def set_BBBB_dihe(self, pose, angle):
"""
set initial B-B-B angle for each residue to a certain value
pose : pyrosetta.Pose() object
angle : angle in degrees
works for any object with 1-bead backbone
"""
for i in range(2, pose.size() - 1):
pose.conformation().set_torsion_angle(
pyrosetta.AtomID(1, int(i - 1)), pyrosetta.AtomID(1, int(i)),
pyrosetta.AtomID(1, int(i + 1)),
pyrosetta.AtomID(1, int(i + 2)), angle * np.pi / 180)
return (pose)
def random_BBBB_dihe(self, pose):
"""
set random initial B-B-B-B angle for each residue
pose : pyrosetta.Pose() object
angle : angle in degrees
works for any object with 1-bead backbone
"""
for i in range(2, pose.size() - 1):
angle = np.random.rand() * 2 * np.pi
pose.conformation().set_torsion_angle(
pyrosetta.AtomID(1, int(i - 1)), pyrosetta.AtomID(1, int(i)),
pyrosetta.AtomID(1, int(i + 1)),
pyrosetta.AtomID(1, int(i + 2)), angle)
return (pose)
def __init__(self, pose, angle=180):
pyrosetta.rosetta.protocols.moves.Mover.__init__(self)
self.pose = pose
self.angle = angle
self.conf = pose.conformation()
self.torsions = []
self.atoms = [pyrosetta.AtomID(1, 1)]
for atom_1 in self.atoms:
# print("Working on", atom_1)
for atom_2 in self.get_neighbors(atom_1):
if self.is_new_atom(atom_2):
self.atoms.append(atom_2)
for atom_3 in self.get_neighbors(atom_2):
if [atom_1.rsd(), atom_1.atomno()
] == [atom_3.rsd(), atom_3.atomno()]:
continue
for atom_4 in self.get_neighbors(atom_3):
if [atom_2.rsd(), atom_2.atomno()
] == [atom_4.rsd(), atom_4.atomno()]:
continue
if pose.has_dof(
self.conf.atom_tree().torsion_angle_dof_id(
atom_1, atom_2, atom_3, atom_4, 0)):
if self.is_new_torsion(
[atom_1, atom_2, atom_3, atom_4]):
self.torsions.append(
[atom_1, atom_2, atom_3, atom_4])
else:
continue
def __init__(self, pose, angle=5):
pyrosetta.rosetta.protocols.moves.Mover.__init__(self)
self.pose = pose
self.angle = angle
self.conf = pose.conformation()
self.bond_angles = []
self.atoms = [pyrosetta.AtomID(1, 1)]
for atom_1 in self.atoms:
# print("Working on", atom_1)
for atom_2 in self.get_neighbors(atom_1):
if self.is_new_atom(atom_2):
self.atoms.append(atom_2)
for atom_3 in self.get_neighbors(atom_2):
# print("Angle Candidate:", atom_1, atom_2, atom_3)
if [atom_1.rsd(), atom_1.atomno()
] == [atom_3.rsd(), atom_3.atomno()]:
continue
if pose.has_dof(self.conf.atom_tree().bond_angle_dof_id(
atom_1, atom_2, atom_3, 0)):
if self.is_new_angle([atom_1, atom_2, atom_3]):
self.bond_angles.append([atom_1, atom_2, atom_3])
# print("Adding Bond Angle!")
# print("A1:", atom_1)
# print("A2:", atom_2)
# print("A3:", atom_3)
else:
continue
def __init__(self, pose, d_bond=0.1):
pyrosetta.rosetta.protocols.moves.Mover.__init__(self)
self.pose = pose
self.d_bond = d_bond
self.conf = pose.conformation()
self.bond_lengths = []
self.atoms = [pyrosetta.AtomID(1, 1)]
for atom_1 in self.atoms:
for atom_2 in self.get_neighbors(atom_1):
if self.is_new_atom(atom_2):
self.atoms.append(atom_2)
if pose.has_dof(self.conf.atom_tree().bond_length_dof_id(
atom_1, atom_2)):
if self.is_new_bond([atom_1, atom_2]):
self.bond_lengths.append([atom_1, atom_2])
else:
continue
def testCGSmallAngleMover():
pose = pyrosetta.pose_from_sequence(
'X[CG11x3:CGLower]X[CG11x3]X[CG11x3][CG11x3:CGUpper]')
x_old = pose.xyz(pyrosetta.AtomID(1, pose.size())).x
y_old = pose.xyz(pyrosetta.AtomID(1, pose.size())).y
z_old = pose.xyz(pyrosetta.AtomID(1, pose.size())).z
small_angle_mover = cg_pyrosetta.CG_movers.CGSmallAngleMover(pose)
for _ in range(200):
small_angle_mover.apply(pose)
x_new = pose.xyz(pyrosetta.AtomID(1, pose.size())).x
y_new = pose.xyz(pyrosetta.AtomID(1, pose.size())).y
z_new = pose.xyz(pyrosetta.AtomID(1, pose.size())).z
assert x_new != x_old
assert y_new != y_old
assert z_new != z_old
def get_neighbors(self, atom):
return (self.conf.bonded_neighbor_all_res(
pyrosetta.AtomID(atom.atomno(), atom.rsd())))
# Build PyMol visualizer
pymol = pyrosetta.PyMOLMover()
# pymol.apply(polyA)
pymol.apply(polyCG)
# Build Score Function
sf = pyrosetta.ScoreFunction()
sf.set_weight(pyrosetta.rosetta.core.scoring.mm_bend, 1)
sf.set_weight(pyrosetta.rosetta.core.scoring.mm_twist, 1)
sf.set_weight(pyrosetta.rosetta.core.scoring.fa_atr, 1)
sf.set_weight(pyrosetta.rosetta.core.scoring.fa_rep, 1)
# Build MoveMap
mm = pyrosetta.MoveMap()
mm.set(
pyrosetta.rosetta.core.id.DOF_ID(pyrosetta.AtomID(3, 2),
pyrosetta.rosetta.core.id.THETA), True)
# Build Minimizer
mini = pyrosetta.rosetta.protocols.minimization_packing.MinMover()
mini.score_function(sf)
mini.movemap(mm)
# Perturb angle
polyA.conformation().set_bond_angle(pyrosetta.AtomID(3, 2),
pyrosetta.AtomID(2, 2),
pyrosetta.AtomID(1, 2), 0.5)
polyCG.conformation().set_bond_angle(pyrosetta.AtomID(3, 2),
pyrosetta.AtomID(2, 2),
pyrosetta.AtomID(1, 2), 0.5)