[Biojava-dev] AFPChain getSimilarity function

[Ambikesh Jayal]

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