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#

v0.4.0 - 2025-07-25#

Added#

  • energy_cost and nutrient_cost methods to compute biosynthesis cost of a peptide according to various parameters.

Changed#

  • Use bytes.translate method to improve performance of sequence encoding on Peptide instantiation.

Fixed#

  • Documentation error in aliphatic_index method (#6).

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.