def test3(self):
pdb_3 = self.pdb.filter(Resolution(34.99, 35.01))
results_3 = pdb_3.keys().collect()
self.assertFalse('2ONX' in results_3)
self.assertFalse('2OLX' in results_3)
self.assertFalse('3REC' in results_3)
self.assertFalse('1LU3' in results_3)
def test2(self):
pdb_2 = self.pdb.filter(Resolution(1.41, 1.43))
results_2 = pdb_2.keys().collect()
self.assertFalse('2ONX' in results_2)
self.assertTrue('2OLX' in results_2)
self.assertFalse('3REC' in results_2)
self.assertFalse('1LU3' in results_2)
def test1(self):
pdb_1 = self.pdb.filter(Resolution(1.51, 1.53))
results_1 = pdb_1.keys().collect()
self.assertTrue('2ONX' in results_1)
self.assertFalse('2OLX' in results_1)
self.assertFalse('3REC' in results_1)
self.assertFalse('1LU3' in results_1)
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]:
# ## Read in MMTF Files
# In[3]:
path = "../../resources/mmtf_reduced_sample/"
pdb = mmtfReader.read_sequence_file(path, sc)
# ## Filter by resolution
#
# Entires without resolution values (eg. NMR structures) will be filtered out
# In[4]:
pdb = pdb.filter(Resolution(0.0, 2.0))
# ## Count number of entires
# In[5]:
count = pdb.count()
print(f"Number of structures : {count}")
# ## Visualize Structures
# In[6]:
structure_names = pdb.keys().collect()
view_structure(structure_names)
# In[2]:
# input parameters
resolution = 2.0
minInteractions = 2
maxInteractions = 4
distanceCutoff = 3.0
bFactorCutoff = 1.645
includeWaters = True
# ## Read PDB and filter by resolution and only include proteins
# In[3]:
pdb = mmtfReader.read_sequence_file(path, sc)
pdb = pdb.filter(Resolution(minResolution=0.0, maxResolution=2.0)).filter(
ContainsLProteinChain(exclusive=True))
# ## Setup criteria for metal interactions
# In[4]:
interactions_filter = InteractionFilter()
interactions_filter.set_distance_cutoff(3.0)
interactions_filter.set_normalized_b_factor_cutoff(1.645)
interactions_filter.set_min_interactions(2)
interactions_filter.set_max_interactions(4)
interactions_filter.set_query_groups(True, ["HOH"])
interactions_filter.set_query_elements(True, "O") # Only use water oxygen
interactions_filter.set_target_elements(True, ["O", "N", "S"])