def makeHMM(Trajectories, topology): top = md.load_prmtop(topology) alpha_carbons = [a.index for a in top.atoms if a.name == 'CA'] filenames = sorted(glob(Trajectories)) first_frame = md.load_frame(filenames[0], 0, top=top) f = SuperposeFeaturizer(alpha_carbons, first_frame) dataset = [] for fragment in filenames: for chunk in md.iterload(fragment, chunk=100, top=top): dataset.append(f.partial_transform(chunk)) hmm = GaussianHMM(n_states=8) hmm.fit(dataset) print(hmm.timescales_) return hmm
def makeHMM(Trajectories, topology): top = md.load_prmtop(topology) alpha_carbons = [a.index for a in top.atoms if a.name == 'CA'] filenames = sorted(glob(Trajectories)) first_frame = md.load_frame(filenames[0], 0, top=top) f = SuperposeFeaturizer(alpha_carbons, first_frame) dataset = [] for fragment in filenames: for chunk in md.iterload(fragment, chunk=100, top=top): dataset.append(f.partial_transform(chunk)) hmm = GaussianHMM(n_states=8) hmm.fit(dataset) print(hmm.timescales_) return hmm
from glob import glob filenames = sorted(glob("05_Prod_*.nc")) topology = md.load_prmtop(glob("*nowat.prmtop")[0]) first_frame = md.load_frame(filenames[0], 0, top=topology) indices = [ atom.index for atom in topology.atoms if atom.element.symbol in ['C', 'O', 'N'] ] featurizer = SuperposeFeaturizer(indices, first_frame) sequences = [] for fragment in filenames: for chunk in md.iterload(fragment, chunk=100, top=topology): sequences.append(featurizer.partial_transform(chunk)) lag_times = [1, 20, 50, 100, 200, 400] hmm_ts0 = {} hmm_ts1 = {} n_states = [n for n in range(2, 11, 2)] for n in n_states: hmm_ts0[n] = [] hmm_ts1[n] = [] for lag_time in lag_times: #pdb.set_trace() strided_data = [ s[i::lag_time] for s in sequences for i in range(lag_time) ] hmm = GaussianHMM(n_states=n, n_init=1).fit(strided_data)
from glob import glob filenames = sorted(glob("05_Prod_*.nc")) topology = md.load_prmtop(glob("*nowat.prmtop")[0]) first_frame = md.load_frame(filenames[0], 0, top=topology) indices = [atom.index for atom in topology.atoms if atom.element.symbol in ['C', 'O', 'N']] featurizer = SuperposeFeaturizer(indices, first_frame) sequences = [] for fragment in filenames: for chunk in md.iterload(fragment, chunk = 100, top = topology): sequences.append(featurizer.partial_transform(chunk)) lag_times = [1, 20, 50, 100, 200, 400] hmm_ts0 = {} hmm_ts1 = {} n_states = [n for n in range(2,11,2)] for n in n_states: hmm_ts0[n] = [] hmm_ts1[n] = [] for lag_time in lag_times: #pdb.set_trace() strided_data = [s[i::lag_time] for s in sequences for i in range(lag_time)] hmm = GaussianHMM(n_states=n, n_init=1).fit(strided_data) timescales = hmm.timescales_ * lag_time