Filter By Sequence Regex Demo¶

This example shows how to filter poteins by their sequence regualar expression.

Imports¶

In [1]:

from pyspark import SparkConf, SparkContext
from mmtfPyspark.io import mmtfReader
from mmtfPyspark.filters import ContainsSequenceRegex
from mmtfPyspark.structureViewer import view_group_interaction

Configure Spark¶

In [2]:

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

Read in MMTF Files¶

In [3]:

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

pdb = mmtfReader.read_sequence_file(path, sc)

Filter by sequence regular expression¶

Zinc Finger Motif regular expression: C.{2,4}C.{12}H.{3,5}H¶

In [8]:

structures = pdb.filter(ContainsSequenceRegex("C.{2,4}C.{12}H.{3,5}H"))

Count number of entires¶

In [9]:

count = structures.count()

print(f"Number of entries containing Zinc figure motif is : {count}")

Number of entries containing Zinc figure motif is : 16

Visualize Structure Zinc interactions¶

In [12]:

structure_names = structures.keys().collect()
view_group_interaction(structure_names, 'ZN', style='line')

Out[12]:

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

Terminate Spark¶

In [13]:

sc.stop()

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