Releases | Open Source Science

cath-tools - v0.16.10

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Published by github-actions[bot] about 5 years ago

cath-tools - Improve docs, build, code

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Published by tonyelewis about 6 years ago

cath-tools - https://github.com/UCLOrengoGroup/cath-tools/releases/tag/v0.16.4

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Published by tonyelewis about 6 years ago

cath-tools - cath-cluster: fast, simple complete-linkage clustering

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Published by tonyelewis over 8 years ago

cath-tools - Add some new features; address some old issues

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: * 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

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Published by tonyelewis over 8 years ago

cath-tools - Improve compatibility of Travis-CI Ubuntu executables with older Ubuntus

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.

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Published by tonyelewis over 8 years ago

cath-tools - Teach cath-resolve-hits to parse hmmscan output

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Published by tonyelewis over 8 years ago

cath-tools - Deprecate cath-resolve-hits' --apply-cath-rules option

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Published by tonyelewis over 8 years ago

cath-tools - cath-map-clusters: a new tool to map between different ways of clustering your data

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Published by tonyelewis almost 9 years ago

cath-tools - Add MacOS executables (via the automatic Travis-CI build)

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Published by tonyelewis almost 9 years ago

cath-tools - Update cath-resolve-hits' options to allow multiple outputs per run; deprecate some previous options

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Published by tonyelewis about 9 years ago

cath-tools - Make cath-resolve-hits substantially faster on complex data-sets (like titin)

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Published by tonyelewis about 9 years ago

cath-tools - Apply breaking changes to cath-resolve-hits: add headers to output, add JSON format, change default trim, add HMMER evalues to output

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

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Published by tonyelewis about 9 years ago