Read Local MMTF Full Demo

Simple example reading 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("ReadLocalMMTFReduced")
sc = SparkContext(conf = conf)

Read in local Hadoop Sequence Files and count number of entries

In [3]:
path = "../../resources/mmtf_reduced_sample/"

pdb = mmtfReader.read_sequence_file(path, sc)

count = pdb.count()

print(f'number of pdb entries read : {count}')
number of pdb entries read : 5395
In [ ]:
## Visualize Structures
In [5]:
structures = pdb.keys().collect()
view_structure(structures, style = 'sphere')
Out[5]:
<function mmtfPyspark.structureViewer.view_structure.<locals>.view3d>

Terminate Spark

In [6]:
sc.stop()