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Diffstat (limited to 'plip/test/test_basic_functions.py')
| -rw-r--r-- | plip/test/test_basic_functions.py | 135 |
1 files changed, 135 insertions, 0 deletions
diff --git a/plip/test/test_basic_functions.py b/plip/test/test_basic_functions.py new file mode 100644 index 0000000..7134f55 --- /dev/null +++ b/plip/test/test_basic_functions.py @@ -0,0 +1,135 @@ +# coding=utf-8 +""" +Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files. +test_basic_functions.py - Unit Tests for basic functionality. +""" + +# Python Standard Library +import unittest +import numpy +import random + +# Own modules +from plip.structure.preparation import PDBComplex +from plip.basic.supplemental import euclidean3d, vector, vecangle, projection +from plip.basic.supplemental import normalize_vector, cluster_doubles, centroid + + +class TestLigandSupport(unittest.TestCase): + """Test for support of different ligands""" + + def test_dna_rna(self): + """Test if DNA and RNA is correctly processed as ligands""" + tmpmol = PDBComplex() + tmpmol.load_pdb('./pdb/1tf6.pdb') + # DNA ligand four times consisting of 31 parts (composite) + self.assertEqual([len(ligand.members) for ligand in tmpmol.ligands].count(31), 4) + for ligset in [set((x[0] for x in ligand.members)) for ligand in tmpmol.ligands]: + if len(ligset) == 4: + # DNA only contains four bases + self.assertEqual(ligset, {'DG', 'DC', 'DA', 'DT'}) + + +class TestMapping(unittest.TestCase): + """Test""" + + def test_ids(self): + """Test if the atom IDs are correctly mapped from internal to original PDB.""" + tmpmol = PDBComplex() + tmpmol.load_pdb('./pdb/1vsn.pdb') + bsid = 'NFT:A:283' + for ligand in tmpmol.ligands: + if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + tmpmol.characterize_complex(ligand) + s = tmpmol.interaction_sets[bsid] + for contact in s.hydrophobic_contacts: + if contact.restype == 'ALA' and contact.resnr == 133: + self.assertEqual(contact.ligatom_orig_idx, 1636) + self.assertEqual(contact.bsatom_orig_idx, 994) + if contact.restype == 'ASP' and contact.resnr == 61: + self.assertEqual(contact.ligatom_orig_idx, 1639) + self.assertEqual(contact.bsatom_orig_idx, 448) + for contact in s.hbonds_ldon + s.hbonds_pdon: + if contact.restype == 'GLN' and contact.resnr == 19: + self.assertEqual(contact.a_orig_idx, 1649) + self.assertEqual(contact.d_orig_idx, 153) + if contact.restype == 'CYS' and contact.resnr == 25: + self.assertEqual(contact.a_orig_idx, 1649) + self.assertEqual(contact.d_orig_idx, 183) + if contact.restype == 'ASN' and contact.resnr == 158: + self.assertEqual(contact.d_orig_idx, 1629) + self.assertEqual(contact.a_orig_idx, 1199) + for contact in s.halogen_bonds: + if contact.restype == 'TYR' and contact.resnr == 67: + self.assertEqual(contact.don.x_orig_idx, 1627) + self.assertEqual(contact.acc.o_orig_idx, 485) + if contact.restype == 'LEU' and contact.resnr == 157: + self.assertEqual(contact.don.x_orig_idx, 1628) + self.assertEqual(contact.acc.o_orig_idx, 1191) + + +class GeometryTest(unittest.TestCase): + """Tests for geometrical calculations in PLIP""" + + def vector_magnitude(self, v): + return numpy.sqrt(sum(x**2 for x in v)) + + # noinspection PyUnusedLocal + def setUp(self): + """Generate random data for the tests""" + # Generate two random n-dimensional float vectors, with -100 <= n <= 100 and values 0 <= i <= 1 + dim = random.randint(1, 100) + self.rnd_vec = [random.uniform(-100, 100) for i in range(dim)] + + def test_euclidean(self): + """Tests for mathematics.euclidean""" + # Are the results correct? + self.assertEqual(euclidean3d([0.0, 0.0, 0.0], [0.0, 0.0, 0.0]), 0) + self.assertEqual(euclidean3d([2.0, 3.0, 4.0], [2.0, 3.0, 4.0]), 0) + self.assertEqual(euclidean3d([4.0, 5.0, 6.0], [4.0, 5.0, 8.0]), 2.0) + # Does the function take vectors or tuples as an input? What about integers? + self.assertEqual(euclidean3d((4.0, 5.0, 6.0), [4.0, 5.0, 8.0]), 2.0) + self.assertEqual(euclidean3d((4.0, 5.0, 6.0), (4.0, 5.0, 8.0)), 2.0) + self.assertEqual(euclidean3d((4, 5, 6), (4.0, 5.0, 8.0)), 2.0) + # Is the output a float? + self.assertIsInstance(euclidean3d([2.0, 3.0, 4.0], [2.0, 3.0, 4.0]), float) + + def test_vector(self): + """Tests for mathematics.vector""" + # Are the results correct? + self.assertEqual(list(vector([1, 1, 1], [0, 1, 0])), [-1, 0, -1]) + self.assertEqual(list(vector([0, 0, 10], [0, 0, 4])), [0, 0, -6]) + # Do I get an Numpy Array? + self.assertIsInstance(vector([1, 1, 1], [0, 1, 0]), numpy.ndarray) + # Do I get 'None' if the points have different dimensions? + self.assertEqual(vector([1, 1, 1], [0, 1, 0, 1]), None) + + def test_vecangle(self): + """Tests for mathematics.vecangle""" + # Are the results correct? + self.assertEqual(vecangle([3, 4], [-8, 6], deg=False), numpy.radians(90.0)) + self.assertEqual(vecangle([3, 4], [-8, 6]), 90.0) + self.assertAlmostEqual(vecangle([-1, -1], [1, 1], deg=False), numpy.pi) + # Correct if both vectors are equal? + self.assertEqual(vecangle([3, 3], [3, 3]), 0.0) + + def test_centroid(self): + """Tests for mathematics.centroid""" + # Are the results correct? + self.assertEqual(centroid([[0, 0, 0], [2, 2, 2]]), [1.0, 1.0, 1.0]) + self.assertEqual(centroid([[-5, 1, 2], [10, 2, 2]]), [2.5, 1.5, 2.0]) + + def test_normalize_vector(self): + """Tests for mathematics.normalize_vector""" + # Are the results correct? + self.assertAlmostEqual(self.vector_magnitude(normalize_vector(self.rnd_vec)), 1) + + def test_projection(self): + """Tests for mathematics.projection""" + # Are the results correct? + self.assertEqual(projection([-1, 0, 0], [3, 3, 3], [1, 1, 1]), [3, 1, 1]) + + def test_cluster_doubles(self): + """Tests for mathematics.cluster_doubles""" + # Are the results correct? + self.assertEqual(set(cluster_doubles([(1, 3), (4, 1), (5, 6), (7, 5)])), {(1, 3, 4), (5, 6, 7)}) |