@sverhoeven sverhoeven released this Mar 28, 2018 · 7 commits to master since this release

Assets 2

Library to interact with Kripo fragment, fingerprint and similarity data files.

KRIPO stands for Key Representation of Interaction in POckets, see reference for more information.

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

@sverhoeven sverhoeven released this Mar 28, 2018 · 24 commits to master since this release

Assets 2

Library to interact with Kripo fragment, fingerprint and similarity data files.

KRIPO stands for Key Representation of Interaction in POckets, see reference for more information.

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)

@sverhoeven sverhoeven released this Jul 21, 2017 · 62 commits to master since this release

Assets 2

Library to interact with Kripo fragment, fingerprint and similarity data files.

KRIPO stands for Key Representation of Interaction in POckets, see reference for more information.

Fixed

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

@sverhoeven sverhoeven released this May 16, 2017 · 69 commits to master since this release

Assets 2

Library to interact with Kripo fragment, fingerprint and similarity data files.

KRIPO stands for Key Representation of Interaction in POckets, see reference for more information.

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

@sverhoeven sverhoeven released this Mar 7, 2017 · 122 commits to master since this release

Assets 2

Library to interact with Kripo fragment, fingerprint and similarity data files.

KRIPO stands for Key Representation of Interaction in POckets, see reference for more information.

Fixed

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

@sverhoeven sverhoeven released this Feb 23, 2017 · 123 commits to master since this release

Assets 2

Library to interact with Kripo fragment, fingerprint and similarity data files.

KRIPO stands for Key Representation of Interaction in POckets, see reference for more information.

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)

@sverhoeven sverhoeven released this Jan 17, 2017 · 152 commits to master since this release

Assets 2

Library to interact with Kripo fragment, fingerprint and similarity data files.

KRIPO stands for Key Representation of Interaction in POckets, see reference for more information.

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)

@sverhoeven sverhoeven released this Jul 14, 2016 · 232 commits to master since this release

Assets 2

Library to interact with Kripo fragment, fingerprint and similarity data files.

KRIPO stands for Key Representation of Interaction in POckets, see reference for more information.

Changed

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

@sverhoeven sverhoeven released this Jun 3, 2016 · 248 commits to master since this release

Assets 2

Library to interact with Kripo fragment, fingerprint and similarity data files.

KRIPO stands for Key Representation of Interaction in POckets, see reference for more information.

Changed

  • Lower webservice cutoff to 0.45 (#18)

@sverhoeven sverhoeven released this May 31, 2016 · 250 commits to master since this release

Assets 2

Library to interact with Kripo fragment, fingerprint and similarity data files.

KRIPO stands for Key Representation of Interaction in POckets, see reference for more information.

Added