imspy.utility package

Submodules

imspy.utility.sequence module

imspy.utility.sequence.tokenize_unimod_sequence(unimod_sequence)

Tokenizes a sequence of modified amino acids. :type unimod_sequence: str :param unimod_sequence: A string representing the sequence of amino acids with modifications.

Return type:

List[str]

Returns:

A list of tokenized amino acids.

imspy.utility.utilities module

class imspy.utility.utilities.ExponentialGaussianDistribution(μ=-3, σ=1, λ=0.25)

Bases: object

class imspy.utility.utilities.NormalDistribution(μ, σ)

Bases: object

class imspy.utility.utilities.TokenSequence(sequence_tokenized=None, jsons=None)

Bases: object

property jsons

imspy.utility.utilities.exp_distribution(x, λ=1)

Exponential function :type x: :param x: :type λ: float :param λ: :return:

imspy.utility.utilities.exp_gaussian(x, μ=-3, σ=1, λ=0.25)

laplacian distribution with exponential decay :type x: :param x: :type μ: float :param μ: :type σ: float :param σ: :type λ: float :param λ: :return:

imspy.utility.utilities.gaussian(x, μ=0, σ=1)

Gaussian function :type x: :param x: :type μ: float :param μ: :type σ: float :param σ: :return:

imspy.utility.utilities.get_aa_num_proforma_sequence(sequence)

get number of amino acids in sequence

Parameters:

sequence (str) – proforma formatted aa sequence

Returns:

Number of amino acids

Return type:

int

imspy.utility.utilities.is_unimod_end(char)

Tests if char is end of unimod bracket

Parameters:

char (str) – Character of a proForma formatted aa sequence

Returns:

Whether char is end of unimod bracket

Return type:

bool

imspy.utility.utilities.is_unimod_start(char)

Tests if char is start of unimod bracket

Parameters:

char (str) – Character of a proForma formatted aa sequence

Returns:

Whether char is start of unimod bracket

Return type:

bool

imspy.utility.utilities.normal_pdf(x, mass, s=0.001, inv_sqrt_2pi=0.3989422804014327, normalize=False)

Parameters:

• x (Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]])

• mass (float)

• s (float)

• inv_sqrt_2pi (float)

• normalize (bool)

imspy.utility.utilities.re_index_indices(ids)

Re-index indices, i.e. replace gaps in indices with consecutive numbers. Can be used, e.g., to re-index frame IDs from precursors for visualization. :type ids: :param ids: Indices.

Returns:

Indices.

imspy.utility.utilities.tokenize_proforma_sequence(sequence)

Tokenize a ProForma formatted sequence string.

Parameters:

sequence (str) – Sequence string (ProForma formatted)

Returns:

List of tokens

Return type:

List

imspy.utility.utilities.tokenizer_from_json(path)

load a pre-fit tokenizer from a json file :type path: str :param path: path to tokenizer as json file :return: a keras tokenizer loaded from json

imspy.utility.utilities.tokenizer_to_json(tokenizer, path)

save a fit keras tokenizer to json for later use :type tokenizer: Tokenizer :param tokenizer: fit keras tokenizer to save :type path: str :param path: path to save json to

Module contents