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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, 0 insertions, 135 deletions
diff --git a/plip/test/test_basic_functions.py b/plip/test/test_basic_functions.py deleted file mode 100644 index 7134f55..0000000 --- a/plip/test/test_basic_functions.py +++ /dev/null @@ -1,135 +0,0 @@ -# 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)}) |