Filter Protein Dna Complexes Demo¶

This example shows how to filter PDB by protein DNA complexes

Imports¶

In [1]:

from pyspark import SparkConf, SparkContext
from mmtfPyspark.io import mmtfReader
from mmtfPyspark.filters import ContainsDnaChain, ContainsLProteinChain
from mmtfPyspark.structureViewer import view_structure

Configure Spark¶

In [2]:

conf = SparkConf().setMaster("local[*]") \
                      .setAppName("FilterProteinDnaComplexDate")
sc = SparkContext(conf = conf)

Read in MMTF Files¶

In [3]:

path = "../../resources/mmtf_reduced_sample/"

pdb = mmtfReader.read_sequence_file(path, sc)

Filter proteins that cotinas Dna chain and L protein chain¶

Retain pdb entires that exclusively contain L-peptide chains
Retain pdb entries that exclusively contain L-Dna

In [4]:

structures = pdb.filter(ContainsLProteinChain()) \
         .filter(ContainsDnaChain())

Count number of entires¶

In [5]:

count = structures.count()

print(f"Number of entires that contain L-protein and L-DNA: {count}")

Number of entires that contain L-protein and L-DNA: 124

Visualize Structures¶

In [7]:

structure_names = structures.keys().collect()
view_structure(structure_names)

Out[7]:

<function mmtfPyspark.structureViewer.view_structure.<locals>.view3d>

Terminate Spark¶

In [6]:

sc.stop()

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