Python InteractionFilter.set_query_atom_names Exemples

Exemple #1

Fichier : test_interactionFilter.py Projet : yuy079/mmtf-pyspark

    def test10(self):
        inFilter = InteractionFilter()
        inFilter.set_query_atom_names(True, ["CA", "CB"])

        self.assertFalse(inFilter.is_query_atom_name('C'))
        self.assertFalse(inFilter.is_query_atom_name('CG'))
        self.assertTrue(inFilter.is_query_atom_name('CA'))
        self.assertTrue(inFilter.is_query_atom_name('CB'))

Exemple #2

    def test2(self):

        interactionFilter = InteractionFilter(distanceCutoff=3.5, minInteractions=1)
        interactionFilter.set_query_groups(True, ['ASP'])
        interactionFilter.set_query_atom_names(True, ['OD1', 'OD2'])
        interactionFilter.set_target_groups(True, ['ARG'])
        interactionFilter.set_target_atom_names(True, ['NH1', 'NH2'])

        interactions = InteractionFingerprinter.get_polymer_interactions(self.pdb, interactionFilter)
        self.assertTrue(interactions.count() == 2)

Exemple #3

# ## Download 1OHR structure

# In[2]:


pdb = mmtfReader.download_mmtf_files(['1OHR'], sc)


# ## Find ASP-ARG salt bridges

# In[3]:


interactionFilter = InteractionFilter(distanceCutoff=3.5, minInteractions=1)
interactionFilter.set_query_groups(True, "ASP")
interactionFilter.set_query_atom_names(True, ['OD1','OD2'])
interactionFilter.set_target_groups(True, "ARG")
interactionFilter.set_target_atom_names(True, ['NH1','NH2'])

interactions = InteractionFingerprinter.get_polymer_interactions(pdb, interactionFilter)
interactions.toPandas().head(10)    


# ## Terminate Spark

# In[ ]:


sc.stop()