Recent Releases of kripodb
kripodb - 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
- Python
Published by sverhoeven about 8 years ago
kripodb - 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)
- Python
Published by sverhoeven about 8 years ago
kripodb - 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)
- Python
Published by sverhoeven almost 9 years ago
kripodb - 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
- Python
Published by sverhoeven about 9 years ago
kripodb - 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)
- Python
Published by sverhoeven over 9 years ago
kripodb - 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)
- Python
Published by sverhoeven over 9 years ago
kripodb - 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 fragmentsby* methods can use local file or webservice
- error when duplicate fragment insert is performed
- Renamed
kripodb similarities servetokripodb serve, as it now also serves the fragments - Switched from nosetest to py.test (#36)
- Python
Published by sverhoeven over 9 years ago
kripodb - 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)
- Python
Published by sverhoeven almost 10 years ago
kripodb - 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
- Python
Published by sverhoeven about 10 years ago
kripodb - v1.4.0
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.
Changed
- Using nested sub-commands instead of long sub-command. For example
kripodb distmatrix_importnow iskripodb distances import
Added
- Faster distance matrix storage format
- Python3 support (#12)
- Automated build to docker hub.
Removed
- CLI argument
--precision
- Python
Published by sverhoeven about 10 years ago
kripodb - v1.3.0
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
- webservice server/client for distance matrix (#16). The CLI and canned commands can now take a local file or a url.
Fixed
- hetseqnr contains non-numbers (#15)
- Python
Published by sverhoeven about 10 years ago
kripodb - v1.2.4
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
- Sub command to convert fpneight distance file to tsv.
- Python
Published by sverhoeven about 10 years ago
kripodb - v1.2.2
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
- Added sub command to read fpneigh formatted distance matrix file (#14)
- Python
Published by sverhoeven over 10 years ago
kripodb - v1.2.1
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.
Added
- Added sub commands to read/write distance matrix in tab delimited format (#13)
- Created repo for Knime example and plugin at https://github.com/3D-e-Chem/knime-kripodb (#8)
- Python
Published by sverhoeven over 10 years ago
kripodb - 1.2.0
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.
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)
- Python
Published by sverhoeven over 10 years ago