v3.0.0

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

v2.4.0

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)

v2.3.1

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)

v2.3.0

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

v2.2.1

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)

v2.2.0

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)

v2.1.0

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)

v2.0.0

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)

v1.4.2

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)

v1.4.1

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 online at http://3d-e-chem.vu-compmedchem.nl/kripodb/ui/
• Ignore upper triangle option in distance import sub command