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Added a CPDB Signatures Alerts Test.
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@olas
olas committed Jul 13, 2010
1 parent dde3f68 commit 53578d2
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Showing 6 changed files with 155 additions and 12 deletions.
2 changes: 1 addition & 1 deletion plugins/net.bioclipse.ds.cpdb.sign/.classpath
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Expand Up @@ -2,6 +2,6 @@
<classpath>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
<classpathentry kind="src" path="src"/>
<classpathentry excluding="net/bioclipse/ds/cpdb/sign/ParseSignFiles.java|net/bioclipse/ds/cpdb/sign/ParseSignInfoFiles.java|net/bioclipse/ds/cpdb/sign/SignaturesAlertsCalculator.java" kind="src" path="src"/>
<classpathentry kind="output" path="bin"/>
</classpath>
4 changes: 3 additions & 1 deletion plugins/net.bioclipse.ds.cpdb.sign/META-INF/MANIFEST.MF
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Expand Up @@ -18,7 +18,9 @@ Require-Bundle: org.eclipse.ui,
org.openscience.cdk.interfaces,
net.bioclipse.ds.signatures,
org.eclipse.core.resources;bundle-version="3.5.2",
net.bioclipse.ds.libsvm;bundle-version="2.91.0"
net.bioclipse.ds.libsvm;bundle-version="2.91.0",
net.bioclipse.ds.common;bundle-version="2.4.0",
net.bioclipse.cdk.ui.sdfeditor;bundle-version="2.4.0"
Bundle-RequiredExecutionEnvironment: J2SE-1.5
Bundle-ActivationPolicy: lazy
Bundle-ClassPath: .
Expand Down
132 changes: 132 additions & 0 deletions plugins/net.bioclipse.ds.cpdb.sign/data/cpdb_atomsign0_5.sdf_exportedSignatures.txt
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@@ -0,0 +1,132 @@
0
1
significantSignature: [S](p[C]p[C]) nrPos: 23 nrTot: 32 pValue: 0.02 Accuracy: 0.72 ActiveCall: True
significantSignature: [C](p[C][N]p[S]) nrPos: 6 nrTot: 7 pValue: 0.08 Accuracy: 0.86 ActiveCall: True
significantSignature: [N]([C]=[N][O]) nrPos: 6 nrTot: 6 pValue: 0.02 Accuracy: 1.00 ActiveCall: True
significantSignature: [O](p[C]p[C]) nrPos: 32 nrTot: 39 pValue: 0.00 Accuracy: 0.82 ActiveCall: True
significantSignature: [N]([C]=[N]) nrPos: 18 nrTot: 25 pValue: 0.04 Accuracy: 0.72 ActiveCall: True
significantSignature: [C]([N]) nrPos: 67 nrTot: 110 pValue: 0.06 Accuracy: 0.61 ActiveCall: True
significantSignature: [C](p[C]p[C]p[O]) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [O](=[N]) nrPos: 161 nrTot: 215 pValue: 0.00 Accuracy: 0.75 ActiveCall: True
significantSignature: [N]([C][C][P]) nrPos: 6 nrTot: 6 pValue: 0.02 Accuracy: 1.00 ActiveCall: True
significantSignature: [N]([N]=[O]) nrPos: 99 nrTot: 119 pValue: 0.00 Accuracy: 0.83 ActiveCall: True
significantSignature: [C](p[C][C]p[O]) nrPos: 8 nrTot: 10 pValue: 0.08 Accuracy: 0.80 ActiveCall: True
significantSignature: [C]([C][N]) nrPos: 148 nrTot: 231 pValue: 0.00 Accuracy: 0.64 ActiveCall: True
significantSignature: [C](p[C]p[N][N]) nrPos: 13 nrTot: 17 pValue: 0.04 Accuracy: 0.76 ActiveCall: True
significantSignature: [C]([C]p[C]p[O]) nrPos: 19 nrTot: 25 pValue: 0.02 Accuracy: 0.76 ActiveCall: True
significantSignature: [N]([C][C][N]) nrPos: 108 nrTot: 135 pValue: 0.00 Accuracy: 0.80 ActiveCall: True
significantSignature: [C]([C]p[N]p[O]) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([Br][C]) nrPos: 7 nrTot: 7 pValue: 0.01 Accuracy: 1.00 ActiveCall: True
significantSignature: [O]([N]) nrPos: 76 nrTot: 118 pValue: 0.01 Accuracy: 0.64 ActiveCall: True
significantSignature: [C](=[C][O]) nrPos: 8 nrTot: 9 pValue: 0.03 Accuracy: 0.89 ActiveCall: True
significantSignature: [C](p[N][N]p[S]) nrPos: 11 nrTot: 12 pValue: 0.01 Accuracy: 0.92 ActiveCall: True
significantSignature: [O](=[P]) nrPos: 12 nrTot: 16 pValue: 0.06 Accuracy: 0.75 ActiveCall: True
significantSignature: [N]([C][O]=[O]) nrPos: 56 nrTot: 91 pValue: 0.06 Accuracy: 0.62 ActiveCall: True
significantSignature: [C](p[C][N]p[O]) nrPos: 25 nrTot: 28 pValue: 0.00 Accuracy: 0.89 ActiveCall: True
2
significantSignature: [C]([C]([C][C][O])=[O][O]([C])) nrPos: 11 nrTot: 13 pValue: 0.02 Accuracy: 0.85 ActiveCall: True
significantSignature: [C]([C]([C])=[C]([C])[C]([C][C][C])) nrPos: 8 nrTot: 10 pValue: 0.08 Accuracy: 0.80 ActiveCall: True
significantSignature: [C](=[C]([O])[C]([C][C])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C]([C]p[N])p[S](p[C])) nrPos: 12 nrTot: 15 pValue: 0.03 Accuracy: 0.80 ActiveCall: True
significantSignature: [C]([C]([N])[C]([O])) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C][C])[O]([C])[O]([C])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C])p[C]([C]p[O])) nrPos: 27 nrTot: 34 pValue: 0.00 Accuracy: 0.79 ActiveCall: True
significantSignature: [C]([C](=[C])[C](p[C]p[C])[C]([O][O])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([N]=[O][O]([C])) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([N])[O]) nrPos: 16 nrTot: 22 pValue: 0.05 Accuracy: 0.73 ActiveCall: True
significantSignature: [Br]([C]([C])) nrPos: 7 nrTot: 7 pValue: 0.01 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C])p[C]([C]p[C])[C]([C]=[O])) nrPos: 8 nrTot: 10 pValue: 0.08 Accuracy: 0.80 ActiveCall: True
significantSignature: [C]([N]([C])[N]([C][N])=[O]) nrPos: 16 nrTot: 18 pValue: 0.00 Accuracy: 0.89 ActiveCall: True
significantSignature: [C]([N][N]([C][N])=[O]) nrPos: 12 nrTot: 13 pValue: 0.00 Accuracy: 0.92 ActiveCall: True
significantSignature: [C]([C]([N])[C]([C][O])) nrPos: 10 nrTot: 10 pValue: 0.00 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C][N])) nrPos: 14 nrTot: 19 pValue: 0.05 Accuracy: 0.74 ActiveCall: True
significantSignature: [C]([C]([C])=[C]([C])[C]([O]=[O])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C])[C]([C][N])[O]([C])) nrPos: 6 nrTot: 6 pValue: 0.02 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([N]([C][N])=[O][O]([C])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([N])) nrPos: 21 nrTot: 29 pValue: 0.03 Accuracy: 0.72 ActiveCall: True
significantSignature: [C]([C]([N])[Cl]) nrPos: 11 nrTot: 14 pValue: 0.05 Accuracy: 0.79 ActiveCall: True
significantSignature: [C]([C]p[C](p[C])p[C](p[C][C])) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C])[C](p[C]p[C])p[C]([C]p[C])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](=[C]([C])[C]([O])[C]([C][N])) nrPos: 6 nrTot: 6 pValue: 0.02 Accuracy: 1.00 ActiveCall: True
significantSignature: [N](p[C]([C]p[C])p[C]([N]p[S])) nrPos: 6 nrTot: 7 pValue: 0.08 Accuracy: 0.86 ActiveCall: True
significantSignature: [O]([C](p[C]p[C])[C]([C][O])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [N]([C]([O]=[O])) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C])p[C](p[C])[N](=[N])) nrPos: 9 nrTot: 11 pValue: 0.05 Accuracy: 0.82 ActiveCall: True
significantSignature: [N](p[C](p[N][N])p[C](p[N][N])) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [O]([C](=[C])[C]([C][O])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C](=[C])[C]([C][C])) nrPos: 6 nrTot: 7 pValue: 0.08 Accuracy: 0.86 ActiveCall: True
significantSignature: [N](=[C]([C][C])[O]) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C]=[C])[C]([C][O])[N]([C][C])) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[S])[C](p[C]p[O])p[N](p[C])) nrPos: 8 nrTot: 9 pValue: 0.03 Accuracy: 0.89 ActiveCall: True
significantSignature: [C]([C][C](=[C])[C]([C][C])[C]([C]=[C])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](=[C][C]([N])) nrPos: 7 nrTot: 7 pValue: 0.01 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C])p[C]([N]p[O])) nrPos: 25 nrTot: 27 pValue: 0.00 Accuracy: 0.93 ActiveCall: True
significantSignature: [C](p[C](p[C][C])p[C](p[C][N])[C]([C]=[O])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C](p[C]p[C])[C](p[C]p[C])=[O]) nrPos: 13 nrTot: 16 pValue: 0.02 Accuracy: 0.81 ActiveCall: True
significantSignature: [O]([C]([C])[C]([N]=[O])) nrPos: 6 nrTot: 6 pValue: 0.02 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C]=[C])[O]([C])) nrPos: 9 nrTot: 9 pValue: 0.00 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C])p[C]([N]p[S])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]=[C]([C][C])) nrPos: 6 nrTot: 6 pValue: 0.02 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([N])=[C]([C][C])) nrPos: 9 nrTot: 9 pValue: 0.00 Accuracy: 1.00 ActiveCall: True
3
significantSignature: [C](p[C](p[C]([C]p[C,0])[O]([C]))p[C](p[C]([C]p[C,0])[O]([C]))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0]))p[C](p[C](p[C,0]))[O]([C]([C][C][C]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [O]([C](p[C](p[C])p[C](p[C]))[C]([C][C][C]([O]=[O]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [N]([C]([N]([C][N])=[O])) nrPos: 12 nrTot: 13 pValue: 0.00 Accuracy: 0.92 ActiveCall: True
significantSignature: [C]([C](=[C]([C][C]))) nrPos: 6 nrTot: 6 pValue: 0.02 Accuracy: 1.00 ActiveCall: True
significantSignature: [N]([C]([C]([C,1]))[C]([C](=[C,0]))[C]([C,0]([C])[C,1]([O]))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C][C]([N]([C][N]))[O]) nrPos: 6 nrTot: 6 pValue: 0.02 Accuracy: 1.00 ActiveCall: True
significantSignature: [O](=[C]([C](p[C]p[C])[C](p[C]p[C]))) nrPos: 13 nrTot: 16 pValue: 0.02 Accuracy: 0.81 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0][N]))p[C]([C](p[C]p[C])p[C]([C]p[C,0]))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [O](=[C]([N][N]([C][N]))) nrPos: 12 nrTot: 13 pValue: 0.00 Accuracy: 0.92 ActiveCall: True
significantSignature: [C]([C](p[C](p[C])p[O](p[C]))=[N]([N]([C][C]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [Cl]([C]([C]([N]))) nrPos: 11 nrTot: 14 pValue: 0.05 Accuracy: 0.79 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0]))p[C](p[C](p[C,0]))[N]([C][C])) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C]([C]))[C]([N]([C][N]))) nrPos: 10 nrTot: 12 pValue: 0.03 Accuracy: 0.83 ActiveCall: True
significantSignature: [O](=[C]([N][O]([C]))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C](=[C])[C]([C][C])[C]([C]=[C]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](=[C]([C]([N]))) nrPos: 7 nrTot: 7 pValue: 0.01 Accuracy: 1.00 ActiveCall: True
significantSignature: [O]([C]([C]([C]=[C])=[O])[C]([C]([C])[C]([C][N]))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C]([C])=[C]([C]))=[O][O]([C]([C][C]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([O])[C]([N]([C][N]))[O]) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C]([C,0])[O])[C]([C]([C,1])[C]([C][C,0]))[C]([C][C](=[C])[C](=[C][C,1]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0]))p[C](p[C](p[C,0])[N](=[N]))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0]))p[C](p[C]([C]p[C,0])[O])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [O](=[C]([C]([C][C][O])[O]([C]))) nrPos: 11 nrTot: 13 pValue: 0.02 Accuracy: 0.85 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0][O]))p[C](p[C](p[C,0][O])[C]([C][C,1]))[O]([C,1]([O]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C]([N])[O])[O]) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [O]([C]([C]([N,0]))[C]([C]([N,0]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [N](=[C]([C](p[C]p[O]))[N]([C]([C])[C]([N]=[O]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [O](=[C]([N]([C][N])[O]([C]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C](p[C](p[C])p[C](p[C][C]))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [N]([C][C][C](p[C](p[C])p[C](p[C]))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0]))p[C](p[C]([C]p[C,0])[C]([C]=[O]))) nrPos: 8 nrTot: 9 pValue: 0.03 Accuracy: 0.89 ActiveCall: True
significantSignature: [O]([C]([C]([C]=[C]))[C]([C]([C][C][O])=[O])) nrPos: 9 nrTot: 9 pValue: 0.00 Accuracy: 1.00 ActiveCall: True
significantSignature: [O]([C]([C]([N]))) nrPos: 16 nrTot: 22 pValue: 0.05 Accuracy: 0.73 ActiveCall: True
significantSignature: [O](=[C]([N]([C])[N]([C][N]))) nrPos: 16 nrTot: 18 pValue: 0.00 Accuracy: 0.89 ActiveCall: True
significantSignature: [C](=[C]([C]([C,0]=[O]))[C]([C][C]([C][C])[C]([C]=[C,0]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C](=[C])[C]([O][O,1]))p[C](p[C](p[C,0])[O,1])p[C](p[C]([C]p[C,0])[O]([C]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
4
significantSignature: [C]([C]([C]([C]([C])))[C]([C]([N]([C][N])))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [O]([C]([C]([C]([N])[O]))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [O]([C]([C][C]([N]([C][N])))) nrPos: 6 nrTot: 6 pValue: 0.02 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0]))[C]([C](p[C](p[C])p[C,1]))p[C](p[C](p[C,0])[C,1](p[C](p[C])))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C](p[C](p[C](p[C,0]))p[C](p[C](p[C,0])[C,2]))[C](p[C](p[C](p[C,1][N]))p[C,2](p[C](p[C,1])))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C]([C]([C])))[C]([C]([C]([N])))) nrPos: 6 nrTot: 7 pValue: 0.08 Accuracy: 0.86 ActiveCall: True
significantSignature: [O]([C]([C]([O])[C]([N]([C][N])))) nrPos: 5 nrTot: 5 pValue: 0.04 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0]([C])))p[C](p[C]([C]([C]=[O])p[C,0]))) nrPos: 7 nrTot: 8 pValue: 0.05 Accuracy: 0.88 ActiveCall: True
significantSignature: [C]([C]([C]([C]([C][C])[C,1]([C])))[C](=[C]([C]([C,0]=[O]))[C]([C][C](=[C,0])[C,1]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C]([N]([C][N]))[O])) nrPos: 6 nrTot: 6 pValue: 0.02 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C][C]([N]([C]([C])[N](=[O])))=[O]) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [O](=[C]([C]([C]([C])=[C]([C]))[O]([C]([C][C])))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0]))p[C](p[C](p[C,0][N](=[N])))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](=[C]([C]([C][C]([C][C])[C,0]([C])))[C]([C](=[C,0])=[O])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C](=[C,1])=[O])=[C]([C]([C]([C,0]))[C]([C][C]([C][C,0])[C,1]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
5
significantSignature: [C](p[C](p[C](p[C,2]))p[C](p[C]([C]([C,1])p[C,2])[C](p[C](p[C](p[C,0]))p[C,1](p[C](p[C,0]))))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [O](=[C]([C][C]([N]([C]([C])[N](=[O]))))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C]([C]([C]([C]))))[C]([C]([C]([C]([N]))))) nrPos: 6 nrTot: 7 pValue: 0.08 Accuracy: 0.86 ActiveCall: True
significantSignature: [C]([C](=[C]([C,1]([C][C]([C][C,0]))))[C](=[C]([C]([C]([C,0]))[C,1]))=[O]) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,1]))p[C]([C]([C](p[C](p[C])p[C,0]))p[C]([C,0](p[C](p[C]))p[C,1]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C]([C]([C]([N]([C]([C])[N](=[O])))=[O])) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
significantSignature: [C](p[C](p[C](p[C,0]([N](=[N]))))p[C](p[C](p[C,0]))) nrPos: 4 nrTot: 4 pValue: 0.08 Accuracy: 1.00 ActiveCall: True
10 changes: 10 additions & 0 deletions plugins/net.bioclipse.ds.cpdb.sign/plugin.xml
View file
Expand Up @@ -11,6 +11,16 @@
class="net.bioclipse.ds.cpdb.sign.CPDBSignSigRunner"
endpoint="net.bioclipse.ds.carcinogenicity">
</test>
<test
id="cpdb.alerts.signatures"
name="CPDB Toxicophores"
endpoint="net.bioclipse.ds.carcinogenicity"
consensus="net.bioclipse.ds.consensus.majority.emptynegative"
class="net.bioclipse.ds.matcher.SignatureAlertsMatcher">
<resource name="file"
path="data/cpdb_atomsign0_5.sdf_exportedSignatures.txt">
</resource>
</test>
</extension>

<!--test
Expand Down
4 changes: 2 additions & 2 deletions plugins/net.bioclipse.ds.cpdb/META-INF/MANIFEST.MF
View file
Expand Up @@ -13,8 +13,8 @@ Require-Bundle: org.eclipse.ui,
net.bioclipse.core,
org.eclipse.help,
org.openscience.cdk.interfaces,
net.bioclipse.ds.common;bundle-version="0.1.1",
net.bioclipse.ds.ui;bundle-version="0.1.1"
net.bioclipse.ds.common,
net.bioclipse.ds.ui
Bundle-RequiredExecutionEnvironment: J2SE-1.5
Bundle-ActivationPolicy: lazy
Import-Package: org.apache.log4j
15 changes: 7 additions & 8 deletions plugins/net.bioclipse.ds.cpdb/src/net/bioclipse/ds/cpdb/calc/SignaturesMatchCalculator.java
View file
Expand Up @@ -10,25 +10,24 @@
******************************************************************************/
package net.bioclipse.ds.cpdb.calc;

import org.apache.log4j.Logger;

import net.bioclipse.ds.prop.calc.BaseDSPropertyCalculator;



/**
*
* @author ola
*
*/
public class SignaturesMatchCalculator extends BaseDSPropertyCalculator{

private static final Logger logger = Logger.getLogger(
SignaturesMatchCalculator.class);

@Override
public String getPropertyName() {
return "CPDB Signatures";
return "CPDB Signatures Matches";
}

@Override
public String getTestID() {
return "cpdb.signatures";
return "CPDB Signatures";
}

}

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