def _criteria(self, model, criteria):
# TODO. REST OF CRITERIA!
P_I = []
if criteria == '1/Mc':
nMicroPerMacro = macroAccumulate(model, np.ones(model.micronum))
P_I = 1 / macroAccumulate(model, model.data.N[model.cluster_ofmicro])
P_I = P_I / nMicroPerMacro
return P_I[model.macro_ofmicro]
def _criteria(self, model, criteria):
# TODO. REST OF CRITERIA!
P_I = []
if criteria == '1/Mc':
nMicroPerMacro = macroAccumulate(model, np.ones(model.micronum))
P_I = 1 / macroAccumulate(model,
model.data.N[model.cluster_ofmicro])
P_I = P_I / nMicroPerMacro
return P_I[model.macro_ofmicro]
def _algorithm(self):
logger.info('Postprocessing new data')
sims = simlist(glob(path.join(self.datapath, '*', '')),
glob(path.join(self.inputpath, '*', 'structure.pdb')),
glob(path.join(self.inputpath, '*', '')))
if self.filter:
sims = simfilter(sims, self.filteredpath, filtersel=self.filtersel)
metr = Metric(sims, skip=self.skip)
metr.set(self.projection)
# if self.contactsym is not None:
# contactSymmetry(data, self.contactsym)
if self.ticadim > 0:
# tica = TICA(metr, int(max(2, np.ceil(self.ticalag)))) # gianni: without project it was tooooo slow
tica = TICA(metr.project(), int(max(2, np.ceil(self.ticalag))))
datadr = tica.project(self.ticadim)
else:
datadr = metr.project()
datadr.dropTraj(
) # Preferably we should do this before any projections. Corrupted sims can affect TICA
datadr.cluster(
self.clustmethod(n_clusters=self._numClusters(datadr.numFrames)))
model = Model(datadr)
self._model = model
self._model.markovModel(self.lag, self._numMacrostates(datadr))
if self.save:
self._model.save('adapt_model_e' + str(self._getEpoch()) + '.dat')
# Undirected component
uc = -model.data.N # Lower counts should give higher score hence the -
if self.statetype == 'micro':
uc = uc[model.cluster_ofmicro]
if self.statetype == 'macro':
uc = macroAccumulate(model, uc[model.cluster_ofmicro])
# Calculating the directed component
dc = self._calculateDirectedComponent(sims, model.data.St,
model.data.N)
if self.statetype == 'micro':
dc = dc[model.cluster_ofmicro]
if self.statetype == 'macro':
dc = macroAccumulate(model, dc[model.cluster_ofmicro])
uc = self._featScale(uc)
dc = self._featScale(dc)
reward = dc + self.ucscale * uc
relFrames = self._getSpawnFrames(reward, self._model, datadr)
self._writeInputs(datadr.rel2sim(np.concatenate(relFrames)))
def _criteria(self, model, criteria):
if criteria == '1/Mc':
nMicroPerMacro = macroAccumulate(model, np.ones(model.micronum))
P_I = 1 / macroAccumulate(model, model.data.N[model.cluster_ofmicro])
P_I = P_I / nMicroPerMacro
ret = P_I[model.macro_ofmicro]
elif criteria == 'pi/Mc':
nMicroPerMacro = macroAccumulate(model, np.ones(model.micronum))
P_I = 1 / macroAccumulate(model, model.data.N[model.cluster_ofmicro])
P_I = P_I / nMicroPerMacro
ret = P_I[model.macro_ofmicro]*model.msm.stationary_distribution
return ret
def _criteria(self, model, criteria):
if criteria == '1/Mc':
nMicroPerMacro = macroAccumulate(model, np.ones(model.micronum))
P_I = 1 / macroAccumulate(model, model.data.N[model.cluster_ofmicro])
P_I = P_I / nMicroPerMacro
ret = P_I[model.macro_ofmicro]
elif criteria == 'pi/Mc':
nMicroPerMacro = macroAccumulate(model, np.ones(model.micronum))
P_I = 1 / macroAccumulate(model, model.data.N[model.cluster_ofmicro])
P_I = P_I / nMicroPerMacro
ret = P_I[model.macro_ofmicro]*model.msm.stationary_distribution
return ret
def _algorithm(self):
sims = self._getSimlist()
if self.nosampledc:
print('Spawning only from top DC conformations without sampling')
goaldata = self._getGoalData(sims)
if not self._checkNFrames(goaldata): return False
datconcat = np.concatenate(goaldata.dat).flatten()
sortedabs = np.argsort(datconcat)[::-1]
if self._debug:
np.save('debug.npy', sortedabs[:self.nmax - self._running])
return True
self._writeInputs(
goaldata.abs2sim(sortedabs[:self.nmax - self._running]))
return True
data = self._getData(sims)
if self.save:
if not path.exists('saveddata'):
os.makedirs('saveddata')
np.savetxt(
path.join('saveddata',
'e{}_report.npy'.format(self._getEpoch())),
[self._getEpoch(), data.numFrames,
len(data.dat)])
if not self._checkNFrames(data): return False
goaldata = self._getGoalData(
data.simlist
) # Using the simlist of data in case some trajectories were dropped
if len(data.simlist) != len(goaldata.simlist):
logger.warning(
'The goal function was not able to project all trajectories that the MSM projection could.'
'Check for possible errors in the goal function.')
data.dropTraj(
keepsims=goaldata.simlist
) # Ensuring that I use the intersection of projected simulations
self._createMSM(data)
model = self._model
data = self._model.data
# Undirected component
uc = model.data.N # Lower counts should give higher score
if self.statetype == 'micro':
uc = uc[model.cluster_ofmicro]
if self.statetype == 'macro':
uc = macroAccumulate(model, uc[model.cluster_ofmicro])
uc = 1 / uc
# Calculating the directed component
dcmeans = dcstds = None
if self.statetype == 'micro':
dcmeans, dcstds = self._calculateDirectedComponent(
goaldata, model.data.St, model.micro_ofcluster)
elif self.statetype == 'macro':
# TODO: Should we weigh by equilibrium population?
dcmeans, dcstds = self._calculateDirectedComponent(
goaldata, model.data.St, model.macro_ofcluster)
ucunscaled = uc.copy()
dcunscaled = dcmeans.copy()
dc = dcmeans / np.sum(dcmeans)
uc = uc / np.sum(uc)
N = self.nmax - self._running
Nuc, Ndc = np.random.multinomial(N, [self.epsilon, 1 - self.epsilon])
rewardDC = self._truncate(uc * dc, Ndc)
rewardUC = self._truncate(uc, Nuc)
relFramesDC, spawncountsDC, truncprobDC = self._getSpawnFrames(
rewardDC, self._model, data, Ndc)
relFramesUC, spawncountsUC, truncprobUC = self._getSpawnFrames(
rewardUC, self._model, data, Nuc)
relFrames = np.concatenate(
(np.concatenate(relFramesDC), np.concatenate(relFramesUC)))
if self.save:
if not path.exists('saveddata'):
os.makedirs('saveddata')
epoch = self._getEpoch()
tosave = {
'ucunscaled': -ucunscaled,
'dcunscaled': dcunscaled,
'uc': uc,
'dc': dc,
'epsilon': self.epsilon,
'spawncountsDC': spawncountsDC,
'spawncountsUC': spawncountsUC,
'truncprobDC': truncprobDC,
'truncprobUC': truncprobUC,
'relFramesDC': relFramesDC,
'relFramesUC': relFramesUC,
'dcmeans': dcmeans,
'dcstds': dcstds,
'rewardDC': rewardDC,
'rewardUC': rewardUC
}
np.save(path.join('saveddata', 'e{}_goalreport.npy'.format(epoch)),
tosave)
np.save(
path.join('saveddata', 'e{}_spawnframes.npy'.format(epoch)),
relFrames)
goaldata.save(
path.join('saveddata', 'e{}_goaldata.dat'.format(epoch)))
if self._debug:
np.save('debug.npy', relFrames)
return True
self._writeInputs(data.rel2sim(relFrames))
return True
def _algorithm(self):
sims = self._getSimlist()
if self.nosampledc:
print('Spawning only from top DC conformations without sampling')
goaldata = self._getGoalData(sims)
if not self._checkNFrames(goaldata): return False
datconcat = np.concatenate(goaldata.dat).flatten()
sortedabs = np.argsort(datconcat)[::-1]
if self._debug: np.save('debug.npy', sortedabs[:self.nmax - self._running]); return True
self._writeInputs(goaldata.abs2sim(sortedabs[:self.nmax - self._running]))
return True
data = self._getData(sims)
if self.save:
if not path.exists('saveddata'):
os.makedirs('saveddata')
np.savetxt(path.join('saveddata', 'e{}_report.npy'.format(self._getEpoch())), [self._getEpoch(), data.numFrames, len(data.dat)])
if not self._checkNFrames(data): return False
goaldata = self._getGoalData(data.simlist) # Using the simlist of data in case some trajectories were dropped
if len(data.simlist) != len(goaldata.simlist):
logger.warning('The goal function was not able to project all trajectories that the MSM projection could.'
'Check for possible errors in the goal function.')
data.dropTraj(keepsims=goaldata.simlist) # Ensuring that I use the intersection of projected simulations
self._createMSM(data)
model = self._model
data = self._model.data
# Undirected component
uc = -model.data.N # Lower counts should give higher score hence the -
if self.statetype == 'micro':
uc = uc[model.cluster_ofmicro]
if self.statetype == 'macro':
uc = macroAccumulate(model, uc[model.cluster_ofmicro])
# Calculating the directed component
dcmeans = dcstds = None
if self.statetype == 'micro':
dcmeans, dcstds = self._calculateDirectedComponent(goaldata, model.data.St, model.micro_ofcluster)
elif self.statetype == 'macro':
# TODO: Should we weigh by equilibrium population?
dcmeans, dcstds = self._calculateDirectedComponent(goaldata, model.data.St, model.macro_ofcluster)
ucunscaled = uc
dcunscaled = dcmeans
uc = self._featScale(uc)
dc = self._featScale(dcmeans)
scale = self.ucscale
if self.autoscale:
scale = AdaptiveGoal._calculateScale(goaldata, self.autoscalediff, self.autoscalemult, self.autoscaletol)
reward = scale * uc + (1 - scale) * dc
N = self.nmax - self._running
reward = self._truncate(reward, N)
relFrames, spawncounts, truncprob = self._getSpawnFrames(reward, self._model, data, N)
if self.save:
if not path.exists('saveddata'):
os.makedirs('saveddata')
epoch = self._getEpoch()
tosave = {'ucunscaled': -ucunscaled, 'dcunscaled': dcunscaled, 'uc': uc, 'dc': dc, 'ucscale': scale,
'spawncounts': spawncounts, 'truncprob': truncprob, 'relFrames': relFrames, 'dcmeans': dcmeans,
'dcstds': dcstds, 'reward': reward}
np.save(path.join('saveddata', 'e{}_goalreport.npy'.format(epoch)), tosave)
np.save(path.join('saveddata', 'e{}_spawnframes.npy'.format(epoch)), relFrames)
goaldata.save(path.join('saveddata', 'e{}_goaldata.dat'.format(epoch)))
if self._debug: np.save('debug.npy', relFrames); return True
self._writeInputs(data.rel2sim(np.concatenate(relFrames)))
return True
def _algorithm(self):
sims = self._getSimlist()
if self.nosampledc:
print('Spawning only from top DC conformations without sampling')
goaldata = self._getGoalData(sims)
if not self._checkNFrames(goaldata): return False
datconcat = np.concatenate(goaldata.dat).flatten()
sortedabs = np.argsort(datconcat)[::-1]
if self._debug: np.save('debug.npy', sortedabs[:self.nmax - self._running]); return True
self._writeInputs(goaldata.abs2sim(sortedabs[:self.nmax - self._running]))
return True
data = self._getData(sims)
if self.save:
if not path.exists('saveddata'):
os.makedirs('saveddata')
np.savetxt(path.join('saveddata', 'e{}_report.npy'.format(self._getEpoch())), [self._getEpoch(), data.numFrames, len(data.dat)])
if not self._checkNFrames(data): return False
goaldata = self._getGoalData(data.simlist) # Using the simlist of data in case some trajectories were dropped
if len(data.simlist) != len(goaldata.simlist):
logger.warning('The goal function was not able to project all trajectories that the MSM projection could.'
'Check for possible errors in the goal function.')
data.dropTraj(keepsims=goaldata.simlist) # Ensuring that I use the intersection of projected simulations
self._createMSM(data)
model = self._model
data = self._model.data
# Undirected component
uc = -model.data.N # Lower counts should give higher score hence the -
if self.statetype == 'micro':
uc = uc[model.cluster_ofmicro]
if self.statetype == 'macro':
uc = macroAccumulate(model, uc[model.cluster_ofmicro])
# Calculating the directed component
dcmeans = dcstds = None
if self.statetype == 'micro':
dcmeans, dcstds = self._calculateDirectedComponent(goaldata, model.data.St, model.micro_ofcluster)
elif self.statetype == 'macro':
# TODO: Should we weigh by equilibrium population?
dcmeans, dcstds = self._calculateDirectedComponent(goaldata, model.data.St, model.macro_ofcluster)
ucunscaled = uc
dcunscaled = dcmeans
uc = self._featScale(uc)
dc = self._featScale(dcmeans)
scale = self.ucscale
if self.autoscale:
scale = AdaptiveGoal._calculateScale(goaldata, self.autoscalediff, self.autoscalemult, self.autoscaletol)
reward = scale * uc + (1 - scale) * dc
N = self.nmax - self._running
reward = self._truncate(reward, N)
relFrames, spawncounts, truncprob = self._getSpawnFrames(reward, self._model, data, N)
if self.save:
if not path.exists('saveddata'):
os.makedirs('saveddata')
epoch = self._getEpoch()
tosave = {'ucunscaled': -ucunscaled, 'dcunscaled': dcunscaled, 'uc': uc, 'dc': dc, 'ucscale': scale,
'spawncounts': spawncounts, 'truncprob': truncprob, 'relFrames': relFrames, 'dcmeans': dcmeans,
'dcstds': dcstds, 'reward': reward}
np.save(path.join('saveddata', 'e{}_goalreport.npy'.format(epoch)), tosave)
np.save(path.join('saveddata', 'e{}_spawnframes.npy'.format(epoch)), relFrames)
goaldata.save(path.join('saveddata', 'e{}_goaldata.dat'.format(epoch)))
if self._debug: np.save('debug.npy', relFrames); return True
self._writeInputs(data.rel2sim(np.concatenate(relFrames)))
return True