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|
import os
import sys
import csb.test as test
from csb.bio.io.wwpdb import EntryID, StandardID, DegenerateID, SeqResID, InvalidEntryIDError, HeaderFormatError
from csb.bio.io.wwpdb import RobustResidueMapper, FastResidueMapper, CombinedResidueMapper, ResidueMappingError, SparseChainSequence
from csb.bio.io.wwpdb import StructureParser, RegularStructureParser, LegacyStructureParser, UnknownPDBResidueError
from csb.bio.io.wwpdb import get, find, FileSystemStructureProvider, RemoteStructureProvider, CustomStructureProvider, StructureNotFoundError
from csb.bio.sequence import SequenceAlphabets, ProteinAlphabet, SequenceTypes, RichSequence
from csb.bio.structure import ChemElements, SecStructures, Structure, Chain
@test.regression
class TestBiomoleculeRegressions(test.Case):
def testCommaSplitting(self):
"""
@see: [CSB 0000067]
"""
pdbfile = self.config.getTestFile('3shm_ca.pdb')
parser = LegacyStructureParser(pdbfile)
s1 = parser.parse_biomolecule(1, True)
self.assertEqual(len(s1.chains), 60)
self.assertEqual(s1.first_chain.id, 'A')
@test.regression
class TestSecStructureRegressions(test.Case):
def testSecStructureParsing(self):
"""
@see: [CSB 0000045]
"""
pdbfile = self.config.getTestFile('1d3z.regular.pdb')
structure = StructureParser(pdbfile).parse_structure(1)
self.assertTrue(structure.chains['A'].secondary_structure is not None)
@test.regression
class TestMappingRegressions(test.Case):
def testHetMapping(self):
"""
@see: [CSB 0000031]
"""
pdbfile = self.config.getTestFile('1d3z.regular.pdb')
structure = StructureParser(pdbfile).parse_structure(1)
residue = structure.chains['A'].find(26)
self.assertTrue(residue.has_structure)
self.assertTrue(residue.atoms.length > 0)
for an in residue.atoms:
self.assertTrue(residue[an].vector.tolist())
def testNonStandardResidueMapping(self):
"""
@see: [CSB 0000052]
"""
pdbfile = self.config.getTestFile('3p1u.pdb')
chain = StructureParser(pdbfile).parse_structure().chains['A']
for residue in chain.residues:
if residue.rank < 15:
self.assertFalse(residue.has_structure)
elif residue.rank in (15, 16):
self.assertTrue(residue.has_structure)
self.assertEqual(chain.residues[2].sequence_number, None)
self.assertEqual(chain.residues[15].sequence_number, 39)
self.assertEqual(chain.residues[16].sequence_number, 40)
@test.unit
class TestStructureParser(test.Case):
def setUp(self):
super(TestStructureParser, self).setUp()
regular_file = self.config.getTestFile('1d3z.regular.pdb')
legacy_file = self.config.getTestFile('1d3z.legacy.pdb')
self.rp = StructureParser(regular_file)
self.lp = StructureParser(legacy_file)
def testFactory(self):
self.assertTrue(isinstance(self.rp, RegularStructureParser))
self.assertTrue(isinstance(self.lp, LegacyStructureParser))
@test.unit
class TestLegacyStructureParser(test.Case):
def setUp(self):
super(TestLegacyStructureParser, self).setUp()
self.pdb = self.config.getTestFile('1d3z.legacy.pdb')
self.parser = LegacyStructureParser(self.pdb)
def testParseModels(self):
ensemble = self.parser.parse_models()
self.assertEqual(ensemble.models.length, 10)
self.assertEqual(ensemble[0].model_id, 1)
self.assertEqual(ensemble.models[1].model_id, 1)
def testParseStructure(self):
structure = self.parser.parse(model=1)
self.assertEqual(self.parser.parse_structure().model_id, 1)
self.assertEqual(structure.accession, '1d3z')
self.assertEqual(structure.model_id, 1)
# Chain level
self.assertEqual(structure.chains.length, 1)
self.assertEqual(len(structure.chains), 1)
self.assertEqual(structure.first_chain.molecule_id, '1')
self.assertEqual(structure.chains['A'].sequence, 'MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG')
self.assertEqual(len(structure.chains['A']), 76)
self.assertEqual(len(structure['A']), 76)
# Residue level
self.assertEqual(len(structure['A'][1:10]), 9)
self.assertEqual(structure['A'][0].type, SequenceAlphabets.Protein.MET)
self.assertEqual(structure['A'][0].label, 'MSE')
self.assertEqual(structure['A'][1].label, 'GLN')
self.assertTrue(structure['A'][0].is_modified)
self.assertFalse(structure['A'][1].is_modified)
# Atom level
self.assertEqual(structure['A'][1].atoms['CA'].element, None)
self.assertNotEqual(structure['A'][2].atoms['CA'].element, None)
self.assertEqual(structure['A'][2].atoms['CA'].element, ChemElements.C)
vector = [51.653, -89.304, 8.833]
self.assertEqual(structure['A'][0]['CA'].vector.tolist(), vector)
def testParseResidue(self):
self.assertEqual(self.parser.parse_residue('AGM'), SequenceAlphabets.Protein.ARG.name) #@UndefinedVariable
self.assertEqual(self.parser.parse_residue('AGM', as_type=SequenceTypes.Protein), SequenceAlphabets.Protein.ARG.name) #@UndefinedVariable
self.assertRaises(UnknownPDBResidueError, self.parser.parse_residue, 'AGM', as_type=SequenceTypes.NucleicAcid)
def testParseResidueSafe(self):
self.assertEqual(self.parser.parse_residue_safe('AGM', as_type=None), SequenceAlphabets.Protein.ARG.name) #@UndefinedVariable
self.assertEqual(self.parser.parse_residue_safe('AGM', as_type=SequenceTypes.Protein), SequenceAlphabets.Protein.ARG.name) #@UndefinedVariable
self.assertEqual(self.parser.parse_residue_safe('AGM', as_type=SequenceTypes.NucleicAcid), SequenceAlphabets.Nucleic.Any.name) #@UndefinedVariable
self.assertEqual(self.parser.parse_residue_safe('junk', as_type=SequenceTypes.Protein), SequenceAlphabets.Unknown.UNK.name) #@UndefinedVariable
def testGuessSequenceType(self):
self.assertEqual(self.parser.guess_sequence_type('AGM'), SequenceTypes.Protein)
self.assertEqual(self.parser.guess_sequence_type('DOC'), SequenceTypes.NucleicAcid)
self.assertRaises(UnknownPDBResidueError, self.parser.guess_sequence_type, 'junk')
def testFileName(self):
self.assertEqual(self.parser.filename, self.pdb)
def testModels(self):
self.assertEqual(self.parser.models(), list(range(1, 11)))
def testParseBiomolecule(self):
pdbfile = self.config.getTestFile('3p1u.pdb')
parser = LegacyStructureParser(pdbfile)
s2 = parser.parse_biomolecule(2)
self.assertEqual(len(s2.chains), 1)
self.assertEqual(s2.first_chain.id, 'B1')
self.assertRaises(KeyError, parser.parse_biomolecule, 3)
def testParseHetMolecules(self):
with self.config.getTempStream() as tmp:
tmp.write('HETATM 1 NA BLM A 1 -14.575 27.241 3.310 1.00 0.00 N ')
tmp.flush()
parser = LegacyStructureParser(tmp.name)
self.assertRaises(HeaderFormatError, parser.parse_structure)
del parser
@test.unit
class TestRegularStructureParser(test.Case):
def setUp(self):
super(TestRegularStructureParser, self).setUp()
self.pdb = self.config.getTestFile('1d3z.regular.pdb')
self.mapping = self.config.getTestFile('mapping.pdb')
self.parser = RegularStructureParser(self.pdb)
def testMapper(self):
p = RegularStructureParser(self.pdb, mapper=None)
self.assertTrue(isinstance(p.mapper, CombinedResidueMapper))
p.mapper = FastResidueMapper()
self.assertTrue(isinstance(p.mapper, FastResidueMapper))
def testCombinedMapping(self):
# default mapper
c = self.parser.parse(self.mapping)['E']
self.assertEqual(c.residues[14].type, ProteinAlphabet.GLU)
self.assertEqual(c.residues[15].type, ProteinAlphabet.GLU)
self.assertEqual(c.residues[16].type, ProteinAlphabet.THR)
self.assertEqual(4, sum([1 for r in c if r.has_structure]))
# explicit combined mapper
self.parser.mapper = CombinedResidueMapper()
c = self.parser.parse(self.mapping)['E']
self.assertEqual(4, sum([1 for r in c if r.has_structure]))
def testFastMapping(self):
self.parser.mapper = FastResidueMapper()
self.assertRaises(ResidueMappingError, self.parser.parse, self.mapping)
mapping2 = self.config.getTestFile('mapping2.pdb')
c = self.parser.parse(mapping2)['E']
self.assertEqual(2, sum([1 for r in c if r.has_structure]))
def testRobustMapping(self):
mapping3 = self.config.getTestFile('mapping3.pdb')
self.parser.mapper = RobustResidueMapper()
self.assertRaises(ResidueMappingError, self.parser.parse, mapping3)
c = self.parser.parse(self.mapping)['E']
self.assertEqual(4, sum([1 for r in c if r.has_structure]))
def testParseModels(self):
ensemble = self.parser.parse_models()
self.assertEqual(ensemble.models.length, 10)
self.assertEqual(ensemble[0].model_id, 1)
self.assertEqual(ensemble.models[1].model_id, 1)
self.assertRaises(ValueError, self.parser.parse_models, (999, 1000))
pdb = self.config.getTestFile('3p1u.pdb')
ensemble = RegularStructureParser(pdb).parse_models()
self.assertEqual(ensemble.models.length, 1)
self.assertEqual(ensemble[0].model_id, 1)
self.assertEqual(ensemble[0].resolution, 2.05)
def testParseStructure(self):
structure = self.parser.parse(model=2)
self.assertEqual(self.parser.parse_structure().model_id, 1)
self.assertEqual(structure.resolution, None)
self.assertEqual(structure.accession, '1d3z')
self.assertEqual(structure.model_id, 2)
# Chain level
self.assertEqual(structure.chains.length, 1)
self.assertEqual(len(structure.chains), 1)
self.assertEqual(structure.chains['A'].sequence, 'MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG')
self.assertEqual(structure.chains['A'].sequence, ''.join([str(r.type) for r in structure.chains['A'] if r.has_structure]))
ss = structure.chains['A'].secondary_structure
self.assertEqual(ss.to_string(), '-EEEEE-----EEEEE-----HHHHHHHHHHHHHH-HHH-EEEEE--EE------HHHHH-----EEEEEE')
self.assertEqual(len(ss.scan(1, 99, filter=SecStructures.Helix)), 3)
self.assertEqual(ss[1].start, 2)
self.assertEqual(ss[1].end, 6)
self.assertEqual(len(structure.chains['A']), 76)
self.assertEqual(len(structure['A']), 76)
# Residue level
self.assertEqual(len(structure['A'][1:10]), 9)
self.assertEqual(structure['A'][0].type, SequenceAlphabets.Protein.MET)
self.assertEqual(structure['A'][0].label, 'MSE')
self.assertEqual(structure['A'][1].label, 'GLN')
# Atom
vector = [52.647, -87.443, 9.674]
self.assertEqual(structure['A'][0]['CA'].vector.tolist(), vector)
def testParseResidue(self):
self.assertEqual(self.parser.parse_residue('AGM'), SequenceAlphabets.Protein.ARG.name) #@UndefinedVariable
self.assertEqual(self.parser.parse_residue('AGM', as_type=SequenceTypes.Protein), SequenceAlphabets.Protein.ARG.name) #@UndefinedVariable
self.assertRaises(UnknownPDBResidueError, self.parser.parse_residue, 'AGM', as_type=SequenceTypes.NucleicAcid)
def testParseResidueSafe(self):
self.assertEqual(self.parser.parse_residue_safe('AGM', as_type=None), SequenceAlphabets.Protein.ARG.name) #@UndefinedVariable
self.assertEqual(self.parser.parse_residue_safe('AGM', as_type=SequenceTypes.Protein), SequenceAlphabets.Protein.ARG.name) #@UndefinedVariable
self.assertEqual(self.parser.parse_residue_safe('AGM', as_type=SequenceTypes.NucleicAcid), SequenceAlphabets.Nucleic.Any.name) #@UndefinedVariable
self.assertEqual(self.parser.parse_residue_safe('junk', as_type=SequenceTypes.Protein), SequenceAlphabets.Unknown.UNK.name) #@UndefinedVariable
def testGuessSequenceType(self):
self.assertEqual(self.parser.guess_sequence_type('AGM'), SequenceTypes.Protein)
self.assertEqual(self.parser.guess_sequence_type('DOC'), SequenceTypes.NucleicAcid)
self.assertRaises(UnknownPDBResidueError, self.parser.guess_sequence_type, 'junk')
def testFileName(self):
self.assertEqual(self.parser.filename, self.pdb)
def testModels(self):
self.assertEqual(self.parser.models(), list(range(1, 11)))
@test.unit
class TestFastResidueMapper(test.Case):
def setUp(self):
super(TestFastResidueMapper, self).setUp()
self.mapper = FastResidueMapper()
def _build(self, string):
id = str(hash(string))
seq = RichSequence(id, "", string, SequenceTypes.Protein)
return SparseChainSequence.create(Chain.from_sequence(seq))
def testMap(self):
ref = self._build("ZABCD")
sparse = self._build("AC")
self.assertRaises(ResidueMappingError, self.mapper.map, sparse, ref)
sparse.residues[2].id = (22, None)
result = self.mapper.map(sparse, ref)
self.assertEqual(result.sequence, "-A-C-")
def testModifiedResidueMapping(self):
"""
Strictly speaking, this is a regression test. But it so essential that
we should keep it here.
@see: [csb: 19]
"""
pdb = self.config.getTestFile('modified.pdb')
structure = StructureParser(pdb, mapper=self.mapper).parse_structure()
chain = structure.first_chain
self.assertFalse(chain.residues[1].has_structure)
self.assertEqual(chain.residues[1].label, "MET")
self.assertTrue(chain.residues[19].has_structure)
self.assertEqual(chain.residues[19].label, "MSE")
@test.unit
class TestRobustResidueMapper(TestFastResidueMapper):
def setUp(self):
super(TestRobustResidueMapper, self).setUp()
self.mapper = RobustResidueMapper()
def testMap(self):
ref = self._build("ABCD")
sparse = self._build("EF")
self.assertRaises(ResidueMappingError, self.mapper.map, sparse, ref)
ref = self._build("ZABCD")
sparse = self._build("AC")
result = self.mapper.map(sparse, ref)
self.assertEqual(result.sequence, "-A-C-")
def testModifiedResidueMapping(self):
pdb = self.config.getTestFile('modified2.pdb')
structure = StructureParser(pdb, mapper=self.mapper).parse_structure()
chain = structure.first_chain
self.assertTrue(chain.residues[1].has_structure)
self.assertEqual(chain.residues[1].label, "MSE")
self.assertFalse(chain.residues[19].has_structure)
self.assertEqual(chain.residues[19].label, "MET")
@test.unit
class TestCombinedResidueMapper(TestFastResidueMapper):
def setUp(self):
super(TestCombinedResidueMapper, self).setUp()
self.mapper = CombinedResidueMapper()
def testMap(self):
ref = self._build("ZABCD")
sparse = self._build("AC")
result = self.mapper.map(sparse, ref)
self.assertEqual(result.sequence, "-A-C-")
@test.unit
class TestFileSystemProvider(test.Case):
def setUp(self):
super(TestFileSystemProvider, self).setUp()
self.path = self.config.data
self.provider = FileSystemStructureProvider()
self.provider.add(self.path)
def testAdd(self):
self.assertEqual(len(self.provider.paths), 1)
self.provider.add('.')
self.assertEqual(self.provider.paths[1], '.')
self.assertEqual(len(self.provider.paths), 2)
self.assertRaises(IOError, self.provider.add, 'non-exi$ting path')
def testRemove(self):
self.assertEqual(len(self.provider.paths), 1)
self.provider.remove(self.path)
self.assertEqual(len(self.provider.paths), 0)
self.assertRaises(ValueError, self.provider.remove, 'non-exi$ting path')
def testFind(self):
f1 = self.provider.find('3p1u')
f2 = self.config.getTestFile('3p1u.pdb')
self.assertEqual(os.path.abspath(f1), os.path.abspath(f2))
self.assertEqual(None, self.provider.find('$'))
def testGet(self):
s = self.provider.get('3p1u')
self.assertEqual(s.accession, '3p1u')
self.assertTrue(isinstance(s, Structure))
self.assertRaises(StructureNotFoundError, self.provider.get, '$')
@test.unit
class TestCustomProvider(test.Case):
def setUp(self):
super(TestCustomProvider, self).setUp()
self.path = self.config.getTestFile('3p1u.pdb')
self.provider = CustomStructureProvider({'3p1u': self.path})
def testAdd(self):
self.assertEqual(len(self.provider.paths), 1)
self.assertEqual(self.provider.paths[0], self.path)
self.provider.add('test', self.config.getTestFile('d1nz0a_.pdb'))
self.assertEqual(len(self.provider.paths), 2)
self.assertRaises(IOError, self.provider.add, 'test', 'non-exi$ting path')
def testRemove(self):
self.assertEqual(len(self.provider.paths), 1)
self.provider.remove('3p1u')
self.assertEqual(len(self.provider.paths), 0)
self.assertRaises(ValueError, self.provider.remove, '$')
def testFind(self):
f1 = self.provider.find('3p1u')
f2 = self.config.getTestFile('3p1u.pdb')
self.assertEqual(os.path.abspath(f1), os.path.abspath(f2))
self.assertEqual(None, self.provider.find('$'))
def testGet(self):
s = self.provider.get('3p1u')
self.assertEqual(s.accession, '3p1u')
self.assertTrue(isinstance(s, Structure))
self.assertRaises(StructureNotFoundError, self.provider.get, '$')
@test.functional
class TestFind(test.Case):
def runTest(self):
f2 = find('3p1u', [self.config.data])
f1 = self.config.getTestFile('3p1u.pdb')
self.assertEqual(os.path.abspath(f1), os.path.abspath(f2))
self.assertEqual(None, find('$', self.config.data))
@test.unit
class TestEntryID(test.Case):
def setUp(self):
super(TestEntryID, self).setUp()
def testFactory(self):
self.assertTrue(isinstance(EntryID.create('abcdE'), StandardID))
self.assertTrue(isinstance(EntryID.create('abcdddE'), DegenerateID))
self.assertTrue(isinstance(EntryID.create('abcd_E'), SeqResID))
@test.unit
class TestStandardID(test.Case):
def setUp(self):
super(TestStandardID, self).setUp()
self.id = StandardID('abCdE')
self.accession = 'abcd'
self.chain = 'E'
def testAccession(self):
self.assertEqual(self.id.accession, self.accession)
def testChain(self):
self.assertEqual(self.id.chain, self.chain)
def testEntryID(self):
self.assertEqual(self.id.entry_id, self.accession + self.chain)
def testFormat(self):
self.assertEqual(self.id.format(), self.accession + self.chain)
def testConstructor(self):
self.assertRaises(InvalidEntryIDError, StandardID, 'aE')
@test.unit
class TestDegenerateID(TestStandardID):
def setUp(self):
super(TestDegenerateID, self).setUp()
self.id = DegenerateID('abCdddE')
self.accession = 'abcddd'
self.chain = 'E'
@test.unit
class TestSeqResID(TestStandardID):
def setUp(self):
super(TestSeqResID, self).setUp()
self.id = SeqResID('abCd_E')
def testFormat(self):
self.assertEqual(self.id.format(), 'abcd_E')
def testConstructor(self):
self.assertRaises(InvalidEntryIDError, SeqResID, 'abcdE')
@test.custom
def TestPDB():
import glob
class PDBTestCase(test.Case):
def runTest(self):
try:
StructureParser(self.entry).parse_structure()
except:
sys.stdout.write("\n{0}\n".format(self.entry))
self.reRaise([self.entry])
var = 'PDBMASK'
suite = test.unittest.TestSuite()
if var in os.environ:
for entry in glob.glob(os.environ[var]):
case = PDBTestCase()
case.entry = entry
suite.addTest(case)
return suite
if __name__ == '__main__':
test.Console()
|
