def setUpClass(self):
from htmd.simlist import simlist, simfilter
from glob import glob
from htmd.projections.metric import Metric
from moleculekit.projections.metricdistance import MetricDistance
from moleculekit.projections.metricdihedral import MetricDihedral
from moleculekit.util import tempname
from htmd.home import home
from os.path import join
sims = simlist(
glob(join(home(dataDir="adaptive"), "data", "*", "")),
glob(join(home(dataDir="adaptive"), "input", "*")),
)
fsims = simfilter(sims, tempname(), "not water")
metr = Metric(fsims)
metr.set(
MetricDistance(
"protein and resid 10 and name CA",
"resname BEN and noh",
periodic="selections",
metric="contacts",
groupsel1="residue",
threshold=4,
)
)
self.data1 = metr.project()
metr.set(MetricDihedral())
self.data2 = metr.project()
def _getSimlist(self):
logger.info('Postprocessing new data')
sims = simlist(glob(path.join(self.datapath, '*', '')), glob(path.join(self.inputpath, '*', '')),
glob(path.join(self.inputpath, '*', '')))
if self.filter:
sims = simfilter(sims, self.filteredpath, filtersel=self.filtersel)
return sims
def _getSimlist(self):
logger.info('Postprocessing new data')
sims = simlist(glob(path.join(self.datapath, '*', '')), glob(path.join(self.inputpath, '*', '')),
glob(path.join(self.inputpath, '*', '')))
if self.filter:
sims = simfilter(sims, self.filteredpath, filtersel=self.filtersel)
return sims
def setUpClass(self):
from htmd.simlist import simlist, simfilter
from glob import glob
from htmd.projections.metric import Metric
from moleculekit.projections.metricdistance import MetricDistance
from moleculekit.projections.metricdihedral import MetricDihedral
from moleculekit.util import tempname
from htmd.home import home
from os.path import join
sims = simlist(glob(join(home(dataDir='adaptive'), 'data', '*', '')),
glob(join(home(dataDir='adaptive'), 'input', '*')))
fsims = simfilter(sims, tempname(), 'not water')
metr = Metric(fsims)
metr.set(
MetricDistance('protein and resid 10 and name CA',
'resname BEN and noh',
metric='contacts',
groupsel1='residue',
threshold=4))
self.data1 = metr.project()
metr.set(MetricDihedral())
self.data2 = metr.project()
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)))
self._model = Model(datadr)
self._model.markovModel(self.lag, self._numMacrostates(datadr))
if self.save:
self._model.save('adapt_model_e' + str(self._getEpoch()) + '.dat')
relFrames = self._getSpawnFrames(self._model, datadr)
self._writeInputs(datadr.rel2sim(np.concatenate(relFrames)))
def _getSimlist(self):
logger.info("Postprocessing new data")
sims = simlist(
glob(path.join(self.datapath, "*", "")),
glob(path.join(self.inputpath, "*", "")),
glob(path.join(self.inputpath, "*", "")),
)
if self.filter:
sims = simfilter(sims, self.filteredpath, filtersel=self.filtersel)
return sims
def _algorithm(self):
logger.info('Postprocessing new data')
datalist = simlist(glob(path.join(self.datapath, '*', '')), glob(path.join(self.inputpath, '*', 'structure.pdb')),
glob(path.join(self.inputpath, '*', '')))
filtlist = simfilter(datalist, self.filteredpath, filtersel=self.filtersel)
if hasattr(self, 'metricsel2') and self.metricsel2 is not None:
proj = MetricDistance(self.metricsel1, self.metricsel2, metric=self.metrictype)
else:
proj = MetricSelfDistance(self.metricsel1, metric=self.metrictype)
metr = Metric(filtlist, skip=self.skip)
metr.projection(proj)
data = metr.project()
#if self.contactsym is not None:
# contactSymmetry(data, self.contactsym)
data.dropTraj()
if self.ticadim > 0:
tica = TICA(data, int(max(2, np.ceil(20/self.skip))))
datadr = tica.project(self.ticadim)
else:
datadr = data
K = int(max(np.round(0.6 * np.log10(datadr.numFrames/1000)*1000+50), 100)) # heuristic
if K > datadr.numFrames / 3: # Freaking ugly patches ...
K = int(datadr.numFrames / 3)
datadr.cluster(self.clustmethod(n_clusters=K), mergesmall=5)
replacement = False
if datadr.K < 10:
datadr.cluster(self.clustmethod(n_clusters=K))
replacement = True
model = Model(datadr)
macronum = self.macronum
if datadr.K < macronum:
macronum = np.ceil(datadr.K / 2)
logger.warning('Using less macrostates than requested due to lack of microstates. macronum = ' + str(macronum))
from pyemma.msm import timescales_msm
timesc = timescales_msm(datadr.St.tolist(), lags=self.lag, nits=macronum).get_timescales()
macronum = min(self.macronum, max(np.sum(timesc > self.lag), 2))
model.markovModel(self.lag, macronum)
p_i = self._criteria(model, self.method)
(spawncounts, prob) = self._spawn(p_i, self.nmax-self.running)
logger.debug('spawncounts {}'.format(spawncounts))
stateIdx = np.where(spawncounts > 0)[0]
_, relFrames = model.sampleStates(stateIdx, spawncounts[stateIdx], statetype='micro', replacement=replacement)
logger.debug('relFrames {}'.format(relFrames))
self._writeInputs(datadr.rel2sim(np.concatenate(relFrames)))
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 _algorithm(self):
""" Select random frames for respawning
"""
from htmd.projections.metric import Metric
from htmd.molecule.molecule import Molecule
from htmd.projections.metriccoordinate import MetricCoordinate
from htmd.simlist import simlist
sims = simlist(glob(path.join(self.datapath, '*', '')), glob(path.join(self.inputpath, '*', 'structure.pdb')),
glob(path.join(self.inputpath, '*', '')))
metr = Metric(sims)
metr.projection(MetricCoordinate(Molecule(sims[0].molfile), 'protein and name CA', 'protein and name CA'))
data = metr.project()
simframes = data.abs2sim(np.random.randint(0, data.numFrames, self.nmax-self.running))
self._writeInputs(simframes)
def _algorithm(self):
""" Select random frames for respawning
"""
from htmd.projections.metriccoordinate import MetricCoordinate
from htmd.simlist import simlist
sims = simlist(glob(path.join(self.datapath, '*', '')),
glob(path.join(self.inputpath, '*', 'structure.pdb')),
glob(path.join(self.inputpath, '*', '')))
data = MetricCoordinate.project(sims, sims[0].molfile,
'protein and name CA',
'protein and name CA')
simframes = data.abs2sim(
np.random.randint(0, data.numFrames, self.nmax - self.running))
self._writeInputs(simframes)
def _getsimlist(self, folder):
from htmd.simlist import simlist
from glob import glob
simfolders = glob(f'{folder}/filtered/*/')
tmp_sims = []
#To avoid problems while merging multiples data sources
clean_names = set([i.split("/")[-2] for i in simfolders])
for sim in simfolders:
tmp_name = sim.split("/")[-2]
if tmp_name in clean_names:
tmp_sims.append(sim)
clean_names.remove(tmp_name)
simfolders = tmp_sims
all_folders = glob(folder)[0]
sims = simlist(simfolders, f'{all_folders}/filtered/filtered.pdb')
return sims
def removeCorrupted():
from htmd.simlist import simlist
from htmd.projections.metric import Metric
from os import path
from glob import glob
import shutil
print("Removing Corrupted Simulations")
try:
sims = simlist(glob("./filtered/*/"), "./filtered/filtered.pdb")
except:
return
met = Metric(sims)
met.set(corruptMetric)
dat = met.project()
for i, s in zip(dat.dat, dat.simlist):
if np.sum(i):
pt = path.dirname(s.trajectory[0])
shutil.move(pt, f"/tmp/{pt}")
mol.read(path.join(home(), 'data', 'metricdistance', 'traj.xtc'))
ref = mol.copy()
ref.coords = np.atleast_3d(ref.coords[:, :, 0])
metr = MetricRmsd(ref, 'protein and name CA')
data = metr.project(mol)
lastrmsd = np.array([
1.30797791, 1.29860222, 1.25042927, 1.31319737, 1.27044261, 1.40294552,
1.25354612, 1.30127883, 1.40618336, 1.18303752, 1.24414587, 1.34513164,
1.31932807, 1.34282494, 1.2261436, 1.36359048, 1.26243281, 1.21157813,
1.26476419, 1.29413617
],
dtype=np.float32)
assert np.all(
np.abs(data[-20:] -
lastrmsd) < 0.001), 'Coordinates calculation is broken'
from htmd.simlist import simlist
from htmd.projections.metric import Metric
dd = home(dataDir="adaptive")
fsims = simlist([dd + '/data/e1s1_1/', dd + '/data/e1s2_1/'],
dd + '/generators/1/structure.pdb')
ref = Molecule(dd + "/generators/1/structure.pdb")
metr2 = Metric(fsims)
metr2.set(MetricRmsd(ref, 'protein and name CA'))
data2 = metr2.project()
assert data2.trajectories[0].projection.shape == (6, 1)
pass
datatica.description = keepdimdesc.append(datatica.description,
ignore_index=True)
return datatica
if __name__ == "__main__":
from htmd.simlist import simlist
from glob import glob
from moleculekit.projections.metricdistance import MetricSelfDistance
from htmd.home import home
from os.path import join
testfolder = home(dataDir="villin")
sims = simlist(glob(join(testfolder, "*", "")),
join(testfolder, "filtered.pdb"))
met = Metric(sims[0:2])
met.set(MetricSelfDistance("protein and name CA"))
data = met.project()
data.fstep = 0.1
tica = TICA(data, 2, dimensions=range(2, 10))
datatica = tica.project(2)
tica5 = TICA(data, 0.2, units="ns", dimensions=range(2, 10))
datatica5 = tica5.project(2)
expected = [
[3.69098878, -0.33862674, 0.85779184],
[3.77816105, -0.31887317, 0.87724227],
[3.83537507, -0.11878026, 0.65236956],
]
assert np.allclose(
datatica.description = keepdimdesc.append(datatica.description,
ignore_index=True)
return datatica
if __name__ == '__main__':
from htmd.simlist import simlist
from glob import glob
from htmd.projections.metricdistance import MetricSelfDistance
from htmd.home import home
from os.path import join
testfolder = home(dataDir='villin')
sims = simlist(glob(join(testfolder, '*', '')),
join(testfolder, 'filtered.pdb'))
met = Metric(sims[0:2])
met.set(MetricSelfDistance('protein and name CA'))
data = met.project()
data.fstep = 0.1
tica = TICA(data, 2, dimensions=range(2, 10))
datatica = tica.project(2)
tica5 = TICA(data, 0.2, units='ns', dimensions=range(2, 10))
datatica5 = tica5.project(2)
expected = [[3.69098878, -0.33862674, 0.85779184],
[3.77816105, -0.31887317, 0.87724227],
[3.83537507, -0.11878026, 0.65236956]]
assert np.allclose(np.abs(datatica.trajectories[0].projection[-3:, -3:]),
np.abs(np.array(expected, dtype=np.float32)),
rtol=0,
if self.dimensions is not None and keepdimdesc is not None: # If TICA is done on a subset of dims
datatica.description = keepdimdesc.append(datatica.description, ignore_index=True)
return datatica
if __name__ == '__main__':
from htmd.simlist import simlist
from glob import glob
from htmd.projections.metricdistance import MetricSelfDistance
from htmd.home import home
from os.path import join
testfolder = home(dataDir='villin')
sims = simlist(glob(join(testfolder, '*', '')), join(testfolder, 'filtered.pdb'))
met = Metric(sims[0:2])
met.projection(MetricSelfDistance('protein and name CA'))
data = met.project()
data.fstep = 0.1
tica = TICA(data, 2, dimensions=range(2, 10))
datatica = tica.project(2)
tica5 = TICA(data, 0.2, units='ns', dimensions=range(2, 10))
datatica5 = tica5.project(2)
expected = [[ 3.69098878, -0.33862674, 0.85779184],
[ 3.77816105, -0.31887317, 0.87724227],
[ 3.83537507, -0.11878026, 0.65236956]]
assert np.allclose(np.abs(datatica.trajectories[0].projection[-3:, -3:]), np.abs(np.array(expected, dtype=np.float32)), rtol=0, atol=0.01)
assert np.allclose(np.abs(datatica5.trajectories[0].projection[-3:, -3:]), np.abs(np.array(expected, dtype=np.float32)), rtol=0, atol=0.01)
assert np.all(datatica.description.iloc[[587, 588]].type == 'tica')
]) # None can be replaced by any other "not in b" value
if __name__ == '__main__':
from htmd.simlist import simlist, simfilter
from glob import glob
from htmd.projections.metric import Metric
from htmd.projections.metricdistance import MetricDistance
from htmd.projections.metricdihedral import MetricDihedral
from htmd.util import tempname
from htmd.home import home
from os.path import join
testfolder = home(dataDir='adaptive')
sims = simlist(glob(join(testfolder, 'data', '*', '')),
glob(join(testfolder, 'input', '*', 'structure.pdb')))
fsims = simfilter(sims, tempname(), 'not water')
metr = Metric(fsims)
metr.set(
MetricDistance('protein and resid 10 and name CA',
'resname BEN and noh',
metric='contacts',
groupsel1='residue',
threshold=4))
data1 = metr.project()
metr.set(MetricDihedral())
data2 = metr.project()
# Testing combining of metrics
data1.combine(data2)
mol = Molecule(path.join(home(), 'data', '1kdx', '1kdx_0.pdb'))
mol.read(path.join(home(), 'data', '1kdx', '1kdx.dcd'))
metric = MetricPlumed2(
['d1: DISTANCE ATOMS=1,200', 'd2: DISTANCE ATOMS=5,6'])
data = metric.project(mol)
ref = np.array([
0.536674, 21.722393, 22.689391, 18.402114, 23.431387, 23.13392,
19.16376, 20.393544, 23.665517, 22.298349, 22.659769, 22.667669,
22.484084, 20.893447, 18.791701, 21.833056, 19.901318
])
assert np.all(
np.abs(ref - data[:, 0]) < 0.01), 'Plumed demo calculation is broken'
# Simlist
# datadirs=glob(path.join(home(), 'data', 'adaptive', 'data', '*' )
# fsims=simlist(glob(path.join(home(), 'data', 'adaptive', 'data', '*', '/')),
# path.join(home(), 'data', 'adaptive', 'generators', '1','structure.pdb'))
fsims = simlist([
'/home/toni/work/htmd/htmd/htmd/data/adaptive/data/e1s1_1/',
'/home/toni/work/htmd/htmd/htmd/data/adaptive/data/e1s2_1/'
], '/home/toni/work/htmd/htmd/htmd/data/adaptive/generators/1/structure.pdb'
)
metr = Metric(fsims)
metr.projection(
MetricPlumed2(['d1: DISTANCE ATOMS=2,3', 'd2: DISTANCE ATOMS=5,6']))
data2 = metr.project()
print(data2.dat)
sim = s
break
if sim is None:
raise NameError(f"Could not find parent of simulation {simname}.")
return sim, prevpiece, prevframe, epo
if __name__ == "__main__":
import htmd
import os
from htmd.simlist import Frame, simlist
from htmd.util import tempname
filedir = htmd.home.home() + "/data/adaptive/"
sims = simlist(
glob(os.path.join(filedir, "data", "*", "")),
glob(os.path.join(filedir, "input", "*", "")),
glob(os.path.join(filedir, "input", "*", "")),
)
outf = tempname()
os.makedirs(outf)
f = Frame(sims[0], 0, 5)
_writeInputsFunction(1, f, 2, outf, "input.coor")
mol = Molecule(sims[0])
mol.read(os.path.join(outf, "e2s2_e1s1p0f5", "input.coor"))
shutil.rmtree(outf)
md.run()
# Cleaning up
inputodel = glob(path.join(home(), 'data', 'adaptive', 'input', 'e2*'))
for i in inputodel:
shutil.rmtree(i, ignore_errors=True, acemd='/shared/acemd/bin/acemd')
os.remove(path.join(home(), 'data', 'adaptive', 'input', 'e2_writeinputs.log'))'''
import htmd
import os
import shutil
from htmd.queues.localqueue import LocalGPUQueue
from htmd.simlist import Frame, simlist
from htmd.util import tempname
filedir = htmd.home.home()+'/data/adaptive/'
sims = simlist(glob(os.path.join(filedir, 'data', '*', '')),
glob(os.path.join(filedir, 'input', '*', '')),
glob(os.path.join(filedir, 'input', '*', '')))
outf = tempname()
os.makedirs(outf)
f = Frame(sims[0], 0, 5)
_writeInputsFunction(1, f, 2, outf, 'input.coor')
mol = Molecule(sims[0])
mol.read(os.path.join(outf, 'e2s2_e1s1p0f5', 'input.coor'))
shutil.rmtree(outf)
def _algorithm(self):
logger.info('Postprocessing new data')
datalist = simlist(
glob(path.join(self.datapath, '*', '')),
glob(path.join(self.inputpath, '*', 'structure.pdb')),
glob(path.join(self.inputpath, '*', '')))
filtlist = simfilter(datalist,
self.filteredpath,
filtersel=self.filtersel)
if hasattr(self, 'metricsel2') and self.metricsel2 is not None:
proj = MetricDistance(self.metricsel1,
self.metricsel2,
metric=self.metrictype)
else:
proj = MetricSelfDistance(self.metricsel1, metric=self.metrictype)
metr = Metric(filtlist, skip=self.skip)
metr.projection(proj)
data = metr.project()
#if self.contactsym is not None:
# contactSymmetry(data, self.contactsym)
data.dropTraj()
if self.ticadim > 0:
tica = TICA(data, int(max(2, np.ceil(20 / self.skip))))
datadr = tica.project(self.ticadim)
else:
datadr = data
K = int(
max(np.round(0.6 * np.log10(datadr.numFrames / 1000) * 1000 + 50),
100)) # heuristic
if K > datadr.numFrames / 3: # Freaking ugly patches ...
K = int(datadr.numFrames / 3)
datadr.cluster(self.clustmethod(n_clusters=K), mergesmall=5)
replacement = False
if datadr.K < 10:
datadr.cluster(self.clustmethod(n_clusters=K))
replacement = True
model = Model(datadr)
macronum = self.macronum
if datadr.K < macronum:
macronum = np.ceil(datadr.K / 2)
logger.warning(
'Using less macrostates than requested due to lack of microstates. macronum = '
+ str(macronum))
from pyemma.msm import timescales_msm
timesc = timescales_msm(datadr.St.tolist(),
lags=self.lag,
nits=macronum).get_timescales()
macronum = min(self.macronum, max(np.sum(timesc > self.lag), 2))
model.markovModel(self.lag, macronum)
p_i = self._criteria(model, self.method)
(spawncounts, prob) = self._spawn(p_i, self.nmax - self.running)
logger.debug('spawncounts {}'.format(spawncounts))
stateIdx = np.where(spawncounts > 0)[0]
_, relFrames = model.sampleStates(stateIdx,
spawncounts[stateIdx],
statetype='micro',
replacement=replacement)
logger.debug('relFrames {}'.format(relFrames))
self._writeInputs(datadr.rel2sim(np.concatenate(relFrames)))
import htmd.home
from htmd.simlist import simlist
from htmd.projections.metricplumed2 import MetricPlumed2
from htmd.projections.metric import Metric
try:
_getPlumedRoot()
except:
print("Tests in %s skipped because plumed executable not found." % __file__)
sys.exit()
# Simlist
dd = htmd.home.home(dataDir="adaptive")
fsims = simlist([dd + '/data/e1s1_1/', dd + '/data/e1s2_1/'],
dd + '/generators/1/structure.pdb')
metr = Metric(fsims)
metr.set(MetricPlumed2(
['d1: DISTANCE ATOMS=2,3',
'd2: DISTANCE ATOMS=5,6']))
data2 = metr.project()
# One simulation
testpath=os.path.join(htmd.home.home(), 'data', '1kdx')
mol = Molecule(os.path.join(testpath, '1kdx_0.pdb'))
mol.read(os.path.join(htmd.home.home(), 'data', '1kdx', '1kdx.dcd'))
metric = MetricPlumed2(['d1: DISTANCE ATOMS=1,200',
'd2: DISTANCE ATOMS=5,6'])
data = metric.project(mol)
return np.array([bind.get(itm, -1) for itm in a]) # None can be replaced by any other "not in b" value
if __name__ == '__main__':
from htmd.simlist import simlist, simfilter
from glob import glob
from htmd.projections.metric import Metric
from htmd.projections.metricdistance import MetricDistance
from htmd.projections.metricdihedral import MetricDihedral
from htmd.util import tempname
from htmd.home import home
from os.path import join
testfolder = home(dataDir='adaptive')
sims = simlist(glob(join(testfolder, 'data', '*', '')), glob(join(testfolder, 'input', '*', 'structure.pdb')))
fsims = simfilter(sims, tempname(), 'not water')
metr = Metric(fsims)
metr.set(MetricDistance('protein and resid 10 and name CA', 'resname BEN and noh', metric='contacts',
groupsel1='residue', threshold=4))
data1 = metr.project()
metr.set(MetricDihedral())
data2 = metr.project()
# Testing combining of metrics
data1.combine(data2)
# Testing dimensions
assert np.array_equal(data1.description.shape, (897, 3)), 'combine not working correct'
assert np.array_equal(data1.trajectories[0].projection.shape, (6, 897)), 'combine not working correct'
assert np.array_equal(np.where(data1.description.type == 'contact')[0], [0, 1, 2, 3, 4, 5, 6, 7, 8]), 'combine not working correct'
from htmd.molecule.molecule import Molecule
from htmd.home import home
import numpy as np
from os import path
mol = Molecule(path.join(home(), 'data', 'metricdistance', 'filtered.pdb'))
mol.read(path.join(home(), 'data', 'metricdistance', 'traj.xtc'))
ref = mol.copy()
ref.coords = np.atleast_3d(ref.coords[:, :, 0])
metr = MetricTMscore(ref, 'protein and name CA')
data = metr.project(mol)
lasttm = np.array([0.9633381, 0.96441294, 0.96553609, 0.96088852, 0.96288511, 0.95677591, 0.96544727, 0.96359811,
0.95658912, 0.96893117, 0.96623924, 0.96064913, 0.96207041, 0.95947848, 0.96657048, 0.95993426,
0.96543296, 0.96806875, 0.96437248, 0.96144066], dtype=np.float32)
assert np.all(np.abs(data[-20:].flatten() - lasttm) < 0.001), 'Coordinates calculation is broken'
from htmd.simlist import simlist
from htmd.projections.metric import Metric
dd = home(dataDir="adaptive")
fsims = simlist([path.join(dd, 'data', 'e1s1_1'), path.join(dd, 'data', 'e1s2_1')],
path.join(dd, 'generators', '1', 'structure.pdb'))
ref = Molecule(path.join(dd, 'generators', '1', 'structure.pdb'))
metr2 = Metric(fsims)
metr2.projection(MetricTMscore(ref, 'protein and name CA'))
data2 = metr2.project()
assert data2.trajectories[0].projection.shape == (6, 1)
def analyze_folder(folder=None,
out_folder="/tmp",
skip=1,
metrics=None,
clu=500,
tica=True,
ticadim=5,
tica_lag=20,
model_lag=10,
model_units='ns',
macro_N=10,
bulk_split=False,
fes=True,
rg_analysis=True,
save=True,
data_fstep=None):
"""Analysis script for create a Markov State Model
Creates and returns a Markov State Model given a data folder.
Intented to follow up the evolution of an adaptive sampling run.
Allows to save the model ans several informative plots
Parameters
----------
folder : str
Data folder where adaptive is running
out_folder : str
Output folder to store derived data
skip : int
Number of frames to skip while projecting the MD data
metrics : [:class: `Metric` object]
Metric array used to project the data
clu : int
Number of cluster to create using the MiniBatchKMeans method.
tica: bool
Wether to use TICA of GWPCA for dimensionality reduction
ticadim : int
Number of TICA dimension to project the data. If None, the model will be created using the raw projected data
tica_lag : int, optional
Description
model_lag : int
Number of ns used to create the model
model_units : str, optional
Description
macro_N : int
Number of macrostate to split the final Markov State Model
fes : bool, optional
If true it will save a plot projecting the first two TICA dimension. Requires ticadim to be defined
rg_analysis : bool, optional
If true, a plot with information relative to the radious of gyration of the molecule will be created.
save : bool, optional
If true, the model will be saved in the outputs folder
Returns
-------
:class:`Model`
Final model
"""
from htmd.model import Model
from htmd.molecule.molecule import Molecule
from htmd.simlist import simlist
from htmd.projections.metric import Metric
from sklearn.cluster import MiniBatchKMeans
from IDP_htmd.IDP_model import plot_RG
from IDP_htmd.model_utils import create_bulk
from glob import glob
import os
try:
os.mkdir(out_folder)
except:
print("Folder already exists")
try:
fsims = np.load(f"{folder}/simlist.npy", allow_pickle=True)
print(f"Loaded {folder}/simlist.npy")
except:
print("Creating simlist")
sims = glob(folder + 'filtered/*/')
fsims = simlist(sims, folder + 'filtered/filtered.pdb')
metr = Metric(fsims, skip=skip)
metr.set(metrics)
#Check if this gives problems to ITS
try:
model = Model(file=f"{out_folder}/model.dat")
out_data = model.data
print(f"Loading model: {out_folder}/model.dat")
except:
if tica and ticadim:
from htmd.projections.tica import TICA
print("Projecting TICA")
tica = TICA(metr, tica_lag)
out_data = tica.project(ticadim)
elif not tica and ticadim:
from htmd.projections.gwpca import GWPCA
data = metr.project()
data.dropTraj()
print("using GWPCA")
gwpca = GWPCA(data, tica_lag)
out_data = gwpca.project(ticadim)
else:
print("Not using TICA")
data = metr.project()
data.dropTraj()
out_data = data
#Avoid some possibles error while clustering
if data_fstep: out_data.fstep = data_fstep
x = True
while x:
try:
out_data.cluster(MiniBatchKMeans(n_clusters=clu), mergesmall=5)
x = False
except Exception as e:
raise Exception("Error " + str(e))
model = Model(out_data)
model.plotTimescales(plot=False, save=f"{out_folder}/1_its.png")
if macro_N:
model.markovModel(model_lag, macro_N, units=model_units)
if bulk_split:
try:
print("Starting bulk splitting")
create_bulk(model, bulk_split)
except Exception as e:
print("Could not perform the bulk splitting")
print(e)
model.eqDistribution(plot=False,
save=f"{out_folder}/1.2_eqDistribution.png")
if rg_analysis:
from IDP_htmd.IDP_analysis import rg_analysis
mol = Molecule(model.data.simlist[0].molfile)
rg_data = rg_analysis(model, skip=skip)
plot_RG(rg_data, mol, save=f"{out_folder}/1.4_rg.png")
# if fes and ticadim:
# model.plotFES(0, 1, temperature=310, states=True,
# plot=False, save=f"{out_folder}/1.3_fes.png")
if save:
model.save(f"{out_folder}/model.dat")
return model
md.datapath = path.join(home(), 'data', 'adaptive', 'data')
md.run()
# Cleaning up
inputodel = glob(path.join(home(), 'data', 'adaptive', 'input', 'e2*'))
for i in inputodel:
shutil.rmtree(i, ignore_errors=True, acemd='/shared/acemd/bin/acemd')
os.remove(path.join(home(), 'data', 'adaptive', 'input', 'e2_writeinputs.log'))'''
import htmd
import os
import shutil
from htmd.queues.localqueue import LocalGPUQueue
from htmd.simlist import Frame, simlist
from htmd.util import tempname
filedir = htmd.home.home() + '/data/adaptive/'
sims = simlist(glob(os.path.join(filedir, 'data', '*', '')),
glob(os.path.join(filedir, 'input', '*', '')),
glob(os.path.join(filedir, 'input', '*', '')))
outf = tempname()
os.makedirs(outf)
f = Frame(sims[0], 0, 5)
_writeInputsFunction(1, f, 2, outf, 'input.coor')
mol = Molecule(sims[0])
mol.read(os.path.join(outf, 'e2s2_e1s1p0f5', 'input.coor'))
shutil.rmtree(outf)
from htmd.molecule.molecule import Molecule
from htmd.home import home
import numpy as np
from os import path
mol = Molecule(path.join(home(), 'data', 'metricdistance', 'filtered.pdb'))
mol.read(path.join(home(), 'data', 'metricdistance', 'traj.xtc'))
ref = mol.copy()
ref.coords = np.atleast_3d(ref.coords[:, :, 0])
metr = MetricTMscore(ref, 'protein and name CA')
data = metr.project(mol)
lasttm = np.array([0.9633381, 0.96441294, 0.96553609, 0.96088852, 0.96288511, 0.95677591, 0.96544727, 0.96359811,
0.95658912, 0.96893117, 0.96623924, 0.96064913, 0.96207041, 0.95947848, 0.96657048, 0.95993426,
0.96543296, 0.96806875, 0.96437248, 0.96144066], dtype=np.float32)
assert np.all(np.abs(data[-20:].flatten() - lasttm) < 0.001), 'Coordinates calculation is broken'
from htmd.simlist import simlist
from htmd.projections.metric import Metric
dd = home(dataDir="adaptive")
fsims = simlist([path.join(dd, 'data', 'e1s1_1'), path.join(dd, 'data', 'e1s2_1')],
path.join(dd, 'generators', '1', 'structure.pdb'))
ref = Molecule(path.join(dd, 'generators', '1', 'structure.pdb'))
metr2 = Metric(fsims)
metr2.set(MetricTMscore(ref, 'protein and name CA'))
data2 = metr2.project()
assert data2.trajectories[0].projection.shape == (6, 1)