cath-ssap segfaults on chain 0 of 1br7

UCLOrengoGroup / cath-tools

Protein structure comparison tools such as SSAP and SNAP

http://cath-tools.readthedocs.io

GNU General Public License v3.0

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Closed tonyelewis closed 6 years ago

tonyelewis commented 6 years ago

The following segfaults:

cath-ssap --prot-src-files PDB 1br7 1zdn --align-regions 'D[1br70]:0' --align-regions 'D[1zdnA]:A'

This is motivated by one of 31 failures, all of which involve 'D[1br7003]430-546:0' and some other different domain.

tonyelewis commented 6 years ago

This turned out to be because:

the chain ID of 0 in the region specification wasn't being considered the same as the PDB lines' (space) so empty data was being read in
multiple opportunities were missed to warn or stop cleanly
secondary structure calculations attempted to build a lattice of empty data which caused a crash

These various issues have been addressed in the commits referencing this issue (and tests added).