[Biojava-dev] AFPChain getSimilarity function

[Andreas Prlic]

Hi Ambikesh,

Sorry for the lack of documentation... will add javadoc for this as
well as set a page up on the wiki.

There are a few methods that provide access to various scores. If you
want to compare the similarity between the two structures,  probably
the most important values to look at are:

getNrEQR()  the number of structurally equivalent residues

getTotalRMSDOpt() the RMSD of the alignment

getProbability() the Probability of the alignment (FATCAT) or the Z-score (CE)

getTMScore() returns the TM-score

 Does that make more sense?

Andreas



On Wed, Jan 5, 2011 at 10:06 AM, Ambikesh Jayal <ambi1999 at gmail.com> wrote:
> Hi,
> Is there a document that explains the purpose of different functions in the
> AFPChain class? Basically I am interested to find how similar two protein
> structures are. The following four functions seem to be returning values
> indicating similarity but I am not sure what is the main difference between
> them. So it will be helpful if someone can explain.
> org.biojava.bio.structure.align.model.AFPChain
> getSimilarity()
> getSimilarity1()
> getSimilarity2()
> getAlignScore()
> I ran the CE and FATCAT algorithms for two proteins and got the following
> results. Not sure how to interpret them. Any help?
> CE, name1 = "1cdg.A"; name2 = "1tim.B";
> **** afpChain.getSimilarity() 0.1951219512195122
> **** afpChain.getSimilarity1() 30
> **** afpChain.getSimilarity2() 83
> **** afpChain.getAlignScore()693.7852267498898
>
>
> FATCAT, name1 = "1cdg.A"; name2 = "1tim.B";
> **** afpChain.getSimilarity() 0.17647058823529413
> **** afpChain.getSimilarity1() 21
> **** afpChain.getSimilarity2() 58
> **** afpChain.getAlignScore()186.61939969257776
>
>
>
>
> FATCAT name1 = "1cdg.A"; name2 = "1cdg.A";
> **** afpChain.getSimilarity() 1.0
> **** afpChain.getSimilarity1() 100
> **** afpChain.getSimilarity2() 100
> **** afpChain.getAlignScore()2040.0
>
> Kind Regards,
> Ambi