peptides.py

Added

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

Fixed

• Peptide methods not being documented in Sphinx documentation.

Added

• PRIN components and VSTPV descriptors to Peptide.

Changed

• Change Sphinx documentation to use the PyData theme.

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.

Initial release.