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CHANGELOG.md

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Change log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning. Formatted as described on http://keepachangelog.com/.

Unreleased

[3.0.0] - 2018-03-28

Changed

  • Fingerprints changed format from intbitset to Roaring bitmap (#52)

Fingerprint data files created with KripoDB < 3 will not work anymore. They must be exported to makebits with old version of KripoDB and imported in new version.

Fixed

  • When generating similarities of the same fingerprints force ignore upper triangle

[2.4.0] - 2018-03-28

Added

  • Commands to
    • Merge fingerprint/fragment/pharmacophore database files
    • Merge fragment database files
    • Convert phar formatted file from/to pharmacophore database file
  • Methods required by kripo (https://github.com/3D-e-Chem/kripo)

Fixed

  • GET /fragments should accept PDB codes in uppercase (#51)
  • Donor and acceptor features are swapped (#50)

[2.3.1] - 2017-07-21

Fixed

  • clients for *.phar and *.svg endpoints have no response (#49)

[2.3.0] - 2017-05-17

Added

  • Similarities
    • Histogram can output raw scores
    • Histogram can read frozen matrices using either lower or upper triangle
    • Export can be filtered by frag1 and/or pdb codes
    • Filter can be filtered by skip list or keep db
  • Use scripts in update steps
  • Pharmacophores
    • Store pharmocophore points in pytables table (#29)
    • Export pharmacophore points in *.phar format
    • Sub command to add points to table from a directory
    • Sub command to filter the pharmacophores points based on a fragments database
    • Sub command and webservice endpoint to fetch the pharmacophore points of a single fragment identifier (#30)
    • Canned method to fetch pharmacophores of a list fragment identifiers
  • Dive
    • Tag pdb in file by filename
    • Scripts to run it

Fixed

  • Connexion internal change broke web service server

[2.2.1] - 2017-03-07

Fixed

  • Web service has internal server error when fragment has no molblock (#45)

[2.2.0] - 2017-02-23

Changed

  • Canned methods can now raise exception with ids which could not be found and data for ids which could

Fixed

  • Fetch fragment with no molblock throws error (#41)
  • Not found response of web service should be JSON (#42)

[2.1.0] - 2017-01-17

Added

  • Webservice endpoint to render 2D fragment in SVG
  • Published documentation on http://kripodb.readthedocs.io
  • Documented update pipeline
  • Documented command line interface in Sphinx
  • Retrieve fragments from webservice based on fragment id and pdb code (#35)

Changed

  • merge similarity pairs files in chunks instead of loading whole source file in memory
  • canned fragments_by_* methods can use local file or webservice
  • error when duplicate fragment insert is performed
  • Renamed kripodb similarities serve to kripodb serve, as it now also serves the fragments
  • Switched from nosetest to py.test (#36)

Removed

  • no longer create indices for similarity pairs file, querying is done on dense matrix

[2.0.0] - 2016-07-14

Changed

  • Renamed distance to similarity (#21)
  • Flag to ignore upper triangle when calculating distances, instead of always ignore (#20)

[1.4.2] - 2016-06-03

Changed

  • Lower webservice cutoff to 0.45 (#18)

[1.4.1] - 2016-05-31

Added

[1.4.0] - 2016-05-03

Changed

  • Using nested sub-commands instead of long sub-command. For example kripodb distmatrix_import now is kripodb distances import

Added

  • Faster distance matrix storage format
  • Python3 support (#12)
  • Automated build to docker hub.

Removed

  • CLI argument --precision

[1.3.0] - 2016-04-23

Added

  • webservice server/client for distance matrix (#16). The CLI and canned commands can now take a local file or a url.

Fixed

  • het_seq_nr contains non-numbers (#15)

[1.2.5] - 2016-03-24

Fixed

  • fpneigh2tsv not available as sub command

[1.2.4] - 2016-03-24

Added

  • Sub command to convert fpneight distance file to tsv.

[1.2.3] - 2016-03-01

Changed

  • Converting distances matrix will load id2label lookup into memory to speed up conversion

[1.2.2] - 2016-02-22

Added

  • Added sub command to read fpneigh formatted distance matrix file (#14)

[1.2.1] - 2016-02-12

Added

[1.2.0] - 2016-02-11

Added

  • Prefix to canned fragments lookups (#11)
  • PDB meta data to fragments db (#6)
  • Limit to distance matrix searches (#5)

Changed

  • Merging of distance matrix files more robust (#10)
  • Tanimoto coefficient is rounded up (#7)

[1.0.0] - 2016-02-05

Added

  • Convert fragments shelve to sqlite
  • Convert SDF molecules file to sqlite
  • Convert Makebits formated file to sqlite
  • Create distance matrix using modified tanimoto coefficient in hdf5 format