Python InteractionFilter.set_query_elements Exemples

Exemple #1

Fichier : test_interactionFilter.py Projet : omc89/mmtf-pyspark

    def test7(self):
        inFilter = InteractionFilter()
        inFilter.set_query_elements(False, ["N", "O"])

        self.assertFalse(inFilter.is_query_element('O'))
        self.assertFalse(inFilter.is_query_element('N'))
        self.assertTrue(inFilter.is_query_element('S'))

Exemple #2

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]: