Filter By Deposition Date Demo¶

Imports¶

In [1]:

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

Configure Spark¶

In [2]:

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

Read in MMTF Files¶

In [3]:

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

pdb = mmtfReader.read_sequence_file(path, sc)

Filter by deposition date¶

In [4]:

pdb = pdb.filter(DepositionDate('1999-02-26','1999-02-28'))

Count number of entires¶

In [5]:

count = pdb.count()

print(f"Number of structure desposited between 1999-02-26 and 1999-02-28 is : {count}")

Number of structure desposited between 1999-02-26 and 1999-02-28 is : 5

View 3D structures¶

In [6]:

pdbIds = pdb.keys().collect()

view_structure(pdbIds)

Out[6]:

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

Terminate Spark¶

In [7]:

sc.stop()

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