def rotate_residue(mol, bond_number, angle):
# --- Identify rotatable bonds ---
rotatable_bonds = struc.find_rotatable_bonds(mol.bonds)
# --- do not rotate about backbone bonds ---
for atom_name in BACKBONE:
index = np.where(mol.atom_name == atom_name)[0][0]
rotatable_bonds.remove_bonds_to(index)
# --- init coordinates for new model ---
coord = mol.coord.copy()
# --- get bond axis ---
atom_i, atom_j, _ = rotatable_bonds.as_array()[bond_number]
axis = coord[atom_j] - coord[atom_i]
# --- get support atom ---
support = coord[atom_i]
# --- need to get atoms only on one side of the bond ---
bond_list_without_axis = mol.bonds.copy()
bond_list_without_axis.remove_bond(atom_i, atom_j)
rotated_atom_indices = struc.find_connected(bond_list_without_axis,
root=atom_j)
# --- rotate atoms ---
coord[rotated_atom_indices] = struc.rotate_about_axis(
coord[rotated_atom_indices], axis, angle, support)
atom_list = []
for i, atom_i in enumerate(mol):
atom_new = struc.Atom(coord[i],
atom_name=atom_i.atom_name,
element=atom_i.element)
atom_list.append(atom_new)
new_mol = struc.array(atom_list)
new_mol.res_id[:] = mol.res_id
new_mol.res_name[:] = mol.res_name
new_mol.bonds = mol.bonds.copy()
return new_mol
def test_find_rotatable_bonds(res_name, expected_bonds):
"""
Check the :func:`find_rotatable_bonds()` function based on
known examples.
"""
molecule = info.residue(res_name)
ref_bond_set = {
tuple(sorted((name_i, name_j)))
for name_i, name_j in expected_bonds
}
rotatable_bonds = struc.find_rotatable_bonds(molecule.bonds)
test_bond_set = set()
for i, j, _ in rotatable_bonds.as_array():
test_bond_set.add(
tuple(sorted((molecule.atom_name[i], molecule.atom_name[j]))))
# Compare with reference bonded atom names
assert test_bond_set == ref_bond_set
# All rotatable bonds must be single bonds
assert np.all(rotatable_bonds.as_array()[:, 2] == struc.BondType.SINGLE)
import biotite.structure as struc
import biotite.structure.io as strucio
import biotite.structure.info as info
import biotite.structure.graphics as graphics
# 'CA' is not in backbone,
# as we want to include the rotation between 'CA' and 'CB'
BACKBONE = ["N", "C", "O", "OXT"]
LIBRARY_SIZE = 9
# Get the structure (including bonds) from the standard RCSB compound
residue = info.residue("TYR")
bond_list = residue.bonds
### Identify rotatable bonds ###
rotatable_bonds = struc.find_rotatable_bonds(residue.bonds)
# Do not rotate about backbone bonds,
# as these are irrelevant for a amino rotamer library
for atom_name in BACKBONE:
index = np.where(residue.atom_name == atom_name)[0][0]
rotatable_bonds.remove_bonds_to(index)
print("Rotatable bonds in tyrosine:")
for atom_i, atom_j, _ in rotatable_bonds.as_array():
print(residue.atom_name[atom_i] + " <-> " + residue.atom_name[atom_j])
### VdW radii of each atom, required for the next step ###
vdw_radii = np.zeros(residue.array_length())
for i, element in enumerate(residue.element):
vdw_radii[i] = info.vdw_radius_single(element)
# The Minimum required distance between two atoms is mean of their
# VdW radii