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)
Beispiel #2
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 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)
Beispiel #3
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 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)