Source code for graphein.protein.features.nodes.aaindex

import logging
from typing import Dict, Tuple

import networkx as nx

from graphein.utils.utils import import_message, protein_letters_3to1_all_caps

log = logging.getLogger(__name__)

    from pyaaisc import Aaindex
except ImportError:
    message = import_message(

[docs]def fetch_AAIndex(accession: str) -> Tuple[str, Dict[str, float]]: """ Fetches AAindex1 dictionary from an accession code. The dictionary maps one-letter AA codes to float values :param accession: Aaindex1 accession code :type accession: str :return: tuple of record titel(str) and dictionary of AA:value mappings :rtype: Tuple[str, Dict[str, float]] """ # Initialise AAindex object and get data aaindex = Aaindex() record = aaindex.get(accession) return record.title, record.index_data
[docs]def aaindex1(G: nx.Graph, accession: str) -> nx.Graph: """Adds AAIndex1 datavalues for a given accession as node features. :param G: nx.Graph protein structure graphein to featurise :type G: nx.Graph :param accession: AAIndex1 accession code for values to use :type accession: str :return: Protein Structure graph with AAindex1 node features added :rtype: nx.Graph """ title, index_data = fetch_AAIndex(accession) # TODO: change to allow for a list of all accession numbers? G.graph["aaindex1"] = accession + ": " + title if G.graph["config"].granularity == "atom": raise NameError( "AAIndex features cannot be added to atom granularity graph" ) for n in G.nodes: residue = n.split(":")[1] residue = protein_letters_3to1_all_caps(residue) aaindex = index_data[residue] G.nodes[n][f"aaindex1_{accession}"] = aaindex return G