def build_msm(clusterer_dir, lag_time):
clusterer = verboseload(clusterer_dir)
n_clusters = np.shape(clusterer.cluster_centers_)[0]
labels = clusterer.labels_
msm_modeler = MarkovStateModel(lag_time=lag_time)
print("fitting msm to trajectories with %d clusters and lag_time %d" %(n_clusters, lag_time))
msm_modeler.fit_transform(labels)
verbosedump(msm_modeler, "/scratch/users/enf/b2ar_analysis/msm_model_%d_clusters_t%d" %(n_clusters, lag_time))
print("fitted msm to trajectories with %d states" %(msm_modeler.n_states_))
#np.savetxt("/scratch/users/enf/b2ar_analysis/msm_%d_clusters_t%d_transmat.csv" %(n_clusters, lag_time), msm_modeler.transmat_, delimiter=",")
#G = nx.from_numpy_matrix(msm_modeler.transmat_)
#nx.write_edgelist(G, "/scratch/users/enf/b2ar_analysis/msm_%d_clusters_t%d_edgelist" %(n_clusters, lag_time), msm_modeler.transmat_, delimiter=",")
transmat = msm_modeler.transmat_
mapping = msm_modeler.mapping_
edges = open("/scratch/users/enf/b2ar_analysis/msm_%d_clusters_t%d_edgelist.csv" %(n_clusters, lag_time), "wb")
for i in range(0, msm_modeler.n_states_):
if i == 0:
for j in range(0, msm_modeler.n_states_):
edges.write(";")
edges.write("%d" %mapping[j])
edges.write("\n")
edges.write("%d" %(mapping[i]))
for j in range(0, msm_modeler.n_states_):
prob = transmat[i][j]
edges.write(";")
if prob > 0.000001:
edges.write("%f" %prob)
else:
edges.write("0")
edges.write("\n")
edges.close()
def build_msm(clusterer_dir, lag_time):
clusterer = verboseload(clusterer_dir)
n_clusters = np.shape(clusterer.cluster_centers_)[0]
labels = clusterer.labels_
msm_modeler = MarkovStateModel(lag_time=lag_time)
print("fitting msm to trajectories with %d clusters and lag_time %d" %(n_clusters, lag_time))
msm_modeler.fit_transform(labels)
verbosedump(msm_modeler, "/scratch/users/enf/b2ar_analysis/msm_model_%d_clusters_t%d" %(n_clusters, lag_time))
print("fitted msm to trajectories with %d states" %(msm_modeler.n_states_))
'''
def build_msm(clusterer_dir,
lag_time,
msm_model_dir,
prior_counts=0.0,
ergodic_cutoff='on'):
clusterer = verboseload(clusterer_dir)
n_clusters = np.shape(clusterer.cluster_centers_)[0]
labels = clusterer.labels_
msm_modeler = MarkovStateModel(lag_time=lag_time,
prior_counts=prior_counts,
ergodic_cutoff=ergodic_cutoff)
print(("fitting msm to trajectories with %d clusters and lag_time %d" %
(n_clusters, lag_time)))
msm_modeler.fit_transform(labels)
print(msm_modeler)
verbosedump(msm_modeler, msm_model_dir)
print(("fitted msm to trajectories with %d states" %
(msm_modeler.n_states_)))
return msm_modeler
'''
def build_msm(clusterer_dir, lag_time):
clusterer = verboseload(clusterer_dir)
n_clusters = np.shape(clusterer.cluster_centers_)[0]
labels = clusterer.labels_
msm_modeler = MarkovStateModel(lag_time=lag_time)
print(("fitting msm to trajectories with %d clusters and lag_time %d" %
(n_clusters, lag_time)))
msm_modeler.fit_transform(labels)
verbosedump(
msm_modeler,
"/scratch/users/enf/b2ar_analysis/msm_model_%d_clusters_t%d" %
(n_clusters, lag_time))
print(("fitted msm to trajectories with %d states" %
(msm_modeler.n_states_)))
#np.savetxt("/scratch/users/enf/b2ar_analysis/msm_%d_clusters_t%d_transmat.csv" %(n_clusters, lag_time), msm_modeler.transmat_, delimiter=",")
#G = nx.from_numpy_matrix(msm_modeler.transmat_)
#nx.write_edgelist(G, "/scratch/users/enf/b2ar_analysis/msm_%d_clusters_t%d_edgelist" %(n_clusters, lag_time), msm_modeler.transmat_, delimiter=",")
transmat = msm_modeler.transmat_
mapping = msm_modeler.mapping_
edges = open(
"/scratch/users/enf/b2ar_analysis/msm_%d_clusters_t%d_edgelist.csv" %
(n_clusters, lag_time), "wb")
for i in range(0, msm_modeler.n_states_):
if i == 0:
for j in range(0, msm_modeler.n_states_):
edges.write(";")
edges.write("%d" % mapping[j])
edges.write("\n")
edges.write("%d" % (mapping[i]))
for j in range(0, msm_modeler.n_states_):
prob = transmat[i][j]
edges.write(";")
if prob > 0.000001:
edges.write("%f" % prob)
else:
edges.write("0")
edges.write("\n")
edges.close()
rs = np.random.RandomState(42)
# Load Fs Peptide Data
trajs = FsPeptide().get().trajectories
# Extract Backbone Dihedrals
featurizer = DihedralFeaturizer(types=['chi1'])
diheds = featurizer.fit_transform(trajs)
# Perform Dimensionality Reduction
tica_model = tICA(lag_time=2, n_components=2)
tica_trajs = tica_model.fit_transform(diheds)
# Perform Clustering
clusterer = MiniBatchKMeans(n_clusters=12, random_state=rs)
clustered_trajs = clusterer.fit_transform(tica_trajs)
# Construct MSM
msm = MarkovStateModel(lag_time=2)
assignments = msm.fit_transform(clustered_trajs)
# Plot Stacked Distributions
a = np.concatenate(assignments, axis=0)
d = np.concatenate(diheds, axis=0)
# Plot Stacked Distributions of the sine of each Chi1 angle
# within an arbitrary set of states {2, 5, 0}
path_data = [d[a == i][:, ::2] for i in [2, 5, 0]]
msme.plot_stackdist(path_data)
lag_time = 10
n_clusters = 2000
sys = 'Src-'
n_timescales = 10
lagTime = 50 # 5ns
# loading the data
dataset = []
import glob
for file in glob.glob('highRMSF_phi_psi/*.npy'):
a = np.array(np.load(file))
dataset.append(a)
# building tica
tica = tICA(n_components=n_components, lag_time=lag_time)
tica.fit(dataset)
tica_traj = tica.transform(dataset)
pickle.dump(tica, open(sys + '_tICs_' + str(n_components) + '.pkl', 'wb'))
# clustering
states = msmbuilder.cluster.KMeans(n_clusters=n_clusters)
states.fit(tica_traj)
io.dump(
states, sys + '_tICs_' + str(n_components) + 'nCluster_' +
str(n_clusters) + '.pkl')
# making MSM
msm = MarkovStateModel(lag_time=lagTime, n_timescales=n_timescales)
msm.fit_transform(cl.labels_)
io.dump(msm, 'MSM' + sys)
def construct_graph(msm_modeler_dir, clusterer_dir, n_clusters, tica_lag_time, msm_lag_time, graph_file, inactive = None, active = None, pnas_clusters_averages = None, tica_clusters_averages = None, docking=None, macrostate = None):
clusterer = verboseload(clusterer_dir)
n_clusters = np.shape(clusterer.cluster_centers_)[0]
labels = clusterer.labels_
if not os.path.exists(msm_modeler_dir):
msm_modeler = MarkovStateModel(lag_time=msm_lag_time, n_timescales = 5, sliding_window = True, verbose = True)
print("fitting msm to trajectories with %d clusters and lag_time %d" %(n_clusters, msm_lag_time))
msm_modeler.fit_transform(labels)
verbosedump(msm_modeler, msm_modeler_dir)
else:
msm_modeler = verboseload(msm_modeler_dir)
graph = nx.DiGraph()
mapping = msm_modeler.mapping_
inv_mapping = {v: k for k, v in mapping.items()}
transmat = msm_modeler.transmat_
for i in range(0, msm_modeler.n_states_):
for j in range(0, msm_modeler.n_states_):
prob = transmat[i][j]
if prob > 0.0:
if prob < 0.001: prob = 0.001
original_i = inv_mapping[i]
original_j = inv_mapping[j]
graph.add_edge(original_i, original_j, prob = float(prob), inverse_prob = 1.0 / float(prob), weight = float(prob))
print(graph.number_of_nodes())
if inactive is not None:
scores = convert_csv_to_map_nocombine(inactive)
for cluster in scores.keys():
cluster_id = int(cluster[7:len(cluster)])
if cluster_id in graph.nodes():
score = scores[cluster][0]
graph.node[cluster_id]["inactive_pnas"] = score
if active is not None:
scores = convert_csv_to_map_nocombine(active)
for cluster in scores.keys():
cluster_id = int(re.search(r'\d+',cluster).group())
if cluster_id in graph.nodes():
score = scores[cluster][0]
graph.node[cluster_id]["active_pnas"] = score
if pnas_clusters_averages is not None:
scores = convert_csv_to_map_nocombine(pnas_clusters_averages)
for cluster in scores.keys():
cluster_id = int(re.search(r'\d+',cluster).group())
if cluster_id in graph.nodes():
graph.node[cluster_id]["tm6_tm3_dist"] = scores[cluster][0]
graph.node[cluster_id]["rmsd_npxxy_active"] = scores[cluster][2]
graph.node[cluster_id]["rmsd_connector_active"] = scores[cluster][4]
if tica_clusters_averages is not None:
scores = convert_csv_to_map_nocombine(tica_clusters_averages)
for cluster in scores.keys():
cluster_id = int(re.search(r'\d+',cluster).group())
if cluster_id in graph.nodes():
for i in range(0,len(scores[cluster])):
graph.node[cluster_id]["tIC%d" %(i+1)] = scores[cluster][i]
if docking is not None:
scores = convert_csv_to_map_nocombine(docking)
for cluster in scores.keys():
cluster_id = int(cluster[7:len(cluster)])
if cluster_id in graph.nodes():
score = scores[cluster][0]
graph.node[cluster_id]["docking"] = score
if macrostate is not None:
macromodel = verboseload(macrostate)
for cluster_id in range(0, n_clusters):
if cluster_id in graph.nodes():
microstate_cluster_id = mapping[cluster_id]
macrostate_cluster_id = macromodel.microstate_mapping_[microstate_cluster_id]
#print(macrostate_cluster_id)
graph.node[cluster_id]["macrostate"] = int(macrostate_cluster_id)
nx.write_graphml(graph, graph_file)
linkage='ward',
metric='rmsd',
landmark_strategy='stride',
random_state=None,
max_landmarks=None,
ward_predictor='ward')
ctrajs = clusterer.fit_transform(trajs)
lags = (np.arange(1, 50, 1) / to_ns).astype(int)
n_timescales = 50
timescales = np.zeros((lags.shape[0], n_timescales))
eigenvalues = np.zeros((lags.shape[0], n_timescales))
for idx, lag in enumerate(lags):
msm = MarkovStateModel(lag_time=lag, n_timescales=n_timescales)
msm.fit_transform(ctrajs)
timescales[idx] = msm.timescales_
eigenvalues[idx] = msm.eigenvalues_[1:]
for idx in range(n_timescales):
plt.plot(lags * to_ns, timescales.T[idx])
plt.savefig('figures/rmsd_timescales.png')
plt.ylim((0, int(np.max(timescales.T[1]))))
plt.savefig('figures/rmsd_timescales-detail.png')
plt.clf()
for idx in range(n_timescales):
plt.plot(lags * to_ns, eigenvalues.T[idx])
plt.savefig('figures/rmsd_eigenvalues.png')
# Make Pipeline
def construct_graph(msm_modeler_dir,
clusterer_dir,
n_clusters,
tica_lag_time=5,
msm_lag_time=10,
graph_file="~/graph_file.graphml",
msm_object=None,
clusterer_object=None,
inactive=None,
active=None,
pnas_clusters_averages=None,
tica_clusters_averages=None,
docking=None,
macrostate=None,
cluster_attributes=None,
msm_attributes=None,
min_prob=1e-4):
"""
Construct a .graphml graph based on an MSM and attributes of clusters and/or MSM states.
Saves .graphml graph to disk and returns it as well.
*needs networkx python package to use*
Parameters
----------
msm_modeler_dir: location on disk of verboseload loadable msm object
clusterer_dir: location on disk of verboseload loadable clusterer object
n_clusters: number of clusters
tica_lag_time: tica lag time
msm_lag_time: msm lag time
graph_file: location on disk for saving graphml file
msm_object: pass msm object directly instead of loading from disk
clusterer_object: pass clusterer object directly instead of loading from disk
cluster_attributes: dictionary that maps names of attributes to lists of size n_clusters
where each entry in the list is the value of that attribute for that cluster. for example,
if n_clusters=3, an example cluster_attributes dict might be:
cluster_attributes = {'tyr75-his319_dist': [7.0, 6.0, 8.0], 'phe289-chi2': [90.0, 93.0, 123.2]}
msm_attributes: dictionary that maps names of attributes to lists of size n_msm_states
where each entry in the list is the value of that attribute for that msm state. for example,
if n_msm_states=3, an example cluster_attributes dict might be:
msm_attributes = {'tyr75-his319_dist': [7.0, 6.0, 8.0], 'phe289-chi2': [90.0, 93.0, 123.2]}
"""
if clusterer_object is None:
clusterer = verboseload(clusterer_dir)
else:
clusterer = clusterer_object
n_clusters = np.shape(clusterer.cluster_centers_)[0]
labels = clusterer.labels_
if not os.path.exists(msm_modeler_dir):
if msm_object is not None:
msm_modeler = msm_object
else:
msm_modeler = MarkovStateModel(lag_time=msm_lag_time,
n_timescales=5,
sliding_window=True,
verbose=True)
print(("fitting msm to trajectories with %d clusters and lag_time %d" %
(n_clusters, msm_lag_time)))
msm_modeler.fit_transform(labels)
verbosedump(msm_modeler, msm_modeler_dir)
else:
msm_modeler = verboseload(msm_modeler_dir)
graph = nx.DiGraph()
mapping = msm_modeler.mapping_
inv_mapping = {v: k for k, v in list(mapping.items())}
transmat = msm_modeler.transmat_
for i in range(0, msm_modeler.n_states_):
for j in range(0, msm_modeler.n_states_):
prob = transmat[i][j]
if prob < min_prob:
continue
original_i = inv_mapping[i]
original_j = inv_mapping[j]
graph.add_edge(original_i,
original_j,
prob=float(prob),
inverse_prob=1.0 / float(prob))
print("Number of nodes in graph:")
print((graph.number_of_nodes()))
if inactive is not None:
scores = convert_csv_to_map_nocombine(inactive)
for cluster in list(scores.keys()):
cluster_id = int(cluster[7:len(cluster)])
if cluster_id in graph.nodes():
score = scores[cluster][0]
graph.node[cluster_id]["inactive_pnas"] = score
if active is not None:
scores = convert_csv_to_map_nocombine(active)
for cluster in list(scores.keys()):
cluster_id = int(re.search(r'\d+', cluster).group())
if cluster_id in graph.nodes():
score = scores[cluster][0]
graph.node[cluster_id]["active_pnas"] = score
if pnas_clusters_averages is not None:
scores = convert_csv_to_map_nocombine(pnas_clusters_averages)
for cluster in list(scores.keys()):
cluster_id = int(re.search(r'\d+', cluster).group())
if cluster_id in graph.nodes():
graph.node[cluster_id]["tm6_tm3_dist"] = scores[cluster][0]
graph.node[cluster_id]["rmsd_npxxy_active"] = scores[cluster][
2]
graph.node[cluster_id]["rmsd_connector_active"] = scores[
cluster][4]
if tica_clusters_averages is not None:
scores = convert_csv_to_map_nocombine(tica_clusters_averages)
for cluster in list(scores.keys()):
cluster_id = int(re.search(r'\d+', cluster).group())
if cluster_id in graph.nodes():
for i in range(0, len(scores[cluster])):
graph.node[cluster_id]["tIC%d" %
(i + 1)] = scores[cluster][i]
if docking is not None:
scores = convert_csv_to_map_nocombine(docking)
for cluster in list(scores.keys()):
cluster_id = int(cluster[7:len(cluster)])
if cluster_id in graph.nodes():
score = scores[cluster][0]
graph.node[cluster_id]["docking"] = score
if macrostate is not None:
macromodel = verboseload(macrostate)
for cluster_id in range(0, n_clusters):
if cluster_id in graph.nodes():
microstate_cluster_id = mapping[cluster_id]
macrostate_cluster_id = macromodel.microstate_mapping_[
microstate_cluster_id]
#print(macrostate_cluster_id)
graph.node[cluster_id]["macrostate"] = int(
macrostate_cluster_id)
if cluster_attributes is not None:
for attribute in cluster_attributes.keys():
for cluster_id in mapping.keys():
graph.node[cluster_id][attribute] = float(
cluster_attributes[attribute][cluster_id])
if msm_attributes is not None:
for attribute in msm_attributes.keys():
for cluster_id in mapping.keys():
graph.node[cluster_id][attribute] = float(
msm_attributes[attribute][mapping[cluster_id]])
nx.write_graphml(graph, graph_file)
return (graph)
import matplotlib
matplotlib.use('Agg')
from msmbuilder.msm import MarkovStateModel
from msmbuilder.msm import implied_timescales
import pylab as plt
import matplotlib as mpl
file = 'dataset_nark.best_nonredu.pkl'
name = file[:-4]
cl = pickle.load(open(name + "-GA-mbkm_mdl.pkl"))
n_timescales = 5
lag_times = range(5, 225, 5)
ts = np.zeros([n_timescales, len(lag_times)])
ns_lt = np.ndarray.tolist(np.array(lag_times))
index = 0
for i in lag_times:
msm = MarkovStateModel(lag_time=i, n_timescales=n_timescales)
clL = cl.labels_
#clL10 = [clL[i][::0] for i in range(len(clL))]
msm.fit_transform(clL)
print(msm.timescales_)
len(msm.timescales_)
ts[:, index] = msm.timescales_
index = index + 1
np.save('nark_best_nonredu_ts10_cl400_ns_lt', ns_lt)
np.save('nark_best_nonredu_ts10_cl400_ts', ts)
font = {'family':'Times New Roman', 'size': 12}
plt.rc('font', **font)
cl = pickle.load(open('clustering.pkl','rb'))
n_timescales=10
stepS = 1.2
lag_times=[1, 2, 3,4, 5,6, 7,8, 9,10,11,12,13,14,15,16,17]
l = len(lag_times)
ts=np.zeros([10,l])
ns_lt=np.ndarray.tolist(stepS*np.array(lag_times))
index = 0
for i in lag_times:
msm=MarkovStateModel(lag_time=i, n_timescales=n_timescales)
msm.fit_transform(cl.labels_)
ts[:,index]=msm.timescales_
index=index+1
io.dump(msm,'MSM'+str(i)+'.pkl')
"""
for i in lag_times:
msm = io.load('MSM'+str(i)+'.pkl')
ts[:,index]=msm.timescales_
index=index+1
"""
fig, ax = plt.subplots(1,1)
for i in range(10):
j=i+1
a = trjN.split('/')[-1]
topN = a.split('_md')[0]
rawtop = 'rawTrj/'+roundN+'-rwTop/'+topN+'.prmtop'
return rawtop
def findRawtrj(trjN):
roundN = trjN.split('/')[1][0:3]
sysName = trjN.split('/')[-1]
rawTrj = 'rawTrj/'+roundN+'-rwTrj/'+sysName
return rawTrj
cluster = pickle.load(open(cl,'rb'))
clL = cluster.labels_
msm = MarkovStateModel(lag_time=10,n_timescales=10)
msm.fit_transform(clL)
trjs = clL
N = n_samples
inits = ad.findStarting([trjs], N, method=method)
T = []
for trj in sorted(glob.glob(Trjs)):
T.append(trj)
count = 0
for init in inits:
structure = msm.draw_samples(clL, 1)[init]
print structure
top = findTop(T[structure[0][0]])
rawTrj = findRawtrj(T[structure[0][0]])
# the address should be the address of trajectories corresponding to dataset
# findStarting(trjs, N, method='random')
import adaptivsamplingMSM as ad
from msmbuilder.msm import MarkovStateModel
cluster=pickle.load(open('clustering.pkl','rb'))
trjs = cluster.labels_
N = n_samples
T = []
for trj in sorted(glob.glob('rawTrj/MD1-rwTrj/*.mdcrd')):
T.append(trj)
inits = ad.findStarting([trjs], N, method='leastPop')
msm=MarkovStateModel(lag_time=1, n_timescales=10)
msm.fit_transform(cluster.labels_)
OPF = []
structure = msm.draw_samples(trjs, 1)
for i in range(n_samples):
try:
init = structure[msm.mapping_[inits[i]]]
except KeyError:
print KeyError
traj = T[init[0][0]]
frame = init[0][1]
OPF.append({'traj':traj, 'frame':frame})
json.dump(OPF, open("ClsInf.txt",'w'))
### Step 5: making the CPPtraj inputs
import json