Filter By Experimental Methods Demo

Example how to filter PDB entries by experimental methods.

To learn more about experimental methods

Imports

In [1]:
from pyspark import SparkConf, SparkContext
from mmtfPyspark.io import mmtfReader
from mmtfPyspark.filters import ExperimentalMethods
from mmtfPyspark.structureViewer import view_structure

Configure Spark

In [2]:
conf = SparkConf().setMaster("local[*]") \
                      .setAppName("FilterByExperimentalMethods")
sc = SparkContext(conf = conf)

Read in MMTF Files

In [3]:
path = "../../resources/mmtf_reduced_sample/"

pdb = mmtfReader.read_sequence_file(path, sc)

Filter by experimental methods

List of supported experimental methods

  • ExperimentalMethods.ELECTRON_CRYSTALLOGRAPHY
  • ExperimentalMethods.ELECTRON_MICROSCOPY
  • ExperimentalMethods.ERP
  • ExperimentalMethods.FIBER_DIFFRACTION
  • ExperimentalMethods.FLUORESCENCE_TRANSFER
  • ExperimentalMethods.INFRARED_SPECTROSCOPY
  • ExperimentalMethods.NEUTRON_DIFFRACTION
  • ExperimentalMethods.POWDER_DIFFRACTION
  • ExperimentalMethods.SOLID_STATE_NMR
  • ExperimentalMethods.SOLUTION_NMR
  • ExperimentalMethods.SOLUTION_SCATTERING
  • ExperimentalMethods.THEORETICAL_MODEL
  • ExperimentalMethods.X_RAY_DIFFRACTION
In [4]:
pdb = pdb.filter(ExperimentalMethods(ExperimentalMethods.NEUTRON_DIFFRACTION, ExperimentalMethods.X_RAY_DIFFRACTION))

Visualize 3D structures of filtered structures

In [6]:
view_structure(filtered_structures)
Out[6]:
<function mmtfPyspark.structureViewer.view_structure.<locals>.view3d>

Terminate Spark

In [7]:
sc.stop()
In [ ]: