Read List Of Entries From Local Hadoop Sequence File¶

Simple example reading a list of PDB entries from local Hadoop Sequence Files

Imports¶

In [1]:

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

Configure Spark¶

In [2]:

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

Read in local Hadoop Sequence Files and count number of entries¶

In [3]:

path = "../../resources/mmtf_full_sample/"
pdbIds = ["1M4L", "1LXJ", "4XPX"]

pdb = mmtfReader.read_sequence_file(path, sc, pdbId = pdbIds,)

count = pdb.count()

print(f'number of pdb entries read : {count}')

number of pdb entries read : 3

Visualize Structures¶

In [4]:

structures = pdb.keys().collect()
view_structure(structures)

Out[4]:

<function mmtfPyspark.structureViewer.view_structure.<locals>.view3d(i=0)>

Terminate Spark¶

In [5]:

sc.stop()

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