Simple example writting a subset of mmtf files
In [2]:
from pyspark import SparkConf, SparkContext
from mmtfPyspark.io import mmtfReader, mmtfWriter
from mmtfPyspark.structureViewer import view_structure
In [3]:
conf = SparkConf().setMaster("local[*]") \
.setAppName("WriteMMTFSubset")
sc = SparkContext(conf = conf)
In [4]:
path = "../../resources/mmtf_full_sample/"
fraction= 0.5
seed = 123
pdb = mmtfReader.read_sequence_file(path, sc, fraction = fraction, seed = seed)
count = pdb.count()
print(f'number of pdb entries read : {count}')
number of pdb entries read : 2215
In [5]:
structures = pdb.keys().collect()
view_structure(structures, style='stick')
Out[5]:
<function mmtfPyspark.structureViewer.view_structure.<locals>.view3d>
In [4]:
write_path = "./mmtf_subset"
mmtfWriter.write_sequence_file(write_path, sc, pdb)
In [5]:
sc.stop()