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)
