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_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 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
