def test_find_connected(bond_list):
"""
Find all connected atoms to an atom in a known example.
"""
for index in (0, 1, 2, 3, 4, 6):
assert struc.find_connected(bond_list,
index).tolist() == [0, 1, 2, 3, 4, 6]
assert struc.find_connected(bond_list, 5).tolist() == [5]
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
# Coordinates for the current rotamer model
coord = residue.coord.copy()
for atom_i, atom_j, _ in rotatable_bonds.as_array():
# The bond axis
axis = coord[atom_j] - coord[atom_i]
# Position of one of the involved atoms
support = coord[atom_i]
# Only atoms at one side of the rotatable bond should be moved
# So the original Bondist is taken...
bond_list_without_axis = residue.bonds.copy()
# ...the rotatable bond is removed...
bond_list_without_axis.remove_bond(atom_i, atom_j)
# ...and these atoms are found by identifying the atoms that
# are still connected to one of the two atoms involved
rotated_atom_indices = struc.find_connected(bond_list_without_axis,
root=atom_i)
accepted = False
while not accepted:
# A random angle between 0 and 360 degrees
angle = np.random.rand() * 2 * np.pi
# Rotate
coord[rotated_atom_indices] = struc.rotate_about_axis(
coord[rotated_atom_indices], axis, angle, support)
# Check if the atoms clash with each other:
# The distance between each pair of atoms must be larger
# than the sum of their VdW radii, if they are not bonded to
# each other
accepted = True
distances = struc.distance(coord[:, np.newaxis],
def test_find_connected(bond_list):
for index in (0,1,2,3,4,6):
assert struc.find_connected(bond_list, index).tolist() == [0,1,2,3,4,6]
assert struc.find_connected(bond_list, 5).tolist() == [5]
# Get the structure (including bonds) from the standard RCSB compound
residue = info.residue("TYR")
bond_list = residue.bonds
### Identify rotatable bonds ###
rotatable_bonds = []
for atom1, atom2, bond_type in bond_list.as_array():
# Can only rotate about single bonds
if bond_type != struc.BondType.SINGLE:
continue
segmented = bond_list.copy()
segmented.remove_bond(atom1, atom2)
conn_atoms1 = struc.find_connected(segmented, atom1)
conn_atoms2 = struc.find_connected(segmented, atom2)
# Rotation makes no sense if one of the atoms is a terminal atom,
# e.g. a hydrogen
if len(conn_atoms1) == 1 or len(conn_atoms2) == 1:
continue
# A bond cannot be rotated in a trivial way,
# if it is inside a cyclic structure
is_circular = atom2 in struc.find_connected(segmented, atom1)
if is_circular:
continue
# Do not rotate about backbone bonds,
# as these are irrelevant for a amino rotamer library