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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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cath-superpose gives confusing options error message #39

Closed tonyelewis closed 6 years ago

tonyelewis commented 7 years ago

cath-ssap two chains without problem:

$ cath-ssap 1bvs 1cuk --align-regions 'D[1bvsA]:A' --align-regions 'D[1cukA]:A'
 1bvsA   1cukA  183  190  85.27  179   94   30   2.93

cath-superpose the two chains without problem:

$ cath-superpose --pdb-infile $PDBDIR/1bvs --pdb-infile $PDBDIR/1cuk --align-regions 'D[1bvsA]:A' --align-regions 'D[1cukA]:A' --ssap-aln-infile 1bvsA1cukA.list
Standard RMSD is : 2.92621
Superposed using select_best_score_percent[70].ca_atoms and actual full RMSD is : 3.08064

Yet if the --ssap-aln-infile argument is omitted, the error message is about an option it previously accepted:

$ cath-superpose --pdb-infile $PDBDIR/1bvs --pdb-infile $PDBDIR/1cuk --align-regions 'D[1bvsA]:A' --align-regions 'D[1cukA]:A'
cath-superpose: the argument ('D[1cukA]:A') for option '--align-regions' is invalid
See 'cath-superpose --help' for usage.
tonyelewis commented 6 years ago

It turned out that the whole-chain region specifications were being mis-handled and the two "without problem" commands above were just failing silently in release builds.

In cbfbb6196848e9af73ddc294063161cfe303cc91, I've fixed the problem and added tests to check that the whole-chain specs are handled better.