[Biojava-dev] Biojava implementation of FATCAT algorithm

[Ambikesh Jayal]

Hi,

What is the function to get the number of twists in FatCatFlexible
algorithm?

I tried AFPChain.getAfpChainTwiNum() but it seems to be giving incorrect
result for those protein sequences for which the FATCAT website reports
non-zero twists.

For example for proteins [3hla.B] AND [2rhe] the Biojava implementation of
FATCAT gives "afpChain.getAfpChainTwiNum() -1" while the number of twists
shown in FATCAT website is 2.

FATCAT website
http://fatcat.burnham.org/fatcat-cgi/cgi/fatcat.pl?-func=pairwise


Regards,
Ambi.