Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

v0.3.4 - 2024-09-09

Added

• AshleyFactors descriptors (#5, by @BenSolomon).

Fixed

• Peptide methods not being documented in Sphinx documentation.

v0.3.3 - 2024-08-26

Added

• PRIN components and VSTPV descriptors to Peptide.

Changed

• Change Sphinx documentation to use the PyData theme.

v0.3.2 - 2023-04-01

Added

• Peptide.svger_descriptors to compute SVGER descriptors from Tong et al. (2016).

Fixed

• Peptide.physical_descriptors not being computed by Peptide.descriptors.

Documentation

• Refactor documentation of individual descriptors into their own class.

• Add missing PCPDescriptors and PhysicalDescriptors to the API documentation.

v0.3.1 - 2022-09-01

Fixed

• peptides.datasets data files missing from the source distribution.

v0.3.0 - 2022-09-01

Added

• Peptide.linker_preference_profile to build a profile like used in the DomCut method from Suyama & Ohara (2002).

• Peptide.profile to build a generic per-residue profile from a data table (#3).

v0.2.1 - 2022-02-05

Fixed

• Peptide.hydrophobic_moment not working properly on sequences smaller than the provided window length (#1).

v0.2.0 - 2021-10-21

Added

• Peptide.counts method to get the number of occurences of each amino acid in the peptide.

• Peptide.frequencies to get the frequencies of each amino acid in the peptide.

• Peptide.pcp_descriptors to compute the PCP descriptors from Mathura & Braun (2001).

• Peptide.sneath_vectors to compute the descriptors from Sneath (1966).

• Hydrophilicity descriptors from Barley (2018).

• Peptide.structural_class to predict the structural class of a protein using one of three reference datasets and one of four distance metrics.

Changed

• Peptide.aliphatic_index now supports unknown Leu/Ile residue (code J).

• Swap order of Peptide.hydrophobic_moment arguments for consistency with profile methods.

• Some Peptide functions now support vectorized code using numpy if available.

v0.1.0 - 2021-10-21

Initial release.