Protein fragmentation

This module is designed to fragment a given protein into smaller, manageable sections or fragments, ideal for use in AlphaFold predictions. It employs a strategy that initially identifies and handles long domains within the protein and then fragments the remaining protein sections. The module ensures that each fragment is within specified size limits where possible, overlapping fragments within specified boundaries.

Functions:

  • fragment_protein: Fragments a given protein into smaller sections based on specified parameters.

Dependencies:

  • time: Used for setting a time limit for recursive fragmentation.

  • .fragmentation_methods.validate_fragmentation_parameters: Validates the parameters used for protein fragmentation.

  • .fragmentation_methods.recursive_fragmentation: Used for recursively fragmenting protein sections that are not classified as long domains.

  • .fragmentation_methods.merge_overlapping_domains: Merges overlapping domains within a list of domains, and outputs as a new list

  • .long_domains.handle_long_domains: Handles the fragmentation of long domains within the protein.

  • .fragmentation_methods.break_in_half: Splits a protein or subsection in half

alphafragment.fragment_protein.fragment_protein(protein, length=None, overlap=None, len_increase=10, time_limit=0.1)

Fragments a given protein into smaller, manageable sections. Initially, it identifies long domains within the protein and organizes fragments around these. Subsequently, it fragments the remaining protein sections. This function is designed to ensure each fragment falls within the specified size limits (where possible - long domains will always have fragments above the max length, and max length will be increased if a solution cannot be found). Protein fragments overlap within specified boundaries. Uses a time limit for recursive fragmentation to prevent infinite loops.

Parameters:

  • protein (Protein): The protein object to be fragmented, containing domain and sequence information.

  • length (dict, optional): Dictionary containing the ideal, minimum, and maximum length values, in the format: {‘min’: min_len, ‘ideal’: ideal_len, ‘max’: max_len} where min_len, ideal_len, and max_len are all integers, with min_len <= ideal_len <= max_len. Default is None, in which case the default values are used

  • overlap (dict, optional): Dictionary containing the ideal, minimum, and maximum overlap values, in the format: {‘min’: min_overlap, ‘ideal’: ideal_overlap, ‘max’: max_overlap} where min_overlap, ideal_overlap and max_overlap are all integers, with min_overlap <= ideal_overlap <= max_overlap. Default is None, in which case the default values are used

  • len_increase (int, optional): The amount by which to incrementally increase the maximum fragment length if a solution cannot be found. Default is 10.

  • time_limit (float, optional): The maximum time allowed for recursive fragmentation, in seconds.

Returns:

  • list of tuples: A sorted list of tuples, where each tuple represents a fragment with its start and end positions within the protein sequence.