def setUpClass(self):
from moleculekit.home import home
from moleculekit.molecule import Molecule
from moleculekit.tools.preparation import proteinPrepare
from moleculekit.tools.autosegment import autoSegment
self.testf = os.path.join(home(), 'test-data', 'test-voxeldescriptors')
mol = Molecule(os.path.join(self.testf, '3PTB.pdb'))
mol.filter('protein')
mol = autoSegment(mol, field='both')
mol = proteinPrepare(mol)
mol.bonds = mol._guessBonds()
self.mol = mol
def setUpClass(self):
from moleculekit.home import home
from moleculekit.molecule import Molecule
from moleculekit.tools.preparation import systemPrepare
from moleculekit.tools.autosegment import autoSegment
self.testf = os.path.join(home(), "test-data", "test-voxeldescriptors")
mol = Molecule(os.path.join(self.testf, "3PTB.pdb"))
mol.filter("protein")
mol = autoSegment(mol, field="both")
mol = systemPrepare(mol, pH=7.0)
mol.bonds = mol._guessBonds()
self.mol = mol
def test_metricsphericalcoordinate(self):
from moleculekit.molecule import Molecule
from moleculekit.home import home
from os import path
mol = Molecule(
path.join(home(dataDir='test-projections'), 'trajectory',
'filtered.pdb'))
ref = mol.copy()
mol.read(
path.join(home(dataDir='test-projections'), 'trajectory',
'traj.xtc'))
mol.bonds = mol._guessBonds()
res = MetricSphericalCoordinate(ref, 'resname MOL',
'within 8 of resid 98').project(mol)
_ = MetricSphericalCoordinate(ref, 'resname MOL',
'within 8 of resid 98').getMapping(mol)
ref_array = np.load(
path.join(home(dataDir='test-projections'),
'metricsphericalcoordinate', 'res.npy'))
assert np.allclose(res, ref_array, rtol=0, atol=1e-04)