Investigate: why does dropping sec files make some SSAP worse

[tonyelewis]

The result of benchmarking the dropping of sec files appears to indicate that the overall homology-discrimination is largely unaffected.

However results for specific pairs are affected - in some cases, the change results in lower scoring alignments and in some cases, higher scoring alignments. See scatter_plot.pdf. Depending on the causes, it may be possible to address some of the regressions without losing the improvements and hence improve the overall performance.

To find the most extreme changes... get the UCLOrengoGroup/cath-tools-supplementary repo, cd into it, then something like:

cd homologue_discrimination_benchmark/results_sets
join v0.12.24-21-g06fbfeb_PDB_DSSP_SEC.full v0.12.24-21-g06fbfeb_PDB_DSSP.full | awk '$6 >= 60 && $15 >=60 && $6 != $15 {print $2 " " $3 " " $6 " " $15 " " ($15 - $6) }' | sort -g  -k 5 | head
join v0.12.24-21-g06fbfeb_PDB_DSSP_SEC.full v0.12.24-21-g06fbfeb_PDB_DSSP.full | awk '$6 >= 60 && $15 >=60 && $6 != $15 {print $2 " " $3 " " $6 " " $15 " " ($15 - $6) }' | sort -rg -k 5 | head