def test_calc_matrix(self):
pdb_structure = prody.parsePDB("data/3_models.pdb")
expected = [ 35.01002624, 47.60315215, 88.64981522, 32.90471145, 87.13023459, 85.76106107]
product_matrix = DihedralRMSDMatrixCalculator.build(pdb_structure)
# print "out", product_matrix.get_data()
# print "out", product_matrix.get_data()
# print product_matrix.get_data()[0]
# print product_matrix[0,1]
numpy.testing.assert_almost_equal(expected, product_matrix.get_data(),8)
def test_get_dihedrals(self):
input = StringIO.StringIO(pdb1)
pdb_structure = prody.parsePDBStream(input)
dihedrals = DihedralRMSDMatrixCalculator.calculateDihedralsForCoordset(
pdb_structure,
pdb_structure.getCoordsets()[0])
# We have to get rid off the unknown values!
numpy.testing.assert_array_almost_equal(
numpy.array(expected_dihedrals[1:-1]),
numpy.array(dihedrals[2:-2]), 2)
def test_calc_matrix(self):
pdb_structure = prody.parsePDB("data/3_models.pdb")
expected = [
35.01002624, 47.60315215, 88.64981522, 32.90471145, 87.13023459,
85.76106107
]
product_matrix = DihedralRMSDMatrixCalculator.build(pdb_structure)
# print "out", product_matrix.get_data()
# print "out", product_matrix.get_data()
# print product_matrix.get_data()[0]
# print product_matrix[0,1]
numpy.testing.assert_almost_equal(expected, product_matrix.get_data(),
8)
def test_get_dihedrals(self):
input = StringIO.StringIO(pdb1)
pdb_structure = prody.parsePDBStream(input)
dihedrals = DihedralRMSDMatrixCalculator.calculateDihedralsForCoordset(pdb_structure,pdb_structure.getCoordsets()[0])
# We have to get rid off the unknown values!
numpy.testing.assert_array_almost_equal(numpy.array(expected_dihedrals[1:-1]), numpy.array(dihedrals[2:-2]), 2)