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/.
- clients for *.phar and *.svg endpoints have no response (#49)
- 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
- Connexion internal change broke web service server
- Web service has internal server error when fragment has no molblock (#45)
- Canned methods can now raise exception with ids which could not be found and data for ids which could
- Fetch fragment with no molblock throws error (#41)
- Not found response of web service should be JSON (#42)
- 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)
- 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 servetokripodb serve, as it now also serves the fragments - Switched from nosetest to py.test (#36)
- no longer create indices for similarity pairs file, querying is done on dense matrix
- Renamed distance to similarity (#21)
- Flag to ignore upper triangle when calculating distances, instead of always ignore (#20)
- Lower webservice cutoff to 0.45 (#18)
- Webservice online at http://3d-e-chem.vu-compmedchem.nl/kripodb/ui/
- Ignore_upper triangle option in distance import sub command
- Using nested sub-commands instead of long sub-command. For example
kripodb distmatrix_importnow iskripodb distances import
- Faster distance matrix storage format
- Python3 support (#12)
- Automated build to docker hub.
- CLI argument
--precision
- webservice server/client for distance matrix (#16). The CLI and canned commands can now take a local file or a url.
- het_seq_nr contains non-numbers (#15)
- fpneigh2tsv not available as sub command
- Sub command to convert fpneight distance file to tsv.
- Converting distances matrix will load id2label lookup into memory to speed up conversion
- Added sub command to read fpneigh formatted distance matrix file (#14)
- 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)
- Prefix to canned fragments lookups (#11)
- PDB meta data to fragments db (#6)
- Limit to distance matrix searches (#5)
- Merging of distance matrix files more robust (#10)
- Tanimoto coefficient is rounded up (#7)
- 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