CHANGELOG.md

Change log

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/.

Unreleased

[2.3.1] - 2017-07-21

Fixed

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

[2.3.0] - 2017-05-17

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

[2.2.1] - 2017-03-07

Fixed

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

[2.2.0] - 2017-02-23

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)

[2.1.0] - 2017-01-17

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)

Removed

• no longer create indices for similarity pairs file, querying is done on dense matrix

[2.0.0] - 2016-07-14

Changed

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

[1.4.2] - 2016-06-03

Changed

• Lower webservice cutoff to 0.45 (#18)

[1.4.1] - 2016-05-31

Added

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

[1.4.0] - 2016-05-03

Changed

• Using nested sub-commands instead of long sub-command. For example kripodb distmatrix_import now is kripodb distances import

Added

• Faster distance matrix storage format
• Python3 support (#12)
• Automated build to docker hub.

Removed

• CLI argument --precision

[1.3.0] - 2016-04-23

Added

• webservice server/client for distance matrix (#16). The CLI and canned commands can now take a local file or a url.

Fixed

• het_seq_nr contains non-numbers (#15)

[1.2.5] - 2016-03-24

Fixed

• fpneigh2tsv not available as sub command

[1.2.4] - 2016-03-24

Added

• Sub command to convert fpneight distance file to tsv.

[1.2.3] - 2016-03-01

Changed

• Converting distances matrix will load id2label lookup into memory to speed up conversion

[1.2.2] - 2016-02-22

Added

• Added sub command to read fpneigh formatted distance matrix file (#14)

[1.2.1] - 2016-02-12

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)

[1.2.0] - 2016-02-11

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)

[1.0.0] - 2016-02-05

Added

• 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