Filter By Polymer Chain Type Demo¶

Simple exmaple of reading an MMTF Hadoop Sequence file, filtering the entries by polymer chain type, L Protein Chain and D Saccharide Chain, and count the number of entires. This example also show show methods can be chained for a more concise syntax

Supported polymer chain type includes (Both string and class variable can be used a input parameter)¶

containsPolymerChainType.D_PEPTIDE_COOH_CARBOXY_TERMINUS = “D-PEPTIDE COOH CARBOXY TERMINUS”
containsPolymerChainType.D_PEPTIDE_NH3_AMINO_TERMINUS = “D-PEPTIDE NH3 AMINO TERMINUS”
containsPolymerChainType.D_PEPTIDE_LINKING = “D-PEPTIDE LINKING”
containsPolymerChainType.D_SACCHARIDE = “D-SACCHARIDE”
containsPolymerChainType.D_SACCHARIDE_14_and_14_LINKING = “D-SACCHARIDE 1,4 AND 1,4 LINKING”
containsPolymerChainType.D_SACCHARIDE_14_and_16_LINKING = “D-SACCHARIDE 1,4 AND 1,6 LINKING”
containsPolymerChainType.DNA_OH_3_PRIME_TERMINUS = “DNA OH 3 PRIME TERMINUS”
containsPolymerChainType.DNA_OH_5_PRIME_TERMINUS = “DNA OH 5 PRIME TERMINUS”
containsPolymerChainType.DNA_LINKING = “DNA LINKING”
containsPolymerChainType.L_PEPTIDE_COOH_CARBOXY_TERMINUS = “L-PEPTIDE COOH CARBOXY TERMINUS”
containsPolymerChainType.L_PEPTIDE_NH3_AMINO_TERMINUS = “L-PEPTIDE NH3 AMINO TERMINUS”
containsPolymerChainType.L_PEPTIDE_LINKING = “L-PEPTIDE LINKING”
containsPolymerChainType.L_SACCHARIDE = “L-SACCHARIDE”
containsPolymerChainType.L_SACCHARIDE_14_AND_14_LINKING = “L-SACCHARDIE 1,4 AND 1,4 LINKING”
containsPolymerChainType.L_SACCHARIDE_14_AND_16_LINKING = “L-SACCHARIDE 1,4 AND 1,6 LINKING”
containsPolymerChainType.PEPTIDE_LINKING = “PEPTIDE LINKING”
containsPolymerChainType.RNA_OH_3_PRIME_TERMINUS = “RNA OH 3 PRIME TERMINUS”
containsPolymerChainType.RNA_OH_5_PRIME_TERMINUS = “RNA OH 5 PRIME TERMINUS”
containsPolymerChainType.RNA_LINKING = “RNA LINKING”
containsPolymerChainType.NON_POLYMER = “NON-POLYMER”
containsPolymerChainType.OTHER = “OTHER”
containsPolymerChainType.SACCHARIDE = “SACCHARIDE”

Imports¶

In [1]:

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

Configure Spark¶

In [2]:

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

Read in MMTF Files, filter and count¶

* Not filter returns the opposite of a particular filter*¶

In [3]:

path = "../../resources/mmtf_reduced_sample/"

structures = mmtfReader.read_sequence_file(path, sc) \
                  .filter(ContainsPolymerChainType("DNA LINKING", ContainsPolymerChainType.RNA_LINKING)) \
                  .filter(NotFilter(ContainsLProteinChain())) \
                  .filter(NotFilter(ContainsDSaccharideChain()))

print(f"Number of pure DNA and RNA entires: {structures.count()}")

Number of pure DNA and RNA entires: 227

View Structures¶

In [4]:

structure_names = structures.keys().collect()
view_structure(structure_names, style='sphere')

Out[4]:

<function mmtfPyspark.structureViewer.view_structure.<locals>.view3d>

Terminate Spark¶

In [5]:

sc.stop()

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