Source code for mmtfPyspark.datasets.secondaryStructureExtractor

#!/user/bin/env python
'''secondaryStructureExtractor.py

Creates a dataset of DSSP secondary structure assignments. The dataset
includes protein sequence, the DSSP 3-state (Q3) and 8-state (Q8)
assignments, and the fraction of alpha, beta, and coil within a chain. The
input to this class must be a single protein chain.

Examples
--------
get dataset of secondary structure assignments:

>>> pdb.flatMapToPair(new StructureToPolymerChains())
...    .filter(new ContainsLProteinChain())
>>> secStruct = SecondaryStructureExtractor.getDataset(pdb)
>>> secStruct.show(10)

'''
__author__ = "Mars (Shih-Cheng) Huang"
__maintainer__ = "Mars (Shih-Cheng) Huang"
__email__ = "marshuang80@gmail.com"
__version__ = "0.2.0"
__status__ = "Done"

from mmtfPyspark.ml import pythonRDDToDataset
from mmtfPyspark.utils import DsspSecondaryStructure
from pyspark.sql import Row


[docs]def get_dataset(structure):
    '''Returns a dataset with protein sequence and secondary structure assignments.

    Parameters
    ----------
    structure : mmtfStructure
       single protein chain

    Returns
    -------
    dataset
       dataset with sequence and secondary structure assignments
    '''

    rows = structure.map(
        lambda x: _get_sec_struct_fractions(x))  # Map or flatMap

    # convert to dataset
    colNames = ["structureChainId", "sequence", "alpha", "beta",
                "coil", "dsspQ8Code", "dsspQ3Code"]

    return pythonRDDToDataset.get_dataset(rows, colNames)


[docs]def get_python_rdd(structure):
    '''Returns a pythonRDD of 3-state secondary structure

    Parameters
    ----------
    structure : mmtfStructure
    '''

    return structure.map(lambda x: _get_sec_struct_fractions(x))


def _get_sec_struct_fractions(t):
    '''Get factions of alpha, beta and coil within a chain
    '''

    key = t[0]
    structure = t[1]
    if structure.num_chains != 1:
        raise Exception(
            "This method can only be applied to single polyer chain.")

    dsspQ8, dsspQ3 = '', ''

    helix = 0
    sheet = 0
    coil = 0
    dsspIndex = 0
    structureIndex = 0

    for code in structure.sec_struct_list:

        seqIndex = structure.sequence_index_list[structureIndex]

        while dsspIndex < seqIndex:
            dsspQ3 += "X"
            dsspQ8 += "X"
            dsspIndex += 1

        structureIndex += 1
        dsspQ8 += DsspSecondaryStructure.get_dssp_code(
            code).get_one_letter_code()
        dsspIndex += 1

        q3 = DsspSecondaryStructure.get_q3_code(code).name
        if q3 == "ALPHA_HELIX":
            helix += 1
            dsspQ3 += "H"
        elif q3 == "EXTENDED":
            sheet += 1
            dsspQ3 += "E"
        elif q3 == "COIL":
            coil += 1
            dsspQ3 += "C"

    while dsspIndex < len(structure.entity_list[0]['sequence']):
        dsspQ8 += "X"
        dsspQ3 += "X"
        dsspIndex += 1

    n = len(structure.sec_struct_list)

    helix /= n
    sheet /= n
    coil /= n

    return Row(key, structure.entity_list[0]['sequence'], helix, sheet,
               coil, dsspQ8, dsspQ3)