def test9(self):
inFilter = InteractionFilter()
inFilter.set_target_elements(False, ["N", "O"])
self.assertFalse(inFilter.is_target_element('O'))
self.assertFalse(inFilter.is_target_element('N'))
self.assertTrue(inFilter.is_target_element('S'))
def test1(self):
interactionFilter = InteractionFilter()
#interactionFilter.set_distance_cutoff(4.0)
interactionFilter.set_distance_cutoff(3.0)
#interactionFilter.set_target_elements(True, ['O'])
interactionFilter.set_target_elements(False, ['C','H','P'])
metals = {"V", "CR", "MN", "MN3", "FE", "FE2", "CO", "3CO", "NI", "3NI", "CU", "CU1", "CU3", "ZN", "MO", "4MO",
"6MO"}
interactionFilter.set_query_groups(True, metals)
#interactionFilter.set_query_elements(False, ['C', 'H', 'P'])
#interactionFilter.set_query_groups(False, "HOH") # ignore water interactions
t0 = time.time()
interactions = InteractionExtractor.get_ligand_polymer_interactions(self.pdb, interactionFilter, level='group')
interactions.show()
print(interactions.count())
t1 = time.time()
print("Interactions: ", t1-t0)
pdb = pdb.filter(Pisces(sequenceIdentity = 30, resolution = 2.5))
# ## Setup criteria for metal interactions
# In[15]:
# Chemical component codes of metals in different oxidation states
metals = {"V","CR","MN","MN3","FE","FE2","CO","3CO","NI","3NI", "CU","CU1","CU3","ZN","MO","4MO","6MO"}
interactions_filter = InteractionFilter(distanceCutoff = 3.0, minInteractions=4, maxInteractions=6)
interactions_filter.set_query_groups(True, metals)
# Exclude non-polar interactions
interactions_filter.set_target_elements(False, ['H','C','P'])
# ## Tabulate interactions in a Dataframe
# In[16]:
interactions = GroupInteractionExtractor().get_interactions(pdb,interactions_filter).cache()
print(f"Metal interactions: {interactions.count()}")
# ## Select interacting atoms and orientational order parameters (q4-q6)
# In[17]:
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"])
# ## Exclude "uninteresting" ligands
# In[5]:
prohibitedGroups = ExcludedLigandSets.ALL_GROUPS
if not includeWaters:
prohibitedGroups.add("HOH")
interactions_filter.set_prohibited_target_groups(prohibitedGroups)
# ## Calculate interactions
# In[6]:
data = GroupInteractionExtractor().get_interactions(