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CHANGELOG.md

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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

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.