def run(self, q, p=None):
p = np.random.standard_normal(q.shape)
p0, q0 = p.copy(), q.copy()
p -= 0.5 * self.dt * self.U.gradient(q)
for t in range(self.T - 1):
q += self.dt * p
p -= self.dt * self.U.gradient(q)
q += self.dt * p
p -= 0.5 * self.dt * self.U.gradient(q)
dH = (np.sum(p**2) - np.sum(p0**2)) / 2 + self.U(q) - self.U(q0)
accept = False
if dH <= 0 or np.log(np.random.uniform()) < -dH:
accept = True
if self.rmsd_max is not None:
accept &= rmsd(q, q0) < self.rmsd_max
if self.adapt_dt:
self.dt *= 1.02 if accept else 0.98
return q
def test_lsq(self):
rotation, score = self.lsq['svd'].optimum()
rmsd_ = [
np.sqrt(score / len(self.coords[0])),
self.lsq['svd'].rmsd(rotation.matrix),
rmsd(*self.coords)
]
lsq_ = [0.5 * score, self.lsq['svd'](rotation.matrix)]
for name in ('euler', 'axisangle', 'expmap', 'axisangle'):
dofs = self.lsq[name].trafo.from_rotation(rotation).dofs
lsq_.append(self.lsq[name](dofs))
rmsd_ = np.round(rmsd_, 5)
lsq_ = np.round(lsq_, 2)
print(make_title('checking LSQ optimization using SVD'))
print('RMSD: {0}'.format(rmsd_))
print(' LSQ: {0}'.format(lsq_))
tol = 1e-10
self.assertTrue(np.all(np.fabs(rmsd_ - rmsd_[0]) < tol))
self.assertTrue(np.all(np.fabs(lsq_ - lsq_[0]) < tol))
self.assertAlmostEqual(spin.distance(
fit(*self.coords)[0], rotation.matrix),
0.,
delta=tol)
def find2SubGraph(self, thres, Clsts):
''' search 2 sub graph which are most likely to be in 1 rigid domain '''
#---------------------------
#Clsts = self.clusters()
# -----------------------
Entry = self['DynDomEntry']
X = Entry.X
# -----------------------
if len(Clsts) <= 2:
print(
'Num of Par is too small to be merged!\n Return original graph'
)
return (None, None, -1)
Clsts_ProtG = []
val_max = -1
c1_max, c2_max = [], []
for idx1, C1 in enumerate(Clsts):
for idx2, C2 in enumerate(Clsts):
if idx1 < idx2:
ProtG_C1 = [
idx for i in C1 for idx in self.vs[i]['Cluster']
]
ProtG_C2 = [
idx for i in C2 for idx in self.vs[i]['Cluster']
]
ProtG_C12 = [
idx for i in C1 + C2 for idx in self.vs[i]['Cluster']
]
X_1 = X[:, ProtG_C1, :]
X_2 = X[:, ProtG_C2, :]
X_12 = X[:, ProtG_C12, :]
#if rmsd(X_1[0], X_1[1]) > rmsd(X_12[0], X_12[1]) or rmsd(X_2[0], X_2[1]) > rmsd(X_12[0], X_12[1]):
# continue
val = (rmsd(X_1[0], X_1[1]) + rmsd(X_2[0], X_2[1])) / rmsd(
X_12[0], X_12[1])
if val > val_max:
val_max = val
c1_max = C1
c2_max = C2
if val_max > thres:
return (c1_max, c2_max, val_max)
else:
return (None, None, val_max)
def report_progress(self, samples):
info = (len(samples['s']), len(samples['X'][-1]),
rmsd(*samples['X'][-2:]), float(samples['s'][-1]),
samples['r_min'][-1], samples['eps'][-1],
self.posteriors['X'].sampler.dt,
np.sum(self.posteriors['X'].likelihood.N < 1.),
radius_of_gyration(samples['X'][-1]))
print GibbsSampler.output.format(*info)
def rmsd(self, Vertex_IDs=None):
if Vertex_IDs is None:
Vertex_IDs = range(len(self.vs))
Entry = self['DynDomEntry']
X = Entry.X
Prot_IDs = [idx for i in Vertex_IDs for idx in self.vs[i]['Cluster']]
X_Part = X[:, Prot_IDs, :]
N = X_Part.shape[0]
Arr = []
for idx1, x1 in enumerate(X_Part):
for idx2, x2 in enumerate(X_Part):
if idx1 < idx2:
Arr.append(rmsd(x1, x2))
return np.max(Arr)
def test_rmsd(self):
R, t = fit(*self.coords)
out = '{0:.2f} ({1})'
print(make_title('RMSD'))
print(out.format(rmsd(*self.coords), 'SVD'))
rmsds = []
for trafo in self.trafos[1:]:
trafo.matrix_vector = R, t
r = np.mean(np.sum((self.coords[0] - trafo(self.coords[1]))**2,
1))**0.5
print(out.format(r, trafo.rotation.name))
rmsds.append(r)
self.assertAlmostEqual(np.std(rmsds), 0., delta=1e-10)
from csb.bio.utils import rmsd
x = cg.load_example('4ake')
N = len(x)
K = N / 20
X = cg.kmeans(x, K)
K = len(X)
k = 10
params = cg.Parameters(x, X)
params2 = cg.Parameters(x, X)
params2._Z = np.zeros((len(x), k), 'i')
print params.Z.shape
print params._Z.shape
L = cg.Likelihood(x, params)
L2 = cg.KDLikelihood(x, params2, k=k)
params.Z[...] = np.equal.outer(L.distances.argmin(1), np.arange(K))
params2.Z[...] = np.equal.outer(L2.distances.argmin(1), np.arange(k))
print L.chi2, L2.chi2
L.update_stats()
L2.update_stats()
print rmsd(L.mu, L2.mu), np.fabs(L.N - L2.N).max()
n_samples,
int(config['replica']['samples_dump_interval']),
burnin=burnin)
ens = np.array([
sample.variables['structures'].reshape(-1, len(knowns[0]), 3)
for sample in samples
])
ens_flat = ens.reshape(ens.shape[0] * ens.shape[1], -1, 3)
figures_folder = output_folder + 'analysis/compare_to_known/'
if not os.path.exists(figures_folder):
os.makedirs(figures_folder)
if True:
## plot histograms of RMSDs to known structures
rmsds = [map(lambda x: rmsd(known, x), ens_flat) for known in knowns]
max_rmsd = np.max(rmsds)
min_rmsd = np.min(rmsds)
fig = plt.figure()
for i, known in enumerate(knowns):
ax = fig.add_subplot(len(knowns), 1, i + 1)
ax.hist(rmsds[i], bins=np.linspace(0.0, 6, np.sqrt(len(ens_flat))))
ax.set_xlabel('RMSD to ' + fnames[i])
#ax.set_xlim((0.3, 4.0))
fig.tight_layout()
if save_figures:
plt.savefig(figures_folder + 'RMSDs.pdf')
else:
plt.show()
ax.plot((true2_rg, true2_rg), (0, max(h[0])), c='b', label=label2)
ax.set_xlabel('radius of gyration')
ax.set_ylabel('# structures')
ax.set_yticks([])
ax.legend()
if show_plots:
plt.show()
if not True:
from csb.bio.utils import rmsd
rgs = map(radius_of_gyration, structures)
rmsds1 = np.array(map(lambda x: rmsd(true1, x), structures))
rmsds2 = np.array(map(lambda x: rmsd(true2, x), structures))
n_bins = 80
fig = plt.figure()
ax = fig.add_subplot(221)
ax.hist(rmsds1, n_bins, label=label1, alpha=0.6)
ax.set_xlabel('RMSD to {}'.format(label1))
ax.set_ylabel('# structures')
ax = fig.add_subplot(222)
ax.hist(rmsds2, n_bins, label=label2, alpha=0.6)
ax.set_xlabel('RMSD to {}'.format(label2))
ax.set_ylabel('# structures')
structures_flipped1 = structures.copy()
cpath = sims['common_path']
n_structures = sims['n_structures']
odirs = sims['output_dirs']
MAP_samples = []
for (n, odir) in zip(n_structures, odirs):
cfg_file = cpath + odir + '/config.cfg'
p = make_posterior(parse_config_file(cfg_file))
samples = load_samples_from_cfg(cfg_file, burnin=60000)
Es = map(lambda x: -p.log_prob(**x.variables), samples)
MAP_sample = samples[np.argmin(Es)]
MAP_samples.append(MAP_sample.variables['structures'].reshape(n, 56, 3))
MAP_samples_flat = np.array([x for y in MAP_samples for x in y])
invar_rmsd = lambda x, y: min(rmsd(x, y), rmsd(x, -y))
tmp = StructureParser(
os.path.expanduser('~/projects/ensemble_hic/data/proteins/1pga.pdb'))
ref_1pga = tmp.parse().get_coordinates(['CA'])
tmp = StructureParser(
os.path.expanduser('~/projects/ensemble_hic/data/proteins/1shf.pdb'))
ref_1shf = tmp.parse().get_coordinates(['CA'])
rmsds_to_1pga = map(lambda x: invar_rmsd(ref_1pga, x), MAP_samples_flat)
rmsds_to_1shf = map(lambda x: invar_rmsd(ref_1shf, x), MAP_samples_flat)
labels = (np.array(rmsds_to_p1) < np.array(rmsds_to_p2))
for i, s in enumerate(MAP_samples_flat):
ref = (ref_1pga, ref_1shf)[labels[i]]
if rmsd(ref, -s) < rmsd(ref, s):
MAP_samples_flat[i] *= -1
MAP_samples_flat[i] = fit_transform(ref, MAP_samples_flat[i])
[rex.history[pair].acceptance_rate() for pair in rex.history.pairs])
if False:
from csb.bio.utils import rmsd
from scipy.spatial.distance import squareform
burnin = -400
thining = 1 #0
mask = np.ones(333, 'i')
mask[:11] = 0
mask[47:66] = 0
x = X[burnin::thining].reshape(-1, 333, 3)
x = np.compress(mask, x, 1)
d = [
rmsd(xx, x[j]) for i, xx in enumerate(x) for j in range(i + 1, len(x))
]
from sklearn.cluster import spectral_clustering
K = 4
membership = spectral_clustering(np.exp(-squareform(d)),
n_clusters=K,
eigen_solver='arpack')
i = np.argsort(membership)
matshow(squareform(d)[i][:, i], origin='lower')
def testRmsdMirrorImage(self):
X, Y = X7, X7.copy()
Y[:, 0] *= -1
rmsd = cbu.rmsd(X, Y)
self.assertAlmostEqual(rmsd, 50.0)
def testRmsd(self):
rmsd = cbu.rmsd(X1, X2)
self.assertAlmostEqual(rmsd, (4./3.)**0.5)