def test9(self): pdb_9 = self.pdb.filter(ExperimentalMethods(ExperimentalMethods.SOLUTION_NMR))\ .filter(ExperimentalMethods(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 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 test10(self): pdb_10 = self.pdb.filter(ExperimentalMethods(ExperimentalMethods.SOLID_STATE_NMR))\ .filter(ExperimentalMethods(ExperimentalMethods.ELECTRON_MICROSCOPY))\ .filter(ExperimentalMethods(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)
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.assertTrue('5LCB' in results_4) self.assertTrue('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.assertTrue('5LCB' in results_3) self.assertTrue('3J07' in results_3)
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.assertTrue('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.assertTrue('5MON' in results_7) self.assertFalse('5LCB' in results_7) self.assertFalse('3J07' in results_7)
# * ExperimentalMethods.ERP # * ExperimentalMethods.FIBER_DIFFRACTION # * ExperimentalMethods.FLUORESCENCE_TRANSFER # * ExperimentalMethods.INFRARED_SPECTROSCOPY # * ExperimentalMethods.NEUTRON_DIFFRACTION # * ExperimentalMethods.POWDER_DIFFRACTION # * ExperimentalMethods.SOLID_STATE_NMR # * ExperimentalMethods.SOLUTION_NMR # * ExperimentalMethods.SOLUTION_SCATTERING # * ExperimentalMethods.THEORETICAL_MODEL # * ExperimentalMethods.X_RAY_DIFFRACTION # In[4]: pdb = pdb.filter( ExperimentalMethods(ExperimentalMethods.NEUTRON_DIFFRACTION, ExperimentalMethods.X_RAY_DIFFRACTION)) # ## Print out entries # In[5]: filtered_structures = pdb.keys().collect() print(filtered_structures) # ## Visualize 3D structures of filtered structures # In[6]: view_structure(filtered_structures)
path = "../../resources/mmtf_full_sample/" fraction = 0.5 seed = 123 pdb = mmtfReader.read_sequence_file(path, sc, fraction=fraction, seed=seed) count = pdb.count() print(f'number of pdb entries read : {count}') # ## Retain high resolution X-ray structures # In[4]: pdb = pdb.filter(ExperimentalMethods( ExperimentalMethods.X_RAY_DIFFRACTION)).filter(Resolution(0, 2.0)).filter( RFree(0, 2.0)) print(f'number of pdb entries left : {pdb.count()}') # ## Visualize Structures # In[5]: structures = pdb.keys().collect() view_structure(structures) # ## Save this subset in a Hadoop Sequence File # In[7]:
# In[10]: path = "../../resources/mmtf_full_sample/" fraction = 0.001 seed = 123 pdb = mmtfReader.read_sequence_file(path, sc, fraction = fraction, seed = seed) # ## Filter by X-Ray Diffraction experimental method # In[11]: pdb = pdb.filter(ExperimentalMethods(ExperimentalMethods.X_RAY_DIFFRACTION)) # ## Map results to a list of information, and print each list # In[12]: pdb.map(lambda t: [t[0], t[1].resolution, t[1].r_free, t[1].r_work]).collect() # ## Terminate Spark # In[13]: