Simple Query Demo¶

pdbj

PDBj Mine 2 RDB keyword search query and MMTF filtering using pdbid.

Imports¶

In [8]:

from pyspark import SparkConf, SparkContext
from mmtfPyspark.webfilters import PdbjMineSearch
from mmtfPyspark.datasets import pdbjMineDataset
from mmtfPyspark.io import mmtfReader

Configure Spark Context¶

In [9]:

conf = SparkConf().setMaster("local[*]") \
                  .setAppName("SimpleQuerySearch")

sc = SparkContext(conf = conf)

Read in MMTF files from local directory¶

In [10]:

path = "../../resources/mmtf_full_sample/"

pdb = mmtfReader.read_sequence_file(path, sc)

Apply a SQL search on PDBj using a filter¶

Very simple query; this gets the pdbids for all entries modified since 2016-06-28 with a resulution better than 1.5 A

In [11]:

sql = "select pdbid from brief_summary where modification_date >= '2016-06-28' and resolution < 1.5"

search = PdbjMineSearch(sql)
count = pdb.filter(search).keys().count()
print(f"Number of entries using sql to filter: {count}")

Number of entries using sql to filter: 11

Apply a SQL search on PDBj and get a dataset¶

In [12]:

dataset = pdbjMineDataset.get_dataset(sql)
dataset.show(5)

+-----------+
|structureId|
+-----------+
|       5U8P|
|       5U8U|
|       5U8V|
|       5U9D|
|       5UAM|
+-----------+
only showing top 5 rows

Terminate Spark Context¶

In [13]:

sc.stop()

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