Filter By RFree Demo¶

Example of reading an MMTF Hadoop Sequence file, filtering the entries by resolution, and counting the number of entries. This example shows how methods can be chained together.

R Free

Imports¶

In [2]:

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

Configure Spark¶

In [3]:

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

Read in MMTF Files, filter by RFree and count¶

In [4]:

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

structures = mmtfReader.read_sequence_file(path, sc) \
                       .filter(RFree(0.15,0.25))

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

Number of structures : 1397

Visualize Structures¶

In [6]:

structure_names = structures.keys().collect()
view_structure(structure_names, style='stick')

Out[6]:

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

Terminate Spark¶

In [7]:

sc.stop()

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