peptides - v0.5.0

Added

• entropy, max_frequency and longest_run methods to Peptide (by Rauf Salamzade @raufs).
• detect_outlier method to detect outlier sequences compared to SwissProt proteins (#8, by Rauf Salamzade @raufs).

Fixed

• Zero division error in auto_correlate (#2).

- Python
Published by github-actions[bot] 6 months ago

peptides - v0.4.0

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).

- Python
Published by github-actions[bot] 7 months ago

peptides - v0.3.4

Added

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

Fixed

• Peptide methods not being documented in Sphinx documentation.

- Python
Published by althonos over 1 year ago

peptides - v0.3.3

Added

• PRIN components and VSTPV descriptors to Peptide.

Changed

• Change Sphinx documentation to use the PyData theme.

- Python
Published by althonos over 1 year ago

peptides - v0.3.2

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.

- Python
Published by github-actions[bot] almost 3 years ago

peptides - v0.3.1

Fixed

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

- Python
Published by github-actions[bot] over 3 years ago

peptides - v0.3.0

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).

- Python
Published by github-actions[bot] over 3 years ago

peptides - v0.2.0

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.

- Python
Published by althonos over 4 years ago

peptides - v0.1.0

Initial release.

- Python
Published by althonos over 4 years ago