Hi, I am trying to implement the Generalized Simulated Annealing routine (Tsalis et al, 1996) and apply it on folding processes.
To do so, I code the mover w.r.t. dihedral angles (each step phi and psi sufer a small, guided perturbation). I am using the pose.set_phi and .set_psi methods to modify pose coordinates.
The problem:
When I do apply the Mover, it wont modify the pose at all. I alread tried several approaches to overload the Mover class, but none of them work. The last atempt will be down here. I also tried modifying the "Basic folding" example to move with all phi and psi at once, but it didn't worked as well. It, strangely, only works if, at each step, I change only phi and psi of one residue (in the same fashion as the basic folding example).
The code:
class GSAMover(pyrosetta.rosetta.protocols.moves.Mover):
"""
GSA Mover:
"""
def __init__(self, **kwargs):
pyrosetta.rosetta.protocols.moves.Mover.__init__(self)
# . . . Just poping parameters from kwargs
def fetch_dihedrals(self, pose):
''' Get protein's dihedral angles '''
seqLen = len(pose.sequence())
dih = np.empty((seqLen,2))
for i in range(seqLen):
dih[i,] = np.asarray([pose.phi(i+1),pose.psi(i+1)])
return dih
def modify_type1(self, pose):
dihs = self.fetch_dihedrals(pose)
# x + g(r)
dihs = np.add(dihs, np.degrees(self.g(self.r_i)))
for i,dih in enumerate(dihs[1:]):
pose.set_phi(i+2,dih[0])
pose.set_psi(i+2,dih[1])
return pose
def apply(self, pose):
"""Applies move to pose."""
self.best_pose = Pose()
self.previous_pose = Pose()
#pose = pose.get()
for self.epoch in range(self.max_iter):
if self.epoch == 0:
self.best_pose.assign(pose)
self.previous_pose.assign(pose)
self.pose_zero = Pose()
self.pose_zero.assign(pose)
self.pose_modified = Pose()
self.pose_modified.assign(self.modifyPose(pose))
pose.assign(self.decisionCriteria(self.pose_modified,
self.pose_zero))
if self.verbose:
print('** Runing iteration: {}'.format(self.epoch))
if self.score(pose) < self.score(self.best_pose):
self.best_pose.assign(pose)
self.log['temperature'].append(self.tqt)
self.log['g'].append(self.g(self.r_i))
self.previous_pose.assign(pose)
Are there any other steps/methods required for me to move the pose?
Thank you for your attention.