def test1a(self):
pdb_1a = self.pdb.flatMap(structureToPolymerChains())
pdb_1a = pdb_1a.filter(
experimentalMethods(experimentalMethods.X_RAY_DIFFRACTION))
results_1a = pdb_1a.keys().collect()
self.assertTrue('2ONX.A' in results_1a)
self.assertFalse('5VLN.A' in results_1a)
def main():
path = "../../resources/mmtf_reduced_sample/"
conf = SparkConf().setMaster("local[*]") \
.setAppName("FilterByDExperimentalMethods")
sc = SparkContext(conf=conf)
MmtfReader.readSequenceFile(path, sc) \
.filter(experimentalMethods(experimentalMethods.NEUTRON_DIFFRACTION, experimentalMethods.X_RAY_DIFFRACTION)) \
.keys() \
.foreach(lambda x: print(x))
sc.stop()
def test5(self):
pdb_5 = self.pdb.filter(
experimentalMethods(experimentalMethods.ELECTRON_CRYSTALLOGRAPHY))
results_2 = pdb_5.keys().collect()
self.assertFalse('2ONX' in results_2)
self.assertFalse('5VLN' in results_2)
self.assertFalse('5VAI' in results_2)
self.assertFalse('5JXV' in results_2)
self.assertTrue('5K7N' in results_2)
self.assertFalse('3PDM' in results_2)
self.assertFalse('5MNX' in results_2)
self.assertFalse('5I1R' in results_2)
self.assertFalse('5MON' in results_2)
self.assertFalse('5LCB' in results_2)
self.assertFalse('3J07' in results_2)
def test4(self):
pdb_4 = self.pdb.filter(
experimentalMethods(experimentalMethods.SOLID_STATE_NMR))
results_4 = pdb_4.keys().collect()
self.assertFalse('2ONX' in results_4)
self.assertFalse('5VLN' in results_4)
self.assertFalse('5VAI' in results_4)
self.assertTrue('5JXV' in results_4)
self.assertFalse('5K7N' in results_4)
self.assertFalse('3PDM' in results_4)
self.assertFalse('5MNX' in results_4)
self.assertFalse('5I1R' in results_4)
self.assertFalse('5MON' in results_4)
self.assertFalse('5LCB' in results_4)
self.assertFalse('3J07' in results_4)
def test3(self):
pdb_3 = self.pdb.filter(
experimentalMethods(experimentalMethods.ELECTRON_MICROSCOPY))
results_3 = pdb_3.keys().collect()
self.assertFalse('2ONX' in results_3)
self.assertFalse('5VLN' in results_3)
self.assertTrue('5VAI' in results_3)
self.assertFalse('5JXV' in results_3)
self.assertFalse('5K7N' in results_3)
self.assertFalse('3PDM' in results_3)
self.assertFalse('5MNX' in results_3)
self.assertFalse('5I1R' in results_3)
self.assertFalse('5MON' in results_3)
self.assertFalse('5LCB' in results_3)
self.assertFalse('3J07' in results_3)
def test2(self):
pdb_2 = self.pdb.filter(
experimentalMethods(experimentalMethods.SOLUTION_NMR))
results_2 = pdb_2.keys().collect()
self.assertFalse('2ONX' in results_2)
self.assertTrue('5VLN' in results_2)
self.assertFalse('5VAI' in results_2)
self.assertFalse('5JXV' in results_2)
self.assertFalse('5K7N' in results_2)
self.assertFalse('3PDM' in results_2)
self.assertFalse('5MNX' in results_2)
self.assertFalse('5I1R' in results_2)
self.assertFalse('5MON' in results_2)
self.assertFalse('5LCB' in results_2)
self.assertFalse('3J07' in results_2)
def test1(self):
pdb_1 = self.pdb.filter(
experimentalMethods(experimentalMethods.X_RAY_DIFFRACTION))
results_1 = pdb_1.keys().collect()
self.assertTrue('2ONX' in results_1)
self.assertFalse('5VLN' in results_1)
self.assertFalse('5VAI' in results_1)
self.assertFalse('5JXV' in results_1)
self.assertFalse('5K7N' in results_1)
self.assertFalse('3PDM' in results_1)
self.assertFalse('5MNX' in results_1)
self.assertFalse('5I1R' in results_1)
self.assertFalse('5MON' in results_1)
self.assertFalse('5LCB' in results_1)
self.assertFalse('3J07' in results_1)
def test7(self):
pdb_7 = self.pdb.filter(
experimentalMethods(experimentalMethods.NEUTRON_DIFFRACTION))
results_7 = pdb_7.keys().collect()
self.assertFalse('2ONX' in results_7)
self.assertFalse('5VLN' in results_7)
self.assertFalse('5VAI' in results_7)
self.assertFalse('5JXV' in results_7)
self.assertFalse('5K7N' in results_7)
self.assertFalse('3PDM' in results_7)
self.assertTrue('5MNX' in results_7)
self.assertFalse('5I1R' in results_7)
self.assertFalse('5MON' in results_7)
self.assertFalse('5LCB' in results_7)
self.assertFalse('3J07' in results_7)
def test9(self):
pdb_9 = self.pdb.filter(
experimentalMethods(experimentalMethods.SOLUTION_NMR,
experimentalMethods.SOLUTION_SCATTERING))
results_9 = pdb_9.keys().collect()
self.assertFalse('2ONX' in results_9)
self.assertFalse('5VLN' in results_9)
self.assertFalse('5VAI' in results_9)
self.assertFalse('5JXV' in results_9)
self.assertFalse('5K7N' in results_9)
self.assertFalse('3PDM' in results_9)
self.assertFalse('5MNX' in results_9)
self.assertTrue('5I1R' in results_9)
self.assertFalse('5MON' in results_9)
self.assertFalse('5LCB' in results_9)
self.assertFalse('3J07' in results_9)
def test10(self):
pdb_10 = self.pdb.filter(
experimentalMethods(experimentalMethods.SOLID_STATE_NMR,
experimentalMethods.ELECTRON_MICROSCOPY,
experimentalMethods.SOLUTION_SCATTERING))
results_10 = pdb_10.keys().collect()
self.assertFalse('2ONX' in results_10)
self.assertFalse('5VLN' in results_10)
self.assertFalse('5VAI' in results_10)
self.assertFalse('5JXV' in results_10)
self.assertFalse('5K7N' in results_10)
self.assertFalse('3PDM' in results_10)
self.assertFalse('5MNX' in results_10)
self.assertFalse('5I1R' in results_10)
self.assertFalse('5MON' in results_10)
self.assertFalse('5LCB' in results_10)
self.assertTrue('3J07' in results_10)