Demo how to calculate polymer interaction data and maps it to polymer chains.
In [1]:
from pyspark import SparkConf, SparkContext
from mmtfPyspark.io import mmtfReader
from mmtfPyspark.interactions import InteractionFilter, InteractionFingerprinter
# Create variables
APP_NAME = "MMTF_Spark"
# Configure Spark
conf = SparkConf().setAppName(APP_NAME).setMaster("local[*]")
sc = SparkContext(conf=conf)
In [2]:
pdb = mmtfReader.download_mmtf_files(['1OHR'], sc)
In [3]:
interactionFilter = InteractionFilter(distanceCutoff=3.5, minInteractions=1)
interactionFilter.set_query_groups(True, "ASP")
interactionFilter.set_query_atom_names(True, ['OD1','OD2'])
interactionFilter.set_target_groups(True, "ARG")
interactionFilter.set_target_atom_names(True, ['NH1','NH2'])
interactions = InteractionFingerprinter.get_polymer_interactions(pdb, interactionFilter)
interactions.toPandas().head(10)
Out[3]:
| structureChainId | queryChainId | targetChainId | groupNumbers | sequenceIndices | sequence | |
|---|---|---|---|---|---|---|
| 0 | 1OHR.A | B | A | [8] | [7] | PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... |
| 1 | 1OHR.B | A | B | [8] | [7] | PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... |