Simple Zinc Interaction Analysis Example¶

Imports¶

In [1]:

from pyspark import SparkConf, SparkContext
from mmtfPyspark.datasets import groupInteractionExtractor
from mmtfPyspark.io import mmtfReader
from mmtfPyspark.webfilters import Pisces

Configure Spark¶

In [2]:

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

sc = SparkContext(conf = conf)

Read PDB in MMTF format¶

In [3]:

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

pdb = mmtfReader.read_sequence_file(path, sc)

Use only representative structures¶

In [4]:

seqId = 40
resolution = 2.0

pdb = pdb.filter(Pisces(seqId, resolution))

Extract proteins with Zn interactions¶

In [5]:

finder = groupInteractionExtractor("ZN",3)

interactions = finder.get_dataset(pdb).cache()

List the top 10 residue types that interact with Zn¶

In [6]:

interactions.printSchema()

interactions.show(20)

print(f"Number of interactions: {interactions.count()}")

root
 |-- structureId: string (nullable = false)
 |-- residue1: string (nullable = false)
 |-- atom1: string (nullable = false)
 |-- element1: string (nullable = false)
 |-- index1: integer (nullable = false)
 |-- residue2: string (nullable = false)
 |-- atom2: string (nullable = false)
 |-- element2: string (nullable = false)
 |-- index2: integer (nullable = false)
 |-- distance: float (nullable = false)

+-----------+--------+-----+--------+------+--------+-----+--------+------+---------+
|structureId|residue1|atom1|element1|index1|residue2|atom2|element2|index2| distance|
+-----------+--------+-----+--------+------+--------+-----+--------+------+---------+
|       1FN9|      ZN|   ZN|      Zn|   730|     CYS|   SG|       S|    50|2.3709755|
|       1FN9|      ZN|   ZN|      Zn|   730|     CYS|   SG|       S|    53|2.3940797|
|       1FN9|      ZN|   ZN|      Zn|   730|     HIS|  NE2|       N|    70|2.2196307|
|       1FN9|      ZN|   ZN|      Zn|   730|     CYS|   SG|       S|    72|2.3465357|
|       1FN9|      ZN|   ZN|      Zn|   731|     CYS|   SG|       S|   415|2.3747551|
|       1FN9|      ZN|   ZN|      Zn|   731|     CYS|   SG|       S|   418|2.3680198|
|       1FN9|      ZN|   ZN|      Zn|   731|     HIS|  NE2|       N|   435|2.1647959|
|       1FN9|      ZN|   ZN|      Zn|   731|     CYS|   SG|       S|   437|2.3763454|
|       1E4M|      ZN|   ZN|      Zn|   519|     HIS|  CE1|       C|    53|2.9807622|
|       1E4M|      ZN|   ZN|      Zn|   519|     HIS|  NE2|       N|    53| 2.040789|
|       1E4M|      ZN|   ZN|      Zn|   519|     ASP|   CG|       C|    67| 2.754825|
|       1E4M|      ZN|   ZN|      Zn|   519|     ASP|  OD1|       O|    67|2.8967845|
|       1E4M|      ZN|   ZN|      Zn|   519|     ASP|  OD2|       O|    67|1.9672809|
|       1BF6|      ZN|   ZN|      Zn|   582|     HIS|  NE2|       N|    10|2.2776458|
|       1BF6|      ZN|   ZN|      Zn|   582|     HIS|  NE2|       N|    12|2.1644206|
|       1BF6|      ZN|   ZN|      Zn|   582|     GLU|  OE2|       O|   123|2.3778422|
|       1BF6|      ZN|   ZN|      Zn|   582|     ASP|  OD1|       O|   241|  2.41581|
|       1BF6|      ZN|   ZN|      Zn|   583|     GLU|   CD|       C|   123|2.7811828|
|       1BF6|      ZN|   ZN|      Zn|   583|     GLU|  OE1|       O|   123|2.1997967|
|       1BF6|      ZN|   ZN|      Zn|   583|     HIS|  ND1|       N|   156|2.2733805|
+-----------+--------+-----+--------+------+--------+-----+--------+------+---------+
only showing top 20 rows

Number of interactions: 238

Show the top 10 interacting groups¶

In [7]:

interactions.groupBy("residue2") \
            .count() \
            .sort("count", ascending = False) \
            .show(10)

+--------+-----+
|residue2|count|
+--------+-----+
|     HIS|   76|
|     CYS|   43|
|     HOH|   37|
|     GLU|   34|
|     ASP|   27|
|     ACT|   12|
|     TRP|    4|
|     LYS|    2|
|     VAL|    2|
|      CL|    1|
+--------+-----+

Terminate Spark¶

In [8]:

sc.stop()

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