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Summary of changes in cath-tools releases

v0.16.5 Improve docs, build, code

2020-04-12  

v0.16.4

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 and nucleic 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:

Fixes:

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  

v0.12.20

2017-01-12  

v0.12.19

2017-01-04  

v0.12.18

2016-12-20  

v0.12.17

2016-11-28  

v0.12.16

2016-11-24  

v0.12.15

2016-11-18  

v0.12.14

2016-11-08  

v0.12.13

2016-11-06  

v0.12.12

2016-11-04  

v0.12.11

2016-11-03  

v0.12.10

2016-11-01  

v0.12.9

2016-10-19  

v0.12.8

2016-10-19