Python ExperimentalMethods Examples

Example #1

File: test_experimentalMethods.py Project: yuy079/mmtf-pyspark

    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)

Example #2

File: test_experimentalMethods.py Project: yuy079/mmtf-pyspark

    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)

Example #3

File: test_experimentalMethods.py Project: yuy079/mmtf-pyspark

    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)

Example #4

File: test_experimentalMethods.py Project: yuy079/mmtf-pyspark

    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)

Example #5

File: test_experimentalMethods.py Project: yuy079/mmtf-pyspark

    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)

Example #6

File: test_experimentalMethods.py Project: yuy079/mmtf-pyspark

    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)

Example #7

File: test_experimentalMethods.py Project: yuy079/mmtf-pyspark

    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)

Example #8

File: test_experimentalMethods.py Project: yuy079/mmtf-pyspark

    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)

Example #9

# * 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)

Example #10

File: WriteMmtfCustomSubsetDemo.ipynb.py Project: fsimkovic/mmtf-pyspark

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]:

Example #11

# 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]: