This example shows how to filter poteins by their sequence regualar expression.
In [1]:
from pyspark import SparkConf, SparkContext
from mmtfPyspark.io import mmtfReader
from mmtfPyspark.filters import ContainsSequenceRegex
from mmtfPyspark.structureViewer import view_group_interaction
In [2]:
conf = SparkConf().setMaster("local[*]") \
.setAppName("FilterBySequenceRegex")
sc = SparkContext(conf = conf)
In [3]:
path = "../../resources/mmtf_reduced_sample/"
pdb = mmtfReader.read_sequence_file(path, sc)
In [8]:
structures = pdb.filter(ContainsSequenceRegex("C.{2,4}C.{12}H.{3,5}H"))
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
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>
In [13]:
sc.stop()