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tonyelewis Attempt to silence false-positives under Mac ASAN
I think this is because of the inconsistent build (about which there are
previous warnings in the Travis-CI logs) :

Latest commit d70c23f Aug 2, 2018


CATH Tools Build Status Documentation Status

Protein structure comparison tools such as SSAP, as used by the Orengo Group in curating CATH.

Executable DOWNLOADS
(for Linux/Mac; chmod them to be executable)
Extras repo


Complete-linkage cluster arbitrary data.
Map names from previous clusters to new clusters based on (the overlaps between) their members (which may be specified as regions within a parent sequence). Renumber any clusters with no equivalents.
Collapse a list of domain matches to your query sequence(s) down to the non-overlapping subset (ie domain architecture) that maximises the sum of the hits' scores.
Structurally align a pair of proteins.
Superpose two or more protein structures using an existing alignment.

Extra Tools

  • build-test Perform the cath-tools tests (which should all pass, albeit with a few warnings)
  • cath-assign-domains Use an SVM model on SSAP+PRC data to form a plan for assigning the domains to CATH superfamilies/folds
  • cath-refine-align Iteratively refine an existing alignment by attempting to optimise SSAP score
  • cath-score-align Score an existing alignment using structural data


The SSAP algorithm (cath-ssap) was devised by Christine A Orengo and William R Taylor.

Please cite: Protein Structure Alignment, Taylor and Orengo, Journal of Molecular Biology 208, 1-22, PMID: 2769748. (PubMed, Elsevier)

Since then, many people have contributed to this code, most notably:


cath-ssap typically uses DSSP, either by reading DSSP files or via its own implementation of the DSSP algorithms.

cath-cluster uses Fionn Murtagh's reciprocal-nearest-neighbour algorithm (see Multidimensional clustering algorithms, volume 4 of Compstat Lectures. Physica-Verlag, Würzburg/ Wien, 1985. ISBN 3-7051-0008-4) as described and refined in Daniel Müllner's Modern hierarchical, agglomerative clustering algorithms (2011, arXiv:1109.2378).


Please tell us about your cath-tools bugs/suggestions here.

If you find this software useful, please spread the word and star the GitHub repo.