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)