[Biojava-dev] Biojava implementation of FATCAT algorithm

[Andreas Prlic]

Hi Ambikesh,

The method you want is afpChain.getBlockNum()

( the afpChain object really needs better documentation...)

Andreas

On Tue, Jun 7, 2011 at 1:09 PM, Ambikesh Jayal <ambi1999 at gmail.com> wrote:
> 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.