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 test_read(self):
inputfiles = self.inputfiles
average = AverModels(inputfiles, self.grid.coordknots)
models = [SASModel(inputfiles[1]), SASModel(inputfiles[0])]
average.read_files(reference=1)
diff = 0.0
for i in range(len(inputfiles)):
diff += (models[i].atoms - average.models[i].atoms).max()
self.assertAlmostEqual(diff, 0.0, 10, msg="Files not read properly")
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_dist_move(self):
m = assign_random_mol()
n = SASModel(m.atoms)
m.canonical_parameters()
n.canonical_parameters()
if abs(n.atoms - m.atoms).max() != 0:
logger.error("molecules are different")
p0 = m.can_param
dist_after_mvt = m.dist_after_movement(p0, n, [1, 1, 1])
self.assertEqual(dist_after_mvt, 0, msg="NSD different of 0: %s!=0" % (dist_after_mvt))
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 spatial_extent(self):
"""
Calculate the maximal extent of input models
:return self.size: 6-list with x,y,z max and then x,y,z min
"""
atoms = []
models_fineness = []
for files in self.inputs:
m = SASModel(files)
if len(atoms) == 0:
atoms = m.atoms
else:
atoms = numpy.append(atoms, m.atoms, axis=0)
models_fineness.append(m.fineness)
mean_fineness = sum(models_fineness) / len(models_fineness)
coordmin = atoms.min(axis=0) - mean_fineness
coordmax = atoms.max(axis=0) + mean_fineness
self.size = [
coordmax[0], coordmax[1], coordmax[2], coordmin[0], coordmin[1],
coordmin[2]
]
return self.size
def test_reverse_transform(self):
m = assign_random_mol()
n = SASModel(m.atoms)
m.canonical_parameters()
m.atoms = m.transform(m.can_param, [1, 1, 1], reverse=None)
m.atoms = m.transform(m.can_param, [1, 1, 1], reverse=True)
dist = m.dist(n, m.atoms, n.atoms)
self.assertAlmostEqual(dist, 0.0, 10, msg="pb with reverse transformation : %s != 0.0" % dist)
def test_makegrid(self):
grid = self.grid
lattice = grid.make_grid()
m = SASModel(lattice)
self.assertAlmostEqual(m.fineness,
2 * grid.radius,
10,
msg="grid do not have the computed radius")
def assign_random_mol(inf=None, sup=None):
if not inf:
inf = 0
if not sup:
sup = 100
molecule = numpy.random.randint(inf, sup, size=400).reshape(100, 4).astype(float)
molecule[:, -1] = 1.0
m = SASModel(molecule)
return m
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 read_files(self, reference=None):
"""
Read all the pdb file in the inputfiles list, creating SASModels.
The SASModels created are save in a list, the reference model is the first model in the list.
:param reference: position of the reference model file in the inputfiles list
"""
ref = reference if reference is not None else 0
inputfiles = self.inputfiles
models = []
models.append(SASModel(inputfiles[ref]))
for i in range(len(inputfiles)):
if i==ref:
continue
else:
models.append(SASModel(inputfiles[i]))
self.models = models
return models
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):
"""
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_gridsize(self):
inputfiles = self.inputfiles
grid = self.grid
size = grid.spatial_extent()
coordmax = numpy.array([size[0:3]], dtype="float")
coordmin = numpy.array([size[3:6]], dtype="float")
pb = 0
for i in inputfiles:
m = SASModel(i)
a = coordmin + m.atoms[:, 0:3]
b = m.atoms[:, 0:3] - coordmax
if (a >= 0.0).any() or (b >= 0.0).any():
pb += 1
self.assertEqual(pb, 0, msg="computed size is not the good one")
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, 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 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_dist(self):
m = assign_random_mol()
n = SASModel(m.atoms)
distance = m.dist(n, m.atoms, n.atoms)
self.assertEqual(distance, 0, msg="NSD different of 0: %s!=0" % (distance))
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))