Filter By Release Date Demo¶

This example demonstrates how to filter structure with specified release date range

Imports¶

In [1]:

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

Configure Spark¶

In [2]:

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

Read in MMTF Files, filter and count¶

In [3]:

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

structures = mmtfReader.read_sequence_file(path, sc) \
                .filter(ReleaseDate("2000-01-28","2017-02-28"))

print(f"Number of structure released between 2000-01-28 and 2017-02-28 is: {structures.count()}")

Number of structure released between 2000-01-28 and 2017-02-28 is: 5395

Visualize Structures¶

In [4]:

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

Out[4]:

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

Terminate Spark¶

In [5]:

sc.stop()

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