def __init__( self, scorefxn, steps, temp, cooling_rate ):
''' '''
assert isScoreFxn( scorefxn )
self._log = ""
self._scorefxn = scorefxn
self._steps = steps # MC steps per annealing cycle
self._temperature = temp
# declare objects
self.__fragidx_pose = FragIdxPose()
self._initialization = "random"
self._cooling_rate = cooling_rate
self._anneal_temp = 0.0
# recover_low ( quench )
self._quench = False
self._lowest_score_pose = FragIdxPose()
self._record_trajectory = False
def __init__(self, score_table, wts, null_frag_score, pose={}):
"""
1. Score methods:
function call operations
> Given a pose, return the total_score
> Given a frag_idx, return the score relatively to the rest of the residues in the pose (update the pose?)
2. Evaluation method:
return stats for evaluation/debug purposes
> Per-residue stats: decomposite scores for each residue level
> Summarize score: overall results for a pose
"""
assert isScoreTable(score_table)
assert isWeights(wts)
self._score_table = score_table
self._wts = wts
self._null_frag_score = null_frag_score
# Private Member
self.__pose = FragIdxPose() # selected_frags_dict
class SimulatedAnnealing:
'''
1. easy to dump the object as a resulting model, and the trajectory?
2. linear cooling rate
'''
def __init__( self, scorefxn, steps, temp, cooling_rate ):
''' '''
assert isScoreFxn( scorefxn )
self._log = ""
self._scorefxn = scorefxn
self._steps = steps # MC steps per annealing cycle
self._temperature = temp
# declare objects
self.__fragidx_pose = FragIdxPose()
self._initialization = "random"
self._cooling_rate = cooling_rate
self._anneal_temp = 0.0
# recover_low ( quench )
self._quench = False
self._lowest_score_pose = FragIdxPose()
self._record_trajectory = False
def set_annealing_temperature( self ):
''' '''
self._anneal_temp = round( self._temperature*self._cooling_rate, 1 )
self._temperature -= self._anneal_temp
def run( self, runid ):
''' run id is a identification for a model to dump '''
self.__fragidx_pose.clear()
self.__fragidx_pose.initialization( self._scorefxn.get_density_score_dict(), self._initialization ) # default initialize by random
#print self.__fragidx_pose.show_state( "initialization" )
mc = MonteCarlo( self._scorefxn, self._temperature )
mc.apply( self.__fragidx_pose, self._steps ) # to prevent a silly bug that at the very first state SCORE==0, such that you wouldn't lower than that during high temperatures sampling
self._lowest_score_pose = self.__fragidx_pose.clone()
tracker = TrajectoryTracker( runid )
tag = "model_" + str( runid )
while self._temperature >=0 : # it would never reach this criteria
if self._quench:
self.recover_low() # retrieve the lowest-score pose from previous runs
mc.apply( self.__fragidx_pose, self._steps )
residual_pose = self._scorefxn.residualize_pose() # residual_pose will be filled with
#print residual_pose.show_state( tag + "_" + str( self._temperature ) )
self.set_annealing_temperature() # update self._temperature
if self._temperature == mc.get_temperature(): break
mc.set_temperature( self._temperature )
if self._record_trajectory: tracker.save( self._temperature, self.__fragidx_pose )
tracker.save( self._temperature, self._scorefxn.residualize_pose() )
tracker.dump_pickle( tag )
residual_pose.show_state( tag + "_final", True ) # True for verbose showing all residues states
def set_to_quench( self ):
self._quench = True
def record_trajectory( self ):
self._record_trajectory = True
def recover_low( self ): # recover_low
'''
last accept score pose, and lowest score pose; the MC.recover_low has this is because it uses Metropolis to thermally accept pose
'''
# this is for the first around
# need to think about a better way to initiate it
if not self._lowest_score_pose._initialized:
self._lowest_score_pose._initialized = self.__fragidx_pose
# .total_score() method will re-evaluate pose whenever it is called
if self.__fragidx_pose.total_score() > self._lowest_score_pose.total_score():
stdout.write("recover previous found lowest-score pose with score: %s\n" % self._lowest_score_pose.total_score() )
self.__fragidx_pose = self._lowest_score_pose.clone()
else:
stdout.write("found a newer lowest-score pose\n")
self._lowest_score_pose = self.__fragidx_pose.clone()
def dump( self, id ):
return
def quench( self ):
return
class ScoreFunction:
"""
The ScoreFucntion object must initialize by having object ScoreTable read in as Dictionary.
> 130909: should I move pose storage out of the class?
"""
def __init__(self, score_table, wts, null_frag_score, pose={}):
"""
1. Score methods:
function call operations
> Given a pose, return the total_score
> Given a frag_idx, return the score relatively to the rest of the residues in the pose (update the pose?)
2. Evaluation method:
return stats for evaluation/debug purposes
> Per-residue stats: decomposite scores for each residue level
> Summarize score: overall results for a pose
"""
assert isScoreTable(score_table)
assert isWeights(wts)
self._score_table = score_table
self._wts = wts
self._null_frag_score = null_frag_score
# Private Member
self.__pose = FragIdxPose() # selected_frags_dict
def __call__(self, input):
"""
Two operations:
1. scorefxn( pose ): #
** noteworthy: the pose object here is Pose
> assign Residue object for each position, and
> return a total score of it
2. scorefxn( frag_idx ):
> return frag score for the frag_idx to a pose
"""
assert isPose(input) or isFragIdx(input)
if isPose(input): # a residual pose
""" 1. update the residue of the verbose_pose to be composed of Residue objects
2. return a total score """
residual_pose = input
self.update_pose(residual_pose) # the frag_idx in the input has been update to self.__pose
# use the new ScoreTable to rescore it residual_pose
output_pose = Pose()
for frag_idx in self.__pose:
output_pose.update_residue(self.score_evaluator(frag_idx, True))
return output_pose
elif isFragIdx(input):
""" return a residue score """
return self.score_evaluator(input)
def residualize_pose(self):
""" Pose() has methods to evaluate the state """
residual_pose = Pose()
for frag_idx in self.__pose:
residual_pose.update_residue(self.score_evaluator(frag_idx, True))
return residual_pose
def get_density_score_dict(self):
return self._score_table.get_density_score_dict()
def get_candidate_frags(self, pos):
""" return candidate fragid objects from a position as a list """
return self._score_table.get_candidate_frags(pos)
def clone(self):
""" would it work? don't know yet """
return copy.deepcopy(self)
def update_score_table(self, new_score_table):
assert isScoreTable(new_score_table)
self._score_table = new_score_table
def update_pose(self, pose):
""" simply assign the coming pose to the in-object pose """
assert isFragIdxPose(pose) or isPose(pose)
if isFragIdxPose(pose):
self.__pose = pose
elif isPose(pose):
for residue in pose:
pos = residue._frag_id._pos
# print pos, residue._score
frag_idx = self._score_table.frag_to_index(residue._frag_id())
self.__pose.update_residue(pos, frag_idx)
def set_weights(self, new_wts):
""" This is in particular useful when you want to interactive use this class to rescore by changing the weights """
assert isWeights(new_wts)
self._wts = new_wts
def set_null_frag_score(self, new_null_frag_score):
""" This is being used whenever low acceptance rate of MonteCarlo object - lower the null_frag_score """
assert new_null_frag_score
self._null_frag_score = new_null_frag_score
#### the main method to score ####
def score_evaluator(self, candidate_frag_idx, verbose=False):
"""
Given a candidate_frag_idx, return a frag_score of the fragment to the selected ones,
1. null_frag - return null_frag_score
2. frag - return frag_score
"""
assert isFragIdxPose(
self.__pose
) # is a Pose instance, and has been initialized; this is because when instance ScoreFunction class, you don't have to give it a Pose class
# skip null fragment: this is for when calculating total_score
if isNullFrag(candidate_frag_idx):
if verbose:
candidate_frag_id = FragID(self._score_table.index_to_frag(candidate_frag_idx)) # make FragID object
return Residue(candidate_frag_id, self._null_frag_score)
else:
return self._null_frag_score
density_score, all_overlap_score, all_closab_score, all_clash_score = (0.0,) * 4
# one-body score:
try:
density_score = self._score_table.density_score_lookup(candidate_frag_idx)
density_score *= self._wts._density_score_wt
rmsd = self._score_table.rmsd_lookup(candidate_frag_idx)
except KeyError:
stderr.write("Error: %s does not have density score\n" % candidate_frag_idx)
exit()
# two-body score: the candidate_frag to the rest selected ones
""" for each candidate placement, calculate frag_score against all selected frags """
for selected_frag_idx in self.__pose: # pose as an iterator of positions
if selected_frag_idx == candidate_frag_idx:
continue # no two-body score to itself
if isNullFrag(selected_frag_idx):
continue # you don't need to compare to null fragment
# overlap using table to do a fast lookup
if self._score_table.overlapping_check_table_lookup(candidate_frag_idx, selected_frag_idx):
# The reason why you don't need to look up clash score for overlapping fragments is because it has been considered while calculating overlap_score
try:
overlap_score = self._score_table.overlap_score_lookup(candidate_frag_idx, selected_frag_idx)
overlap_score *= self._wts._overlap_score_wt
all_overlap_score += overlap_score
except KeyError:
stderr.write(
"WARNING: %s %s don't have overlap score\n"
% (
self._score_table.index_to_frag(candidate_frag_idx),
self._score_table.index_to_frag(selected_frag_id),
)
)
continue
else:
try:
closab_score = self._score_table.closab_score_lookup(candidate_frag_idx, selected_frag_idx)
closab_score *= self._wts._closab_score_wt
all_closab_score += closab_score
clash_score = self._score_table.clash_score_lookup(candidate_frag_idx, selected_frag_idx)
clash_score *= self._wts._clash_score_wt
all_clash_score += clash_score
except KeyError:
stderr.write(
"WARNING: %s %s don't have nonoverlap score\n"
% (
self._score_table.index_to_frag(candidate_frag_idx),
self._score_table.index_to_frag(selected_frag_id),
)
)
continue
#### end of calculating "the candidate_frag" to the selected ones ####
frag_score = density_score + all_overlap_score + all_closab_score + all_clash_score
if verbose:
""" This is to be used at the very end of stage of simulation to dump residual decomposed scores;
preferably will only be called in scorefxn.show_state() """
candidate_frag_id = FragID(self._score_table.index_to_frag(candidate_frag_idx)) # make FragID object
residue = Residue(
candidate_frag_id, frag_score, density_score, all_overlap_score, all_closab_score, all_clash_score, rmsd
) # missing Boltzmann
return residue
else:
return frag_score