Version 0.10.0 (Python version)

See 0.10.0.

v0.10.0

This release adds the following major points:

• Added glycan rendering
• Added some missing information in glycans and fixed some bugs
• Added trait IsAminoAcid (note that this renamed some of the methods on AminoAcid)
• Split Model in FragmentationModel and MatchingParameters
• Added much more complexity in FragmentationModel
  • More complex satellite ions
  • More neutral loss types, based on the amino acid/monosaccharide and side chain losses
  • Added options for glycan fragmentation on peptide fragments
• Added pKA and isoelectric point estimations for peptides (thanks to @aukeheerdink)
• Updated built in fragmentation models to use the added complexity and added ones for EAD, EACID, and UVPD
• Added basic CSV format
• Added the options to keep all CSV lines when parsing an identified peptides file
• Added mzPAF exporting for fragments
• Restructured some parts of the API surface
• Updated all databases
• Fixed many bugs and performance issues

Many of these introduce breaking changes so any code written for earlier version will needs some (minor to medium) revisions. If there is anything unclear please reach out.

For a full run down of the changed API use 'cargo-public-api' (this changelog is too big for inclusion here).

v0.9.0

This release adds the following major points:

• Integration with mzdata for raw file handling
• Full ProForma 2.0 compliance by adding support for cross-links, note that many functions and types are renamed
• More control over fragmentation model
• Many more identified peptide file formats
• Updated and somewhat expanded Python bindings
• More reliability thanks to fuzzing efforts
• Updated complexity API, any Peptidoform (formerly LinearPeptide), SequenceElement, and CheckedAminoAcid now has its maximal complexity tracked. This changes many functions on these elements, but should be straightforward to change.
• Added a simple function to open any identified peptides file (see open_identified_peptides_file)
• Updated Unimod, GNOme, and IMGT to the newest versions
• Updated the documentation
• Many many bug fixes
• Optimised memory usage, mostly for identified peptides file (should expect ~20% of the original memory usage)

Many of these introduce breaking changes so any code written for earlier version will needs some (minor to medium) revisions. If there is anything unclear please reach out.

For a full run down of the changed API use 'cargo-public-api' (this changelog is too big for inclusion here).

v0.9.0-alpha.3p

This is a retry of alpha 3 as the last time the Python release failed.

v0.9.0-alpha.3

Third alpha release for v0.9.0. This release adds the following major points:

• Safer API for peptides, peptidoforms, and compound peptidoforms
• Added general open peptides file function
• Added many new identified peptides file formats (MZTab, more peaks versions, deepnovo, powernovo, novob, pgpointnovo, pointnovo, plink, instanovo)
• Many many bug fixes
• Optimised memory usage, mostly for identified peptides file (should expect ~20% of the original memory usage)

For a full run down of the changed API use 'cargo-public-api' (this changelog is too big for inclusion here).

v0.9.0-alpha.2

This is the second alpha release for v0.9.0. Below are the changes compared to v0.9.0-alpha.1.

• Updated complexity API, any LinearPeptide, SequenceElement, and CheckedAminoAcid now has its maximal complexity tracked. This changes many functions on these elements, but should be straightforward to change.
• Added a simple function to open any identified peptides file (see open_identified_peptides_file)
• Updated Unimod, GNOme, and IMGT to the newest versions
• Updated the documentation
• Fixed some bugs

For all changes since v0.8.3 also see the previous alpha release.

v0.9.0-alpha.1

Alpha release for v0.9.0. This release adds the following major points:

• Integration with mzdata for raw file handling
• Full ProForma 2.0 compliance by adding support for cross-links
• More control over fragmentation model
• More identified peptide file formats (now allows Fasta, MaxQuant, MSFragger, Novor, OPair, Peaks, and Sage)
• Updated and somewhat expanded Python bindings
• More reliability thanks to fuzzing efforts

Many of these introduce breaking changes so any code written for earlier version will needs some (minor to medium) revisions. If there is anything unclear please reach out.

For a full run down of the changed API use 'cargo-public-api' (this changelog is too big for inclusion here).

This is an alpha release with the intent to release a stable version in a couple of weeks. The major fields of potential breaking changes in the mean time are:

• Integration with mzdata, where more tight integration with the spectrum types will be experimented with.
• The API for linear peptides, this will be changed to enforce the peptide simplicity rules.
• There might be more identified peptide file formats added which might need some small changes to the underlying structures.
• The Python API is not envisioned to change but requests for adding bindings to more of the Rust side logic could be accepted.

Python hotpatch

v0.8.3.1

Update Cargo.toml

Version 0.8.3

• Fixed output of some Pro Forma features, notable charge and adduct ions
• Updated models to be more cohesive, added more neutral losses where they are expected
• Added Modification::ontology_url to get the url for modifications from ontologies
• Added Modification::search which searches for ontology modifications matching the modification given
• Updated ontologies and IMGT database

Version 0.8.2

• Added python bindings (thanks to @RalfG)
• Added MultiChemical::charge
• Added MolecularFormula::from_pro_forma (was private)
• Added MolecularFormula::from_psi_mod (was private)
• Made MolecularCharge public
• Updated IMGT database, notably improved for Human IGHA1&2