Being able to specify N/C terminus as the ‘mobile’ part is easier to think about!
If I understand correctly, I need to pass the correct side of the bond for being smaller to make use of the “move_smaller_side” argument.
So, if I’m looking at the C-alpha, then the psi angle would be on the N-terminal side and the phi angle would be on the C-terminal side?
So I’ve got this written up (can’t afford to get fancy at the moment) to just assign the angles and move either the N/C terminal side:
def straighten_v2(session, mobile_sel, mobile_terminal, noise=5.0):
"""
Args:
mobile_sel (selection): selection of residue regions to be moved, must be a
single
contiguous region
mobile_terminal (str): 'N' or 'C' terminal side
noise (float): gaussian standard deviation to 'jitter' angles
"""
import random
mobile_terminal = mobile_terminal.upper()
assert mobile_terminal.lower() in (
"c",
"n",
), "mobile_terminal can only be N or C"
for i, res in enumerate(mobile_sel):
# find backbone C-alpha
atom = res.find_atom("CA")
# handle proline differently (for now)
if res.name != "PRO":
# bond.smaller_side returns the atom that is on the smaller side
for nb, bond in zip(atom.neighbors, atom.bonds):
# look at peptide bond atoms only (no beta-carbons)
if nb.name == "N":
# N-CA -> psi bond (N-terminal)
move_smaller_psi = (
bond.smaller_side.name == mobile_terminal
)
elif nb.name == "C":
# Ca-C -> phi bond (C-terminal)
move_smaller_phi = (
bond.smaller_side.name == mobile_terminal
)
psi_assgn = random.normalvariate(mu=165.0, sigma=noise)
phi_assgn = random.normalvariate(mu=-165.0, sigma=noise)
res.set_psi(psi_assgn, move_smaller_side=move_smaller_psi)
res.set_phi(phi_assgn, move_smaller_side=move_smaller_phi)
It seems to work correctly in some small test cases… but I’ve got a feeling that I did not implement what you meant properly. Is this roughly what you were thinking?