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test_molecules_fileIO.py

Source:test_molecules_fileIO.py

1import unittest2import numpy as np3import os4import filecmp5from bumpy import Molecules, Metadata6from tests.testutils import PDBComp, GROComp7referenceFilePath = os.path.join(os.path.dirname(__file__), "reference_files/test_molecules_fileIO/")8class test_read_input(unittest.TestCase):9    # TODO : add checks for ignoring HETATOMS, etc10    def test_argument_sanity_checks(self):11        pass12    def test_read_pdb(self):13        inputPDBPath = referenceFilePath + "read_pdb.pdb"14        testMolecule = Molecules(infile=inputPDBPath)15        # test coordinates16        self.assertEqual(testMolecule.coords.shape, (3, 3))17        self.assertAlmostEqual(testMolecule.coords[0, 0], 0)18        self.assertAlmostEqual(testMolecule.coords[1, 1], -10)19        self.assertAlmostEqual(testMolecule.coords[2, 2], 0.7)20        # test atomnames21        self.assertEqual(testMolecule.metadata.atomname[0].strip(), "A")22        self.assertEqual(testMolecule.metadata.atomname[1].strip(), "B")23        self.assertEqual(testMolecule.metadata.atomname[2].strip(), "A")24        # test resnames25        self.assertEqual(testMolecule.metadata.resname[0], "MOLA")26        self.assertEqual(testMolecule.metadata.resname[1], "MOLA")27        self.assertEqual(testMolecule.metadata.resname[2], "MOLB")28    def test_read_gro(self):29        inputGROPath = referenceFilePath + "read_gro.gro"30        testMolecule = Molecules(infile=inputGROPath)31        # test coordinates32        self.assertEqual(testMolecule.coords.shape, (3, 3))33        self.assertAlmostEqual(testMolecule.coords[0, 0], 0)34        self.assertAlmostEqual(testMolecule.coords[1, 1], -10)35        self.assertAlmostEqual(testMolecule.coords[2, 2], 0.7)36        # test atomnames37        self.assertEqual(testMolecule.metadata.atomname[0].strip(), "A")38        self.assertEqual(testMolecule.metadata.atomname[1].strip(), "B")39        self.assertEqual(testMolecule.metadata.atomname[2].strip(), "A")40        # test resnames41        self.assertEqual(testMolecule.metadata.resname[0], "MOLA")42        self.assertEqual(testMolecule.metadata.resname[1], "MOLA")43        self.assertEqual(testMolecule.metadata.resname[2], "MOLB")44        # TODO: test resnums45    def test_ignore_resnames(self):46        inputPDBPath = referenceFilePath + "read_pdb.pdb"47        testMolecule = Molecules(infile=inputPDBPath, ignore="MOLB")48        self.assertEqual(testMolecule.coords.shape, (2, 3))49        self.assertAlmostEqual(testMolecule.coords[0, 0], 0)50        self.assertAlmostEqual(testMolecule.coords[1, 1], -10)51        # test atomnames52        self.assertEqual(testMolecule.metadata.atomname[0].strip(), "A")53        self.assertEqual(testMolecule.metadata.atomname[1].strip(), "B")54        # test resnames55        self.assertEqual(testMolecule.metadata.resname[0], "MOLA")56        self.assertEqual(testMolecule.metadata.resname[1], "MOLA")57class test_write_coordinates(unittest.TestCase):58    def setUp(self):59        ''' Sets up a molecule with equivalent fields to the reference files used for reading tests. Not just60            loading a molecule directly from file because if the reading gets broken then the writing tests would61            likely break too62        '''63        metadata = Metadata(atomname=np.array(("A", "B", "A"), dtype="<U4"),64                            resname=np.array(("MOLA", "MOLA", "MOLB"), dtype="<U4"),65                            ressize=np.array((2, 0, 1)))66        coords = np.array([[0.000, -5.000, 0.500],67                           [5.000, -10.000, 0.600],68                           [10.000, -20.000, 0.700]])69        boxdims = np.array([100, 100, 80])70        self.simple_system = Molecules(metadata=metadata, coords=coords, boxdims=boxdims)71    def tearDown(self):72        ''' Removes temporary files generated during output tests '''73        written_test_files = ["test_write_simple.pdb", "test_write_simple.gro"]74        for file in written_test_files:75            if os.path.exists(file):76                os.remove(file)77    def test_write_pdb(self):78        ''' Want exact match with reference PDB, turn off position changing'''79        temporaryOutputPath = "test_write_simple.pdb"80        self.simple_system.write_coordinates(temporaryOutputPath, position=False, reorder=False)81        self.assertTrue(PDBComp.compareAtomFields(temporaryOutputPath, referenceFilePath + "read_pdb.pdb"))82    def test_write_gro(self):83        ''' Want exact match with reference GRO, turn off position changing'''84        temporaryOutputPath = "test_write_simple.gro"85        self.simple_system.write_coordinates("test_write_simple.gro", position=False, reorder=False)86        self.assertTrue(GROComp.compareAtomFields(temporaryOutputPath, referenceFilePath + "read_gro.gro"))87class test_write_topology(unittest.TestCase):88    def setUp(self):89        metadata = Metadata(atomname=np.array(("A", "A", "B", "B"), dtype="<U4"),90                            resname=np.array(("MOLA", "MOLA", "MOLB", "MOLB"), dtype="<U4"),91                            ressize=np.array((1, 1, 2, 0)))92        self.simple_system = Molecules(metadata=metadata)93    def tearDown(self):94        ''' Removes temporary files generated during output tests '''95        written_test_files = ["test_write_simple.top"]96        for file in written_test_files:97            if os.path.exists(file):98                os.remove(file)99    def test_basic_functionality(self):100        temporaryOutputPath = "test_write_simple.top"101        self.simple_system.write_topology(temporaryOutputPath)102        self.assertTrue(filecmp.cmp(temporaryOutputPath, referenceFilePath + "reference_basic_top.top"))103class test_write_index(unittest.TestCase):104    def setUp(self):105        metadata = Metadata(atomname=np.array(("A", "A", "B", "B"), dtype="<U4"),106                            resname=np.array(("MOLA", "MOLA", "MOLB", "MOLB"), dtype="<U4"),107                            leaflets=np.array((0, 1, 1, 1)),108                            ressize=np.array((1, 1, 2, 0)))109        self.simple_system = Molecules(metadata=metadata)110    def tearDown(self):111        written_test_files = ["test_write_simple.ndx", "test_write_top_leaflet_only.ndx",112                              "test_write_molB_as_dummy.ndx"]113        for file in written_test_files:114            if os.path.exists(file):115                os.remove(file)116    def test_writes_fields(self):117        temporaryOutputPath = "test_write_simple.ndx"118        self.simple_system.write_index(temporaryOutputPath)119        self.assertTrue(filecmp.cmp(temporaryOutputPath, referenceFilePath + "reference_basic_index.ndx"))120    def test_handles_zero_indices(self):121        temporaryOutputPath = "test_write_top_leaflet_only.ndx"122        self.simple_system.metadata.leaflets = np.array((1, 1, 1, 1))123        self.simple_system.write_index(temporaryOutputPath)124        self.assertTrue(filecmp.cmp(temporaryOutputPath, referenceFilePath + "reference_top_index_only.ndx"))125    def test_writes_dummy_particles(self):126        # In this case, we'll just treat MOL B as a dummy particle127        temporaryOutputPath = "test_write_molB_as_dummy.ndx"128        self.simple_system.write_index(temporaryOutputPath, dummy_name="MOLB")129        self.assertTrue(filecmp.cmp(temporaryOutputPath, referenceFilePath + "reference_dummy_index.ndx"))130if __name__ == "__main__":...

test_write.py

Source:test_write.py

1import openmetadata as om2import openmetadata.tests3class TestWrite(openmetadata.tests.DynamicTestCase):4    def test_write_simple(self):5        om.write(self.root_path, 'simple', 'value')6        self.assertEquals(om.read(self.root_path, 'simple'), 'value')7    def test_write_deep(self):8        om.write(self.root_path, '/deep/data/key', 'value')9        self.assertEquals(om.read(self.root_path, '/deep/data/key'), 'value')10    def test_write_invalidgroup(self):11        om.write(self.root_path, '/deep/data.string/key', 'value')...

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