def test_init(self):
m = SASModel()
m.read(self.testfile)
n = SASModel(self.testfile)
param1 = m.rfactor
param2 = n.rfactor
self.assertEqual(param1, param2, msg="pdb file not read correctly")
def assign_models(self, molecule=None):
"""
Create SASModels from pdb files saved in self.inputfiles and saved them in self.models.
Center of mass, inertia tensor and canonical parameters are computed for each SASModel.
:param molecule: optional 2d array, coordinates of the atoms for the model to create
:return self.models: list of SASModel
"""
if not self.inputfiles and len(molecule) == 0:
logger.error("No input files")
if self.inputfiles:
for inputpdb in self.inputfiles:
model = SASModel()
model.read(inputpdb)
model.centroid()
model.inertiatensor()
model.canonical_parameters()
self.sasmodels.append(model)
if len(self.inputfiles) != len(self.sasmodels):
logger.error("Problem of assignment\n%s models for %s files" % (len(self.sasmodels), len(self.inputfiles)))
elif len(molecule) != 0:
model = SASModel()
model.atoms = molecule
model.centroid()
model.inertiatensor()
model.canonical_parameters()
self.sasmodels.append(model)
return self.sasmodels
def test_same(self):
m = SASModel()
m.read(self.testfile)
m.save(self.outfile)
infile = open(self.testfile).read()
outfile = open(self.outfile).read()
self.assertEqual(infile, outfile, msg="file content is the same")
def assign_models(self, molecule=None):
"""
Create SASModels from pdb files saved in self.inputfiles and saved them in self.models.
Center of mass, inertia tensor and canonical parameters are computed for each SASModel.
:param molecule: optional 2d array, coordinates of the atoms for the model to create
:return self.models: list of SASModel
"""
if not self.inputfiles and len(molecule) == 0:
logger.error("No input files")
if self.inputfiles:
for inputpdb in self.inputfiles:
model = SASModel()
model.read(inputpdb)
model.centroid()
model.inertiatensor()
model.canonical_parameters()
self.sasmodels.append(model)
if len(self.inputfiles) != len(self.sasmodels):
logger.error("Problem of assignment\n%s models for %s files" %
(len(self.sasmodels), len(self.inputfiles)))
elif len(molecule) != 0:
model = SASModel()
model.atoms = molecule
model.centroid()
model.inertiatensor()
model.canonical_parameters()
self.sasmodels.append(model)
return self.sasmodels
def test_distance(self):
m = SASModel()
n = SASModel()
m.read(self.testfile1)
n.read(self.testfile2)
f_np = m.dist(n, m.atoms, n.atoms, False)
f_cy = m.dist(n, m.atoms, n.atoms, True)
self.assertAlmostEqual(f_np, f_cy, 10,
"distance is the same %s!=%s" % (f_np, f_cy))
def test_same(self):
m = SASModel()
n = SASModel()
m.read(self.testfile1)
n.read(self.testfile1)
numpy.random.shuffle(n.atoms)
f_np = m.dist(n, m.atoms, n.atoms, False)
f_cy = m.dist(n, m.atoms, n.atoms, True)
self.assertAlmostEqual(f_np, 0, 10, "NSD not nul with np")
self.assertAlmostEqual(f_cy, 0, 10, "NSD not nul with cy")
def test_invariants(self):
m = SASModel()
m.read(self.testfile1)
f_np, r_np, d_np = m.calc_invariants(False)
f_cy, r_cy, d_cy = m.calc_invariants(True)
self.assertAlmostEqual(f_np, f_cy, 10,
"fineness is the same %s!=%s" % (f_np, f_cy))
self.assertAlmostEqual(r_np, r_cy, 10,
"Rg is the same %s!=%s" % (r_np, r_cy))
self.assertAlmostEqual(d_np, d_cy, 10,
"Dmax is the same %s!=%s" % (d_np, d_cy))
def assign_models(self):
"""
Create SASModels from pdb files saved in self.inputfiles and saved them in self.models.
Center of mass, inertia tensor and canonical parameters are computed for each SASModel.
:return self.models: list of SASModel
"""
for inputpdb in self.inputfiles:
model = SASModel()
model.read(inputpdb)
model.centroid()
model.inertiatensor()
model.canonical_parameters()
self.models.append(model)
if len(self.inputfiles) != len(self.models):
logger.error("Problem of assignment\n%s models for %s files" % (len(self.models), len(self.inputfiles)))
return self.models
def assign_models(self):
"""
Create SASModels from pdb files saved in self.inputfiles and saved them in self.models.
Center of mass, inertia tensor and canonical parameters are computed for each SASModel.
:return self.models: list of SASModel
"""
for inputpdb in self.inputfiles:
model = SASModel()
model.read(inputpdb)
model.centroid()
model.inertiatensor()
model.canonical_parameters()
self.models.append(model)
if len(self.inputfiles) != len(self.models):
logger.error("Problem of assignment\n%s models for %s files" %
(len(self.models), len(self.inputfiles)))
return self.models
def test_rfactor(self):
m = SASModel()
m.read(self.testfile)
n = SASModel()
n.read(self.testfile)
self.assertEqual(m.rfactor, n.rfactor, msg="R-factor is not the same %s != %s"%(m.rfactor, n.rfactor))