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Releases: 3D-e-Chem/kripodb

v3.0.0

28 Mar 18:10
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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

28 Mar 12:28
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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

21 Jul 13:58
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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

16 May 08:55
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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

07 Mar 13:11
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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

23 Feb 19:34
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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

17 Jan 15:09
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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

14 Jul 10:00
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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

03 Jun 12:05
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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

31 May 14:42
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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