def save_new_ref(filename, data):
""" Saves a new version of the reference data, and backs up the old """
ext = filename.split('.')[-1]
if (data == None):
print "WARNING: Error generating file: %s" % filename
print "Skipped... try again."
return
if os.path.exists(filename):
os.system('mv %s %s' % (filename, BACKUP_DIR))
if ext in ['h5', 'lh5']:
if scipy.sparse.issparse(data):
data = data.toarray()
Serializer.SaveData(filename, data)
elif ext == 'mtx':
io.mmwrite(filename, data)
elif ext == 'pkl':
f = open(filename, 'w')
pickle.dump(f, data)
f.close()
else:
raise ValueError('Could not understand extension (.%s) for %s' %
(ext, filename))
return
assignments = Serializer.LoadData(args.assignments)
ratemtx_fn = pjoin(args.outdir, 'K.mtx')
tcounts_fn = pjoin(args.outdir, 'tCounts.mtx')
unsym_fn = pjoin(args.outdir, 'tCounts.UnSym.mtx')
mapping_fn = pjoin(args.outdir, 'Mapping.dat')
fixed_fn = pjoin(args.outdir, 'Assignments.Fixed.h5')
pops_fn = pjoin(args.outdir, 'Populations.dat')
if not os.path.exists(args.outdir):
os.mkdir(args.outdir)
outlist = [ratemtx_fn, tcounts_fn, unsym_fn, fixed_fn, pops_fn]
for e in outlist:
arglib.die_if_path_exists(e)
# if lag time is not one, there's going to be a unit mispatch between
# what you get and what you're expecting.
lag_time = 1
counts, rev_counts, t_matrix, populations, mapping = MSMLib.build_msm(
assignments, lag_time=lag_time, symmetrize=args.symmetrize)
K = MSMLib.estimate_rate_matrix(rev_counts, assignments)
np.savetxt(pops_fn, populations)
np.savetxt(mapping_fn, mapping, "%d")
scipy.io.mmwrite(ratemtx_fn, K)
scipy.io.mmwrite(tcounts_fn, rev_counts)
scipy.io.mmwrite(unsym_fn, counts)
Serializer.SaveData(fixed_fn, assignments)
for e in outlist:
logger.info('Saved %s' % e)
def GetPhi(X):
return GetAllPhiDipeptide(C1,
NumResi=NumResi,
a=a,
aC=aC,
aN=aN,
aCA=aCA,
X=X)
Phi = P1.EvaluateObservableAcrossProject(GetPhi)
def GetPsi(X):
return GetAllPsiDipeptide(C1,
NumResi=NumResi,
a=a,
aC=aC,
aN=aN,
aCA=aCA,
X=X)
Psi = P1.EvaluateObservableAcrossProject(GetPsi)
print(Phi)
Serializer.SaveData("./Phi.h5", Phi)
Serializer.SaveData("./Psi.h5", Psi)
