Releases · UCLOrengoGroup/cath-tools

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:

Improvements to cath-map-clusters:

Fixes:

Improve cath-ssap's response to being run in a readonly directory
Fix handling of regions when writing SSAP alignments (3c2c549)
Re-enable cath-superpose's ability to read a SSAP scores file for a single PDB (29a0bf8)
Improve identification of "nearby" ligands to include in superpositions by stopping extending via water (81b1254)
Fix problem writing large temperature factor to PDB files (ad7313b)
Fix problem writing residues with the same ID (a9ebe87)
Fix bug dereferencing possibly empty optional value (ab0c204)

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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