 - from Biopython's documentation - biopython/Bio/PDB/Atom.py Line 422
def transform(self, rot, tran):
"""Apply rotation and translation to the atomic coordinates.
:param rot: A right multiplying rotation matrix
:type rot: 3x3 Numeric array
:param tran: the translation vector
:type tran: size 3 Numeric array
Examples
--------
This is an incomplete but illustrative example::
from numpy import pi, array
from Bio.PDB.vectors import Vector, rotmat
rotation = rotmat(pi, Vector(1, 0, 0))
translation = array((0, 0, 1), 'f')
atom.transform(rotation, translation)
"""
self.coord = np.dot(self.coord, rot) + tran
Solution
OK kind of late but, my attempt; given input as (pymol generated peptide no
real folding at all) avgwpt_A.pdb :
ATOM 1 N ALA A 1 67.846 51.727 15.161 1.00 0.00 N
ATOM 2 CA ALA A 1 68.522 53.021 15.161 1.00 0.00 C
ATOM 3 C ALA A 1 70.022 52.847 15.161 1.00 0.00 C
ATOM 4 O ALA A 1 70.553 51.730 15.150 1.00 0.00 O
ATOM 5 CB ALA A 1 68.014 53.813 16.378 1.00 0.00 C
ATOM 6 N VAL A 2 70.773 53.896 15.173 1.00 0.00 N
ATOM 7 CA VAL A 2 72.223 53.728 15.173 1.00 0.00 C
ATOM 8 C VAL A 2 72.922 55.066 15.188 1.00 0.00 C
ATOM 9 O VAL A 2 72.296 56.134 15.198 1.00 0.00 O
ATOM 10 CB VAL A 2 72.665 52.877 13.916 1.00 0.00 C
ATOM 11 CG1 VAL A 2 74.193 52.762 13.664 1.00 0.00 C
ATOM 12 CG2 VAL A 2 72.143 51.420 13.932 1.00 0.00 C
ATOM 13 N GLY A 3 74.212 55.098 15.190 1.00 0.00 N
ATOM 14 CA GLY A 3 74.888 56.392 15.204 1.00 0.00 C
ATOM 15 C GLY A 3 76.388 56.218 15.203 1.00 0.00 C
ATOM 16 O GLY A 3 76.917 55.104 15.192 1.00 0.00 O
ATOM 17 N LEU A 4 77.138 57.267 15.215 1.00 0.00 N
ATOM 18 CA LEU A 4 78.589 57.099 15.215 1.00 0.00 C
ATOM 19 C LEU A 4 79.288 58.437 15.230 1.00 0.00 C
ATOM 20 O LEU A 4 78.660 59.507 15.241 1.00 0.00 O
ATOM 21 CB LEU A 4 79.040 56.251 13.992 1.00 0.00 C
ATOM 22 CG LEU A 4 78.445 54.825 13.832 1.00 0.00 C
ATOM 23 CD1 LEU A 4 79.094 54.113 12.637 1.00 0.00 C
ATOM 24 CD2 LEU A 4 78.610 53.968 15.098 1.00 0.00 C
ATOM 25 N TRP A 5 80.577 58.469 15.232 1.00 0.00 N
ATOM 26 CA TRP A 5 81.254 59.763 15.246 1.00 0.00 C
ATOM 27 C TRP A 5 82.754 59.589 15.245 1.00 0.00 C
ATOM 28 O TRP A 5 83.281 58.478 15.233 1.00 0.00 O
ATOM 29 CB TRP A 5 80.817 60.551 16.512 1.00 0.00 C
ATOM 30 CG TRP A 5 79.341 60.958 16.536 1.00 0.00 C
ATOM 31 CD1 TRP A 5 78.304 60.258 17.187 1.00 0.00 C
ATOM 32 CD2 TRP A 5 78.731 62.003 15.872 1.00 0.00 C
ATOM 33 CE2 TRP A 5 77.340 61.929 16.130 1.00 0.00 C
ATOM 34 CE3 TRP A 5 79.257 63.017 15.031 1.00 0.00 C
ATOM 35 NE1 TRP A 5 77.049 60.848 16.950 1.00 0.00 N
ATOM 36 CZ2 TRP A 5 76.464 62.876 15.556 1.00 0.00 C
ATOM 37 CZ3 TRP A 5 78.372 63.946 14.482 1.00 0.00 C
ATOM 38 CH2 TRP A 5 76.996 63.879 14.742 1.00 0.00 C
ATOM 39 N PRO A 6 83.505 60.638 15.257 1.00 0.00 N
ATOM 40 CA PRO A 6 84.959 60.560 15.257 1.00 0.00 C
ATOM 41 C PRO A 6 85.498 60.036 16.599 1.00 0.00 C
ATOM 42 O PRO A 6 84.724 59.735 17.507 1.00 0.00 O
ATOM 43 CB PRO A 6 85.354 62.018 14.978 1.00 0.00 C
ATOM 44 CG PRO A 6 84.201 62.829 15.588 1.00 0.00 C
ATOM 45 CD PRO A 6 82.967 61.980 15.271 1.00 0.00 C
ATOM 46 N THR A 7 86.770 59.913 16.774 1.00 0.00 N
ATOM 47 CA THR A 7 87.263 59.414 18.054 1.00 0.00 C
ATOM 48 C THR A 7 88.771 59.342 18.062 1.00 0.00 C
ATOM 49 O THR A 7 89.436 59.668 17.100 1.00 0.00 O
ATOM 50 CB THR A 7 86.639 58.014 18.376 1.00 0.00 C
ATOM 51 CG2 THR A 7 87.080 57.358 19.702 1.00 0.00 C
ATOM 52 OG1 THR A 7 85.224 58.110 18.479 1.00 0.00 O
TER
END
pic :
with this code :
import Bio
print('########## Biopython VERSION ##########################################')
print('\n\n BIOPYTHON_VERSION : ', Bio.__version__)
print('###################################################################')
from Bio.PDB import (
PDBParser,
Atom,
PDBIO
)
import numpy as np
import random
from Bio.PDB.vectors import Vector, rotmat
structure_code = 'avgwpt_A'
structure_name = structure_code
parser_pdb= PDBParser(QUIET=False) ### shows warnings
structure_whole = parser_pdb.get_structure(structure_name, structure_name+".pdb")
translation = np.random.rand(3)
print('--------------------')
print('translation : ', translation)
print('--------------------')
p = Vector(random.uniform(0, 1), random.uniform(0, 1), random.uniform(0, 1))
q = Vector(random.uniform(0, 1), random.uniform(0, 1), random.uniform(0, 1))
rotation = rotmat(p,q)
print('rotation : ', rotation)
print('--------------------')
structure_whole_copy = structure_whole.copy()
for model in structure_whole_copy :
for chain in model:
if chain.get_id() == "A":
chain.id = 'B'
for residue in chain:
for atom in residue:
atom.transform(rotation, translation)
for model in structure_whole_copy :
for chain in model:
chain.detach_parent()
structure_whole[0].add(chain)
io=PDBIO()
io.set_structure(structure_whole)
io.save(structure_name+"_transformed.pdb" , preserve_atom_numbering = False)
output , one example , given the random translation/rotation avgwpt_A_transformed.pdb:
ATOM 1 N ALA A 1 67.846 51.727 15.161 1.00 0.00 N
ATOM 2 CA ALA A 1 68.522 53.021 15.161 1.00 0.00 C
ATOM 3 C ALA A 1 70.022 52.847 15.161 1.00 0.00 C
ATOM 4 O ALA A 1 70.553 51.730 15.150 1.00 0.00 O
ATOM 5 CB ALA A 1 68.014 53.813 16.378 1.00 0.00 C
ATOM 6 N VAL A 2 70.773 53.896 15.173 1.00 0.00 N
ATOM 7 CA VAL A 2 72.223 53.728 15.173 1.00 0.00 C
ATOM 8 C VAL A 2 72.922 55.066 15.188 1.00 0.00 C
ATOM 9 O VAL A 2 72.296 56.134 15.198 1.00 0.00 O
ATOM 10 CB VAL A 2 72.665 52.877 13.916 1.00 0.00 C
ATOM 11 CG1 VAL A 2 74.193 52.762 13.664 1.00 0.00 C
ATOM 12 CG2 VAL A 2 72.143 51.420 13.932 1.00 0.00 C
ATOM 13 N GLY A 3 74.212 55.098 15.190 1.00 0.00 N
ATOM 14 CA GLY A 3 74.888 56.392 15.204 1.00 0.00 C
ATOM 15 C GLY A 3 76.388 56.218 15.203 1.00 0.00 C
ATOM 16 O GLY A 3 76.917 55.104 15.192 1.00 0.00 O
ATOM 17 N LEU A 4 77.138 57.267 15.215 1.00 0.00 N
ATOM 18 CA LEU A 4 78.589 57.099 15.215 1.00 0.00 C
ATOM 19 C LEU A 4 79.288 58.437 15.230 1.00 0.00 C
ATOM 20 O LEU A 4 78.660 59.507 15.241 1.00 0.00 O
ATOM 21 CB LEU A 4 79.040 56.251 13.992 1.00 0.00 C
ATOM 22 CG LEU A 4 78.445 54.825 13.832 1.00 0.00 C
ATOM 23 CD1 LEU A 4 79.094 54.113 12.637 1.00 0.00 C
ATOM 24 CD2 LEU A 4 78.610 53.968 15.098 1.00 0.00 C
ATOM 25 N TRP A 5 80.577 58.469 15.232 1.00 0.00 N
ATOM 26 CA TRP A 5 81.254 59.763 15.246 1.00 0.00 C
ATOM 27 C TRP A 5 82.754 59.589 15.245 1.00 0.00 C
ATOM 28 O TRP A 5 83.281 58.478 15.233 1.00 0.00 O
ATOM 29 CB TRP A 5 80.817 60.551 16.512 1.00 0.00 C
ATOM 30 CG TRP A 5 79.341 60.958 16.536 1.00 0.00 C
ATOM 31 CD1 TRP A 5 78.304 60.258 17.187 1.00 0.00 C
ATOM 32 CD2 TRP A 5 78.731 62.003 15.872 1.00 0.00 C
ATOM 33 CE2 TRP A 5 77.340 61.929 16.130 1.00 0.00 C
ATOM 34 CE3 TRP A 5 79.257 63.017 15.031 1.00 0.00 C
ATOM 35 NE1 TRP A 5 77.049 60.848 16.950 1.00 0.00 N
ATOM 36 CZ2 TRP A 5 76.464 62.876 15.556 1.00 0.00 C
ATOM 37 CZ3 TRP A 5 78.372 63.946 14.482 1.00 0.00 C
ATOM 38 CH2 TRP A 5 76.996 63.879 14.742 1.00 0.00 C
ATOM 39 N PRO A 6 83.505 60.638 15.257 1.00 0.00 N
ATOM 40 CA PRO A 6 84.959 60.560 15.257 1.00 0.00 C
ATOM 41 C PRO A 6 85.498 60.036 16.599 1.00 0.00 C
ATOM 42 O PRO A 6 84.724 59.735 17.507 1.00 0.00 O
ATOM 43 CB PRO A 6 85.354 62.018 14.978 1.00 0.00 C
ATOM 44 CG PRO A 6 84.201 62.829 15.588 1.00 0.00 C
ATOM 45 CD PRO A 6 82.967 61.980 15.271 1.00 0.00 C
ATOM 46 N THR A 7 86.770 59.913 16.774 1.00 0.00 N
ATOM 47 CA THR A 7 87.263 59.414 18.054 1.00 0.00 C
ATOM 48 C THR A 7 88.771 59.342 18.062 1.00 0.00 C
ATOM 49 O THR A 7 89.436 59.668 17.100 1.00 0.00 O
ATOM 50 CB THR A 7 86.639 58.014 18.376 1.00 0.00 C
ATOM 51 CG2 THR A 7 87.080 57.358 19.702 1.00 0.00 C
ATOM 52 OG1 THR A 7 85.224 58.110 18.479 1.00 0.00 O
TER 53 THR A 7
ATOM 53 N ALA B 1 4.769 85.111 -17.356 1.00 0.00 N
ATOM 54 CA ALA B 1 4.366 86.307 -18.089 1.00 0.00 C
ATOM 55 C ALA B 1 5.440 87.367 -18.026 1.00 0.00 C
ATOM 56 O ALA B 1 6.507 87.185 -17.426 1.00 0.00 O
ATOM 57 CB ALA B 1 3.025 86.783 -17.506 1.00 0.00 C
ATOM 58 N VAL B 2 5.239 88.497 -18.615 1.00 0.00 N
ATOM 59 CA VAL B 2 6.277 89.521 -18.553 1.00 0.00 C
ATOM 60 C VAL B 2 5.855 90.764 -19.299 1.00 0.00 C
ATOM 61 O VAL B 2 4.760 90.847 -19.870 1.00 0.00 O
ATOM 62 CB VAL B 2 7.631 88.949 -19.135 1.00 0.00 C
ATOM 63 CG1 VAL B 2 8.790 89.968 -19.315 1.00 0.00 C
ATOM 64 CG2 VAL B 2 8.231 87.791 -18.302 1.00 0.00 C
ATOM 65 N GLY B 3 6.661 91.771 -19.344 1.00 0.00 N
ATOM 66 CA GLY B 3 6.253 92.973 -20.065 1.00 0.00 C
ATOM 67 C GLY B 3 7.327 94.032 -20.003 1.00 0.00 C
ATOM 68 O GLY B 3 8.390 93.850 -19.405 1.00 0.00 O
ATOM 69 N LEU B 4 7.125 95.161 -20.592 1.00 0.00 N
ATOM 70 CA LEU B 4 8.164 96.186 -20.530 1.00 0.00 C
ATOM 71 C LEU B 4 7.742 97.429 -21.276 1.00 0.00 C
ATOM 72 O LEU B 4 6.644 97.512 -21.847 1.00 0.00 O
ATOM 73 CB LEU B 4 9.508 95.635 -21.086 1.00 0.00 C
ATOM 74 CG LEU B 4 10.114 94.373 -20.414 1.00 0.00 C
ATOM 75 CD1 LEU B 4 11.485 94.055 -21.027 1.00 0.00 C
ATOM 76 CD2 LEU B 4 10.248 94.519 -18.890 1.00 0.00 C
ATOM 77 N TRP B 5 8.547 98.436 -21.321 1.00 0.00 N
ATOM 78 CA TRP B 5 8.139 99.638 -22.043 1.00 0.00 C
ATOM 79 C TRP B 5 9.214 100.697 -21.980 1.00 0.00 C
ATOM 80 O TRP B 5 10.274 100.515 -21.384 1.00 0.00 O
ATOM 81 CB TRP B 5 6.825 100.184 -21.418 1.00 0.00 C
ATOM 82 CG TRP B 5 5.606 99.274 -21.592 1.00 0.00 C
ATOM 83 CD1 TRP B 5 5.124 98.353 -20.639 1.00 0.00 C
ATOM 84 CD2 TRP B 5 4.815 99.108 -22.710 1.00 0.00 C
ATOM 85 CE2 TRP B 5 3.864 98.098 -22.424 1.00 0.00 C
ATOM 86 CE3 TRP B 5 4.846 99.731 -23.984 1.00 0.00 C
ATOM 87 NE1 TRP B 5 4.036 97.612 -21.136 1.00 0.00 N
ATOM 88 CZ2 TRP B 5 2.929 97.709 -23.408 1.00 0.00 C
ATOM 89 CZ3 TRP B 5 3.906 99.336 -24.937 1.00 0.00 C
ATOM 90 CH2 TRP B 5 2.960 98.341 -24.653 1.00 0.00 C
ATOM 91 N PRO B 6 9.013 101.827 -22.569 1.00 0.00 N
ATOM 92 CA PRO B 6 9.995 102.902 -22.558 1.00 0.00 C
ATOM 93 C PRO B 6 10.123 103.538 -21.163 1.00 0.00 C
ATOM 94 O PRO B 6 9.445 103.122 -20.224 1.00 0.00 O
ATOM 95 CB PRO B 6 9.422 103.865 -23.608 1.00 0.00 C
ATOM 96 CG PRO B 6 7.906 103.632 -23.526 1.00 0.00 C
ATOM 97 CD PRO B 6 7.795 102.123 -23.291 1.00 0.00 C
ATOM 98 N THR B 7 10.946 104.514 -20.977 1.00 0.00 N
ATOM 99 CA THR B 7 11.053 105.104 -19.647 1.00 0.00 C
ATOM 100 C THR B 7 12.063 106.226 -19.633 1.00 0.00 C
ATOM 101 O THR B 7 12.678 106.551 -20.629 1.00 0.00 O
ATOM 102 CB THR B 7 11.424 104.011 -18.588 1.00 0.00 C
ATOM 103 CG2 THR B 7 11.581 104.497 -17.131 1.00 0.00 C
ATOM 104 OG1 THR B 7 10.412 103.014 -18.524 1.00 0.00 O
TER 105 THR B 7
END
pic :
as per biopython//Bio/PDB/vectors.py line 180
code :
def rotmat(p, q):
"""Return a (left multiplying) matrix that rotates p onto q.
:param p: moving vector
:type p: L{Vector}
:param q: fixed vector
:type q: L{Vector}
:return: rotation matrix that rotates p onto q
:rtype: 3x3 NumPy array
Examples
--------
>>> from Bio.PDB.vectors import rotmat
>>> p, q = Vector(1, 2, 3), Vector(2, 3, 5)
>>> r = rotmat(p, q)
>>> print(q)
<Vector 2.00, 3.00, 5.00>
>>> print(p)
<Vector 1.00, 2.00, 3.00>
>>> p.left_multiply(r)
<Vector 1.21, 1.82, 3.03>
"""
rot = np.dot(refmat(q, -p), refmat(p, -p))
return rot
rotmat accepts args p and q as Vector (Bio.PDB.Vector) where Vector args does raise ValueError("Vector: x is not a list/tuple/array of 3 numbers") if not a list/tuple/array of 3 numbers ;
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