def setUp(self): conf = SparkConf().setMaster( "local[*]").setAppName('blastClustersTest') self.sc = SparkContext(conf=conf) pdbIds = ["1O06", "2ONX"] self.pdb = download_mmtf_files(pdbIds, self.sc)
def setUp(self): conf = SparkConf().setMaster("local[*]").setAppName( 'chemicalStructureQueryTest') self.sc = SparkContext(conf=conf) pdbIds = ["1HYA", "2ONX", "1F27", "4QMC", "2RTL"] self.pdb = download_mmtf_files(pdbIds, self.sc)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("blastClustersTest") \ .getOrCreate() pdbIds = ["1O06", "2ONX"] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("wildTypeTest") \ .getOrCreate() pdbIds = ["1PEN", "1OCZ", "2ONX"] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("mineSearchTest") \ .getOrCreate() pdbIds = ["5JDE", "5CU4", "5L6W", "5UFU", "5IHB"] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): conf = SparkConf().setMaster("local[*]").setAppName('PiscesTest') self.sc = SparkContext(conf=conf) # "4R4X.A" and "5X42.B" should pass filter pdbIds = ["5X42", "4R4X", "2ONX", "1JLP"] self.pdb = download_mmtf_files(pdbIds, self.sc)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("secondaryStructureExtractorTest") \ .getOrCreate() pdbIds = ["1STP"] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("chemicalStructureQueryTest") \ .getOrCreate() pdbIds = ["1HYA", "2ONX", "1F27", "4QMC", "2RTL"] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): conf = SparkConf().setMaster("local[*]").setAppName( 'secondaryStructureSegmentExtractorTest') self.sc = SparkContext(conf=conf) pdbIds = ["1STP"] self.pdb = download_mmtf_files(pdbIds, self.sc)
def setUp(self): conf = SparkConf().setMaster( "local[*]").setAppName('PolymerInteractionFingerprint') self.sc = SparkContext(conf=conf) # download structure 1OHR self.pdb = download_mmtf_files(['1OHR'], self.sc)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("PolymerInteractionFingerprint") \ .getOrCreate() # download structure 1OHR self.pdb = download_mmtf_files(['1OHR'])
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("polymerSequenceExtractorTest") \ .getOrCreate() pdbIds = ["1STP", "4HHB"] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("columnarStructure") \ .getOrCreate() self.pdb = mmtfReader.download_mmtf_files(['1STP']) structure = self.pdb.values().first() self.cs = ColumnarStructure(structure, True)
def setUp(self): conf = SparkConf().setMaster( "local[*]").setAppName('containsDProteinChainTest') self.sc = SparkContext(conf=conf) pdbIds = ['2ONX', '1JLP', '5X6H', '5L2G', '2MK1', '2V5W', '5XDP', '5GOD'] self.pdb = download_mmtf_files(pdbIds, self.sc)
def test1(self): pdbIds = ["1I1G"] self.pdb = download_mmtf_files(pdbIds) pdb_1 = self.pdb.flatMap(StructureToBioassembly()) \ .flatMap(StructureToProteinDimers(8, 20, False, True)) self.assertTrue(pdb_1.count() == 4)
def setUp(self): conf = SparkConf().setMaster("local[*]").setAppName( 'columnarStructure') self.sc = SparkContext(conf=conf) self.pdb = mmtfReader.download_mmtf_files(['1STP'], self.sc) structure = self.pdb.values().first() self.cs = ColumnarStructure(structure, True)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("PiscesTest") \ .getOrCreate() # "4R4X.A" and "5X42.B" should pass filter pdbIds = ["5X42", "4R4X", "2ONX", "1JLP"] self.pdb = download_mmtf_files(pdbIds)
def test2(self): pdbIds = ["5NV3"] self.pdb = download_mmtf_files(pdbIds, self.sc) pdb_2 = self.pdb.flatMap(StructureToBioassembly()) \ .flatMap(StructureToProteinDimers(8, 20, False, True)) self.assertTrue(pdb_2.count() == 12)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("ContainsAlternativeLocationsTests") \ .getOrCreate() # 4QXX: has alternative location ids # 2ONX: has no alternative location ids pdbIds = ['4QXX', '2ONX'] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): conf = SparkConf().setMaster("local[*]").setAppName( 'ExperimentalMethodsTest') pdbIds = [ "2ONX", "5VLN", "5VAI", "5JXV", "5K7N", "3PDM", "5MNX", "5I1R", "5MON", "5LCB", "3J07" ] self.sc = SparkContext(conf=conf) self.pdb = download_mmtf_files(pdbIds, self.sc)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("containsDProteinChainTest") \ .getOrCreate() pdbIds = [ '2ONX', '1JLP', '5X6H', '5L2G', '2MK1', '2V5W', '5XDP', '5GOD' ] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): conf = SparkConf().setMaster("local[*]").setAppName('RFreeFilterTest') self.sc = SparkContext(conf=conf) # 2ONX: 0.202 rfree x-ray resolution # 2OLX: 0.235 rfree x-ray resolution # 3REC: n/a NMR structure # 1LU3: n/a EM structure pdbIds = ['2ONX', '2OLX', '3REC', '1LU3'] self.pdb = download_mmtf_files(pdbIds, self.sc)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("containsSequenceRegexTest") \ .getOrCreate() # 5KE8: contains Zinc finger motif # 1JLP: does not contain Zinc finger motif # 5VAI: contains Walker P loop pdbIds = ['5KE8', '1JLP', '5VAI'] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("ExperimentalMethodsTest") \ .getOrCreate() pdbIds = [ "2ONX", "5VLN", "5VAI", "5JXV", "5K7N", "3PDM", "5MNX", "5I1R", "5MON", "5LCB", "3J07" ] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): conf = SparkConf().setMaster("local[*]").setAppName( 'containsSequenceRegexTest') self.sc = SparkContext(conf=conf) # 5KE8: contains Zinc finger motif # 1JLP: does not contain Zinc finger motif # 5VAI: contains Walker P loop pdbIds = ['5KE8', '1JLP', '5VAI'] self.pdb = download_mmtf_files(pdbIds, self.sc)
def setUp(self): conf = SparkConf().setMaster("local[*]").setAppName( 'ContainsAlternativeLocationsTests') self.sc = SparkContext(conf=conf) # 4QXX: has alternative location ids # 2ONX: has no alternative location ids pdbIds = ['4QXX', '2ONX'] self.pdb = download_mmtf_files(pdbIds, self.sc) self.pdb = self.pdb.map(lambda x: (x[0], x[1].set_alt_loc_list()))
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("RWorkFilterTest") \ .getOrCreate() # 2ONX: 0.172 rwork x-ray resolution # 2OLX: 0.183 rfree x-ray resolution # 3REC: n/a NMR structure # 1LU3: n/a EM structure pdbIds = ['2ONX', '2OLX', '3REC', '1LU3'] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("testResolutionFilter") \ .getOrCreate() # 2ONX: 1.52 A x-ray resolution # 2OLX: 1.42 A x-ray resolution # 3REC: n/a NMR structure # 1LU3: 16.8 A EM resolution pdbIds = ['2ONX', '2OLX', '3REC', '1LU3'] self.pdb = download_mmtf_files(pdbIds)
def setUp(self): conf = SparkConf().setMaster("local[*]").setAppName( 'releaseDateFilterTest') pdbIds = ['1O6Y', '4MYA', '3VCO', '5N0Y'] # 1O6Y: released on 2003-01-30 # 4MYA: released on 2014-01-01 # 3VCO: released on 2013-03-06 # 5N0Y: released on 2017-05-24 self.sc = SparkContext(conf=conf) self.pdb = download_mmtf_files(pdbIds, self.sc)
def setUp(self): self.spark = SparkSession.builder.master("local[*]") \ .appName("DepositionDateFilterTest") \ .getOrCreate() # 4MYA: deposited on 2013-09-27 # 1O6Y: deposited on 2002-10-21 # 3VCO: deposited on 2012-01-04 # 5N0Y: deposited on 2017-02-03 pdbIds = ['1O6Y', '4MYA', '3VCO', '5N0Y'] self.pdb = download_mmtf_files(pdbIds)