Map To Protein Dimers Demo¶

Example demonstrating how to extract protein dimers from PDB entries. This example uses a flatMap function to transform a strucure to its dimers.

Protein Dimers

Imports¶

In [1]:

from pyspark import SparkConf, SparkContext
from mmtfPyspark.io import mmtfReader
from mmtfPyspark.mappers import StructureToProteinDimers, StructureToBioassembly

Configure Spark¶

In [2]:

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

Download Protein 1STP in MMTF format¶

In [3]:

protein = mmtfReader.download_mmtf_files(["1STP"], sc)

Map protein structure to Bioassembly, then map to protein dimers¶

In [4]:

cutoffDistance = 8.0
contacts = 20
useAllAtoms = False
exclusive = True

dimers = protein.flatMap(StructureToBioassembly()) \
                .flatMap(StructureToProteinDimers(cutoffDistance, contacts, useAllAtoms, exclusive))

Count number of structures¶

In [5]:

print(f"Number of structures : {dimers.count()}")

Number of structures : 2

Terminate Spark¶

In [6]:

sc.stop()

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