Utility functions for protein fragmentation

” Internal utility functions for protein fragmention process.

Functions:

• validate_fragmentation_parameters: Validates the parameters used for protein fragmentation.

• merge_overlapping_domains: Merges overlapping domains within a list of domains.

• check_valid_cutpoint: Helper function to validate potential fragment boundaries.

• recursive_fragmentation: Main function for recursively generating fragments.

Dependencies:

• Domain: A class representing a domain within a protein sequence.

• Protein: A class representing a protein sequence.

alphafragment.fragmentation_methods.check_valid_cutpoint(res, domains, sequence_end)

Checks if a slicing index is a valid cutpoint.

Parameters:

• res (int): The residue position to check (will be sliced before this residue).

• domains (list of Domain): The domains within the protein.

• sequence_end (int): The last residue position in the protein sequence.

Returns:

• bool: True if the residue position is a valid cutpoint; False otherwise.

alphafragment.fragmentation_methods.merge_overlapping_domains(domains)

Merges overlapping domains within a list of domains.

Parameters:

• domains (list of Domain): List of domain objects.

Returns:

• list of Domain: A list of domains where overlapping domains have been merged into single entries.

alphafragment.fragmentation_methods.recursive_fragmentation(protein, domains, fragment_start, min_len, max_len, overlap, cutpoints=None)

Recursively splits a protein sequence into overlapping fragments, avoiding breaking domains.

Parameters:

• protein (Protein): The protein object to fragment.

• domains (list of Domain): The list of domains within the protein - doesn’t use protein.domain_list as overlapping domains should be merged.

• fragment_start (int): The starting position for fragmentation.

• min_len (int): Minimum allowed fragment length.

• max_len (int): Maximum allowed fragment length. (May be increased in the fragmentation process)

• overlap (dict): 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.

• cutpoints (list of tuples, optional): Accumulator for storing fragment cutpoints.

Returns:

• list of tuples or None: The list of fragment cutpoints if successful; otherwise, None.

alphafragment.fragmentation_methods.validate_fragmentation_parameters(protein, min_len, max_len, overlap)

Validates the parameters used for protein fragmentation.

Parameters:

• protein (Protein): The protein object to be fragmented.

• min_len (int): Minimum acceptable length for a protein fragment.

• max_len (int): Maximum acceptable length for a protein fragment.

• overlap (dict): 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.

Returns:

• None

Raises:

• ValueError: If any of the parameter validations fail.

• TypeError: If the protein input is not an instance of the Protein class.