def test_mm_twist():
# Set CG1-CG1-CG1-CG1 torsion
cg_pyrosetta.change_parameters.changeTorsionParameters(
{'CG2 CG1 CG1 CG2': [10, 6, 35]})
# Build 1-1 CG model
pose = pyrosetta.pose_from_sequence(
'X[CG31:CGLower]X[CG31]X[CG31]X[CG31]X[CG31]X[CG31]X[CG31]X[CG31:CGUpper]'
)
# Randomize torsion in backbone
randomize = cg_pyrosetta.CG_movers.randomizeBackBone(pose)
randomize.apply(pose)
# Scorefunction w/o mm_twist
scorefunction = pyrosetta.ScoreFunction()
scorefunction.set_weight(pyrosetta.rosetta.core.scoring.fa_atr, 1)
scorefunction.set_weight(pyrosetta.rosetta.core.scoring.fa_rep, 1)
# Scorefunction w/ mm_twist
scorefunction_mm = pyrosetta.ScoreFunction()
scorefunction_mm.set_weight(pyrosetta.rosetta.core.scoring.fa_atr, 1)
scorefunction_mm.set_weight(pyrosetta.rosetta.core.scoring.fa_rep, 1)
scorefunction_mm.set_weight(pyrosetta.rosetta.core.scoring.mm_twist, 1)
print(scorefunction(pose))
print(scorefunction_mm(pose))
assert not math.isclose(scorefunction(pose), scorefunction_mm(pose))
def main():
for s in range(10):
kt_i = 100
kt_anneal = [kt_i * (0.9)**i for i in range(50)]
obj = CGFoldingAlgorithm(
'X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]X[CG11]',
file_name='outputs/traj_anneal.pdb')
obj.add_folding_move('default', obj.pymol)
obj.PDB_writer.stride(2000)
obj.small.angle = 180
obj.shear.angle = 180
obj.add_folding_move('default', obj.PDB_writer)
obj.run_anneal_fold('default', 150, kt_anneal)
obj.mc.lowest_score_pose().dump_pdb('outputs/11_lowest_energy_' +
str(s) + '.pdb')
lj_scorefxn = pyrosetta.ScoreFunction()
lj_scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_twist, 0.1)
lj_scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_inter_rep,
1)
lj_scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_inter_atr,
1)
lj_scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_intra_rep,
1)
lj_scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_intra_atr,
1)
with open('outputs/11_lowest_energy_' + str(s) + '.pdb', 'a') as f:
f.write('# LJ Energy : ' +
str(lj_scorefxn(obj.mc.lowest_score_pose())))
def build_energy_function(self, score_term_weight_map):
score = pyrosetta.ScoreFunction()
for term in score_term_weight_map.keys():
if term in self.methods.keys():
score.set_weight(
eval('pyrosetta.rosetta.core.scoring.' + term),
score_term_weight_map[term])
else:
warnings.warn(
"Energy Term not implemented :" + term +
"\n Skipping term", UserWarning)
return (score)
def build_scorefxn(cgmodel, mm=False):
"""
Given a cgmodel class object, this function uses its definitions to build a PyRosetta scoring function.
(Used to confirm energetic agreement between PyRosetta and OpenMM for identical model parameters and an identical structural ensemble.)
Parameters
----------
cgmodel: CGModel() class object
Returns
-------
scorefxn: A PyRosetta ScoreFunction() class object, containing all scoring function components that are defined/requested within the cgmodel() class object.
"""
scorefxn = pyrosetta.ScoreFunction()
if mm:
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_intra_rep, 1)
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_intra_atr, 1)
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_inter_atr, 1)
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_inter_rep, 1)
else:
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_elec, 1)
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_rep, 1)
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_atr, 1)
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_intra_atr, 1)
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_intra_rep, 1)
cg_pyrosetta.change_parameters.changeTorsionParameters({
'CG1 CG1 CG1 CG1': [0, 0, 0],
'CG2 CG1 CG1 CG2': [0, 0, 0],
'CG2 CG1 CG1 CG1': [0, 0, 0],
'X CG2 CG1 CG1': [0, 0, 0]
})
cg_pyrosetta.change_parameters.changeAngleParameters({
'CG1 CG1 CG1': [0, 0],
'CG2 CG1 CG1': [0, 0],
'CG1 CG1 CG2': [0, 0],
'X CG2 CG1': [0, 0]
})
# scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_twist, 0.1)
return (scorefxn)
def build_scorefxn(cgmodel):
"""
Given a cgmodel class object, this function uses its definitions to build a PyRosetta scoring function.
(Used to confirm energetic agreement between PyRosetta and OpenMM for identical model parameters and an identical structural ensemble.)
Parameters
----------
cgmodel: CGModel() class object
Returns
-------
scorefxn: A PyRosetta ScoreFunction() class object, containing all scoring function components that are defined/requested within the cgmodel() class object.
"""
scorefxn = pyrosetta.ScoreFunction()
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_atr, 1)
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_rep, 1)
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_intra_atr, 1)
scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_intra_rep, 1)
# scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_twist, 0.1)
return(scorefxn)
def setup_scorefxn():
py.init()
scorefxn = py.ScoreFunction()
fa_rep = py.rosetta.core.scoring.ScoreType.fa_rep
scorefxn.set_weight(fa_rep, 1.0)
return scorefxn
small_sc_mover.angle = 180
# repeat_sc_mover = pyrosetta.RepeatMover(small_sc_mover, 5)
# folding_object.add_folding_move('AngleMC', repeat_sc_mover)
small_bb_angle_mover = cg_pyrosetta.CG_movers.CGSmallAngleMover(
folding_object.pose)
small_bb_angle_mover.angle = 10
# repeat_bb_angle_mover = pyrosetta.RepeatMover(small_bb_angle_mover, 2)
# folding_object.add_folding_move('AngleMC', repeat_bb_angle_mover)
# Adding a PyMOL object to the folding sequence so we can see output
folding_object.add_folding_move(
'AngleMC', pyrosetta.RepeatMover(folding_object.mini, 10))
pymol = pyrosetta.PyMOLMover()
folding_object.add_folding_move('AngleMC', pymol)
# Runs a folding MC simulation with 200 repeats of the 'default' folder at each kt
folding_object.run_anneal_fold('AngleMC', 10, kt_anneal)
# Dump the lowest energy structure from the MC simulation
folding_object.mc.lowest_score_pose().dump_pdb(
'fold_from_sequence_output/' + names[i] + '_example_angles_' +
str(rep) + '.pdb')
twist_score = pyrosetta.ScoreFunction()
twist_score.set_weight(pyrosetta.rosetta.core.scoring.mm_twist, 1)
# print(twist_score(folding_object.pose))
def __init__(self,
sequence,
BBB_angle=120,
BBBB_dihe=180,
file_name='outputs/traj.pdb',
energy_graph_output=False):
"""
folding object used for easily implementing different
movers into a single folding algorithm.
Arguments
---------
sequence : str
Sequence of CG residues
BBB_angle : float
Desired angle of all B-B-B angles. Generalizes to all backbone models (not working)
BBBB_angle : float
Desired dihedral of all B-B-B-B torsion angles. Generalizes to all backbone models (not working)
"""
# Build CG model and set desired initial angles
self.pose = pyrosetta.pose_from_sequence(sequence, auto_termini=False)
self.energy_graph_output = energy_graph_output
# self.pose = self.set_BBB_angles(self.pose, BBB_angle)
# self.pose = self.set_BBBB_dihe(self.pose, BBBB_dihe)
# PyMOL mover, if wanting to visualize
self.pymol = pyrosetta.PyMOLMover()
self.pymol.apply(self.pose)
# randomizer = CG_movers.randomizeBackBone(self.pose)
# randomizer.apply(self.pose)
self.pymol.apply(self.pose)
# Building PDBTrajWriter object, used for writing multiple structures
# to a single file
self.PDB_writer = pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder(
)
# self.PDB_writer.apply(self.pose) # write initial structure
self.PDB_writer.file_name('outputs/traj.pdb')
self.PDB_writer.stride(100)
# Define scorefunction terms
self.scorefxn = pyrosetta.ScoreFunction()
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_rep, 1)
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_atr, 1)
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_intra_atr,
1)
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.fa_intra_rep,
1)
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_twist, 1)
self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_bend, 1)
# self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_inter_rep, 1) # segfaults beware!
# self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_inter_atr, 1)
# self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_intra_rep, 1)
# self.scorefxn.set_weight(pyrosetta.rosetta.core.scoring.mm_lj_intra_atr, 1)
# Build standard CG 1-1 movers
self.small = CG_movers.CGSmallMover(self.pose)
# self.shear = CG_movers.CGShearMover(self.pose)
self.small_angle = CG_movers.CGSmallAngleMover(self.pose)
# Build minimization movers
self.mini = pyrosetta.rosetta.protocols.minimization_packing.MinMover()
self.mini.min_type('lbfgs_armijo_nonmonotone')
self.movemap = pyrosetta.MoveMap()
self.mini.score_function(self.scorefxn)
# for atom in self.small_angle.bb_atoms:
# self.movemap.set(pyrosetta.rosetta.core.id.DOF_ID(atom , pyrosetta.rosetta.core.id.THETA), True)
self.movemap.set_bb_true_range(1, self.pose.size())
self.mini.movemap(self.movemap)
# Build MC object + Trial Mover (empty for now)
self.mc = pyrosetta.MonteCarlo(self.pose, self.scorefxn, 1)
self.trial_mc = pyrosetta.TrialMover()
# Building variable to store various folding algorithms
self.folding_protocols = {}
# Adding a default mover
self.build_fold_alg('default')
self.add_folding_move('default', pyrosetta.RepeatMover(self.small, 10))
# self.add_folding_move('default', pyrosetta.RepeatMover(self.shear, 10))
self.add_folding_move('default', pyrosetta.RepeatMover(self.mini, 10))
def score_function():
score = pyrosetta.ScoreFunction()
score.set_weight(pyrosetta.rosetta.core.scoring.fa_atr, 1)
score.set_weight(pyrosetta.rosetta.core.scoring.fa_rep, 1)
return (score)
def load_score_fxn_with_weights(filename):
filename = str(filename)
sf = pyrosetta.ScoreFunction()
sf.add_weights_from_file(filename)
return sf
import pyrosetta
cg_pyrosetta.pyrosetta.init("-extra_mm_params_dir mm_atom_type_sets")
# Build models
polyA = pyrosetta.pose_from_sequence('AAAAAAAA')
polyCG = pyrosetta.pose_from_sequence(
'X[CG31:CGLower]X[CG31]X[CG31]X[CG31]X[CG31:CGUpper]')
# 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)