Skip to content

v0.3.0

Pre-release
Pre-release
Compare
Choose a tag to compare
@dominiquesydow dominiquesydow released this 30 Jun 07:25
· 136 commits to main since this release
v0.3.0
197b82e
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

This release contains a lot of big changes to the code base and new features. (In the future cut releases earlier!)

New

Package

  • Replace angles and ratios in SideChainOrientationFeature and SolventExposureFeature with categories (1, 2, 3) PR
  • Add viewer module with StructureViewer, StructurePairViewer, KinaseViewer PR and PR
  • Use opencadd.databases.klifs to fetch structural information from KLIFS (local or remote) PR
  • Use opencadd.structure.pocket to calculate subpocket centers; update anchor residues so that less fingerprints contain NaN values because of missing residues PR
  • Add CLI with sub-commands (kissim encode; kissim compare; kissim outliers; ...) including a structure outlier removal option PR and PR
  • @AJK-dev: Add kinase matrix clustering and tree generation (kissim.comparison.tree module) PR
  • Save FeatureDistancesGenerator and FingerprintDistanceGenerator data as CSV files and FingerprintGenerator data as JSON file PR
  • Add fingeprint pair bit coverage minimum option PR

Repo structure and development workflow

  • Rename repo from kinsim_structure to kissim PR
  • Rename master to main branch
  • Add unit tests and CI for Linux/MacOS/Windows
  • Add tutorials for each module; set up RTD documentation
  • Add CodeCov

Changes

Package

  • Change side chain orientation calculation PR
    • Before: Calculate angle between pocket centroid, residue CA atom and residue's side chain centroid
    • Now: Calculate angle between pocket centroid, residue CA atom and residue's side chain representative (furthest atom from CA) and map angles into categories
  • Use NGLview instead of PyMol for visualization
  • Remove MOL2-to-PDB conversion; use KLIFS started to offer PDB files directly
    • Add PocketBioPython and PocketDataFrame as data classes for the encoding step
    • Add KlifsToKissimData (streamline KLIFS data into KiSSim's required data format)
  • Restructure code base (split large files into a module with multiple submodules)
  • Rename similarity > comparison module PR
  • Rename ExposureFeature > SolventExposureFeature as part of this PR
  • Fingerprints are not normalized by default any more; instead distances are calculated per feature type (thus dimensions match) and can be weighted user-defined to produce the final fingerprint distance PR
  • Move structure/kinase matrix generation in FingerprintDistanceGenerator class method to kissim.comparison.matrix module PR

Repo structure and development workflow

Bug fixes

  • Fix SiteAlign feature implementation for THR's charge (was positively charged but must be neutral) PR
Assets 2
Loading