another update to new similarity calculation

andreasprlic · andreasprlic · commit a62a8b50f5a3 · 2016-08-05T07:50:20.000-07:00
diff --git a/biojava-integrationtest/src/test/resources/ce_1fdo.A_2iv2.X.out b/biojava-integrationtest/src/test/resources/ce_1fdo.A_2iv2.X.out
@@ -1,4 +1,4 @@
-<AFPChain name1="1FDO.A" name2="2IV2.X" method="jCE" version="1.2" alnLength="720" blockNum="1" gapLen="28" optLength="692" totalLenIni="697" alignScore="1551.34" chainRmsd="0.91" identity="0.9569" normAlignScore="0.00" probability="8.40e+00" similarity="0.9569" similarity1="97" similarity2="99" totalRmsdIni="1.36" totalRmsdOpt="0.91" ca1Length="715" ca2Length="697" afpNum="4" alignScoreUpdate="0.00" time="-1">
+<AFPChain name1="1FDO.A" name2="2IV2.X" method="jCE" version="1.2" alnLength="720" blockNum="1" gapLen="28" optLength="692" totalLenIni="697" alignScore="1551.34" chainRmsd="0.91" identity="0.9957" normAlignScore="0.00" probability="8.40e+00" similarity="0.9957" similarity1="97" similarity2="99" totalRmsdIni="1.36" totalRmsdOpt="0.91" ca1Length="715" ca2Length="697" afpNum="4" alignScoreUpdate="0.00" time="-1">
   <block blockNr="0" blockSize="0" blockScore="0.00" blockRmsd="0.91" blockGap="0">
     <eqr eqrNr="0" pdbres1="1" chain1="A" pdbres2="1" chain2="X" />
     <eqr eqrNr="1" pdbres1="2" chain1="A" pdbres2="2" chain2="X" />

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<AFPChain name1="1FDO.A" name2="2IV2.X" method="jCE" version="1.2" alnLength="720" blockNum="1" gapLen="28" optLength="692" totalLenIni="697" alignScore="1551.34" chainRmsd="0.91" identity="0.9569" normAlignScore="0.00" probability="8.40e+00" similarity="0.9569" similarity1="97" similarity2="99" totalRmsdIni="1.36" totalRmsdOpt="0.91" ca1Length="715" ca2Length="697" afpNum="4" alignScoreUpdate="0.00" time="-1">`
	`1`	`+<AFPChain name1="1FDO.A" name2="2IV2.X" method="jCE" version="1.2" alnLength="720" blockNum="1" gapLen="28" optLength="692" totalLenIni="697" alignScore="1551.34" chainRmsd="0.91" identity="0.9957" normAlignScore="0.00" probability="8.40e+00" similarity="0.9957" similarity1="97" similarity2="99" totalRmsdIni="1.36" totalRmsdOpt="0.91" ca1Length="715" ca2Length="697" afpNum="4" alignScoreUpdate="0.00" time="-1">`
`2`	`2`	`<block blockNr="0" blockSize="0" blockScore="0.00" blockRmsd="0.91" blockGap="0">`
`3`	`3`	`<eqr eqrNr="0" pdbres1="1" chain1="A" pdbres2="1" chain2="X" />`
`4`	`4`	`<eqr eqrNr="1" pdbres1="2" chain1="A" pdbres2="2" chain2="X" />`