I do not know if there is a function in Biopython.PDB for dihedral space transformations, but due to the lack of answers I would say no. Biopython.PDB is nice and clean, but I would use something with more molecular mechanics power... or should I say potential (:drum::laughing:).
Personally, I use PyRosetta, but it is not open source (code available to academics), so others may opt for OpenForceField.
PyRosetta requires a licence (free for academia), which is different from the Rosetta proper licence.
The code below uses a helper module I wrote, so I'll use the installer therein (which is shorthand for the official pip wheel, which provides different options etc., while the official shorthand is actually pyrosettacolabsetup)
pip3 install pyrosetta-help
install_pyrosetta -u 👾👾👾 -p 👾👾👾
Ligands?
First lets make sure there's nothing interesting ligand wise.
NB. RCSB has a new shiny API which may be better... Not tried it: currently using European.
import requests
def retrieve_nonpolymer_data(entry_id: str) -> dict:
"""cf. https://www.ebi.ac.uk/pdbe/api/doc/"""
response: requests.Response = requests.get(f' https://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/{entry_id.lower()}')
response.raise_for_status()
return response.json()[entry_id.lower()]
info = retrieve_nonpolymer_data('1enh')
chem_resns = [c for entity in info for c in entity.get('chem_comp_ids', [])]
print(chem_resns) # ['HOH']
If is were something that is not water, I made a list here, which is based off Peter Curran's repo for the HotSpots algorithm, which allows the elimination of worthless ligands like glycol.
I mention this because the route differs if there is a ligand.
Init and read
import pyrosetta
import pyrosetta_help as ph
from types import ModuleType
logger = ph.configure_logger()
pyrosetta.init(extra_options=ph.make_option_string(no_optH=False,
ex1=None,
ex2=None,
#mute='all',
ignore_unrecognized_res=True,
load_PDB_components=False,
ignore_waters=True)
)
# shorthand for sanity
prc: ModuleType = pyrosetta.rosetta.core
# this route strips ligands
pose: Pyrosetta.Pose = pyrosetta.toolbox.pose_from_rcsb('1enh')
Note ignore_unrecognized_res, load_PDB_components and ignore_waters.
Angles
This will not happen to an non-Rosetta user, but I get tripped out by the fact that ψ & φ data is not stored in residue, but in the pose.
for residue in pose.residues: #: prc.conformation.Residue
# residue.get_phi() # ---> Error!
pass
For the residue index in pose, Rosetta was written in Fortran so is one-indexed.
import numpy as np
import numpy.typing as npt
phi:npt.NDArray[float] = np.fromiter(map(pose.phi, range(1, pose.total_residue()+1)), dtype=float)
psi:npt.NDArray[float] = np.fromiter(map(pose.psi, range(1, pose.total_residue()+1)), dtype=float)
Change φ/ψ angles
Time for some fun in dihedral space, say:
r = 2
phi = 180
pose.set_phi(r, phi)
For modelling, I wrote some code for setting spans with the archetypical angles for different SS: here. I do not recall whence the data came (maybe Wikipedia?), but it may be handy anyway.
Save
To save a PDB file:
pose.dump_pdb('👾👾👾.pdb')
There is also pose.dump_scored_pdb, but that is only for friends of J. Willard Gibbs.
Minimisation
It is said in the comments that energy minimisation is not required. But here is a snippet that minimises the sidechains only
scorefxn = pyrosetta.get_fa_scorefxn() # ref2015 will do.
before: float = scorefxn(pose)
cycles = 5
movemap = pyrosetta.MoveMap()
movemap.set_bb(False) # backbone
movemap.set_chi(True) # sidechain
relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn, cycles)
relax.set_movemap(movemap)
relax.apply(pose)
after: float = scorefxn(pose)
print(after - before) # Willard says "Remember free energy is a potential so it should be negative"
If the BB tweaks are minimal, there's also the option of scoring/minimising against the electron density etc.
