v0.16.5 Improve docs, build, code
2020-04-12
2020-04-12
v0.16.2 cath-cluster: fast, simple complete-linkage clustering
2018-01-09
v0.16.0 Add some new features; address some old issues
2018-01-03 Improvements to cath-superpose
:
- Add
--align-refining
option to refine the alignment being used - Add
--do-the-ssaps
option to automatically perform the required SSAPs - Orient structures in superpositions (rather than relying on PyMOL's
orient
command) - Add default of firing up PyMOL when no other output is specified
- Add
protein
andnucleic
selections to PyMOL scripts
Improvements to cath-resolve-hits
:
- Add JavaScript to HTML output to allow the hits to be collapsed/expanded
- Add a version to the standard output
Improvements to cath-map-clusters
:
- Substantially improve speed
- Improve usage and error messages (b1bd3209ce295549fc675e5ce161b422235b69c9, cfe208bbff3edea26a688dbeba50f6e31b8544a)
Fixes:
- Improve
cath-ssap
's response to being run in a readonly directory - Fix handling of regions when writing SSAP alignments (3c2c54954f0ee99313fab00dcd42735e3ec06081)
- Re-enable
cath-superpose
's ability to read a SSAP scores file for a single PDB (29a0bf8204fc5fd9257f47ffff208aa4babf23a2) - Improve identification of "nearby" ligands to include in superpositions by stopping extending via water (81b125412407d7676402093b91db0813129bc913)
- Fix problem writing large temperature factor to PDB files (ad7313bc31469bd970f592670a306ab3859f04b3)
- Fix problem writing residues with the same ID (a9ebe8782df48a1d1c4b59c88b1929190b3bcce1)
- Fix bug dereferencing possibly empty optional value (ab0c204b35890333080a46d5c01d89e89a4d13df)
Resolve GitHub issues:
- 2 ("Run structural comparisons within cath-superpose") as mentioned above
- 39 ("cath-superpose gives confusing options error message")
- 42 ("[dependency: v14.2 onwards] {cath-superpose.ubuntu14.04} libstdc++.so.6: version
GLIBCXX_3.4.22
not found") - 43 ("Problem parsing CORA alignment file")
- 44 ("Resolve conflict of CRH hidden options that are in Gene3D docs")
- 46 ("cath-ssap segfaults on chain 0 of 1br7")
- 47 ("cath-refine-align doesn't respect --align-regions when writing alignments")
- 52 ("Alignment as shown in supn for 4tsvA vs 4tswB is clearly wrong")
- 55 ("cath-superpose segfaults on mismatching residues in alignment")
Also: add new executable cath-extract-pdb
(currently intended for internal use)
Also: make many improvements to code, build configuration etc
v0.15.3 Improve compatibility of Travis-CI Ubuntu executables with older Ubuntus
2017-09-20 The changes to the Travis-CI build in v0.14.2 meant that the resulting executables didn't work on Ubuntu ≤ 16.04 (out-of-the-box).
This release improves things so that the executables should now work on Ubuntu ≥ 14.10.
See 42 and a2d5fa12d1eb0fb0936cf0b1e2ab32ccb48aaaac for more info.
v0.15.2 Teach cath-resolve-hits to parse hmmscan output
2017-09-14
v0.15.1 Deprecate cath-resolve-hits' --apply-cath-rules option
2017-09-08
v0.14.4 cath-map-clusters: a new tool to map between different ways of clustering your data
2017-08-07
v0.14.2 Add MacOS executables (via the automatic Travis-CI build)
2017-07-28
v0.14.1 Update cath-resolve-hits' options to allow multiple outputs per run; deprecate some previous options
2017-05-31
v0.13.1 Make cath-resolve-hits substantially faster on complex data-sets (like titin)
2017-04-28
v0.13.0 Apply breaking changes to cath-resolve-hits: add headers to output, add JSON format, change default trim, add HMMER evalues to output
2017-03-31 Apply [potentially breaking] changes to cath-resolve-hits:
- add headers and HMMER evalues to standard output, see example
- add option
--json-output
to output in JSON, see example - change default trim from 50/30 to 30/10
v0.12.26 Fix bug in cath-resolve-hits's handling of short segments
2017-03-10 See 31 and cca8fb43e712e710c8eaee4553fa723e137d1c2a for details.
v0.12.25 Make cath-ssap run directly from PDB files
2017-02-28
v0.12.24 Improve cath-resolve-hits HTML output (eg: full result shown in single line; input data limitable)
2017-02-02
v0.12.23 Store superposition colour schemes under PyMOL scenes (accessed via the function keys)
2017-01-31
v0.12.22 Handle DNA ATOM records in PDBs
2017-01-27
2017-01-12
2017-01-04
2016-12-20
2016-11-28
2016-11-24
2016-11-18
2016-11-08
2016-11-06
2016-11-04
2016-11-03
2016-11-01
2016-10-19
2016-10-19