Menu
▾
▴
[DL-Learner SVN] SF.net SVN: dl-learner:[3324] trunk
|
From: <km...@us...> - 2011-10-26 11:38:22
|
Revision: 3324
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3324&view=rev
Author: kmpf
Date: 2011-10-26 11:38:13 +0000 (Wed, 26 Oct 2011)
Log Message:
-----------
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
Added Paths:
-----------
trunk/test/pdb/1XFF/
trunk/test/pdb/1XFF/1XFF.A.Alanine.conf
trunk/test/pdb/1XFF/1XFF.A.Alanine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Alanine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Arginine.conf
trunk/test/pdb/1XFF/1XFF.A.Arginine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Arginine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Asparagine.conf
trunk/test/pdb/1XFF/1XFF.A.Asparagine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Asparagine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.conf
trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Cysteine.conf
trunk/test/pdb/1XFF/1XFF.A.Cysteine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Cysteine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.conf
trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Glutamine.conf
trunk/test/pdb/1XFF/1XFF.A.Glutamine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Glutamine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Glycine.conf
trunk/test/pdb/1XFF/1XFF.A.Glycine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Glycine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Histidine.conf
trunk/test/pdb/1XFF/1XFF.A.Histidine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Histidine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Isoleucine.conf
trunk/test/pdb/1XFF/1XFF.A.Isoleucine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Isoleucine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Leucine.conf
trunk/test/pdb/1XFF/1XFF.A.Leucine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Leucine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Lysine.conf
trunk/test/pdb/1XFF/1XFF.A.Lysine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Lysine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Methionine.conf
trunk/test/pdb/1XFF/1XFF.A.Methionine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Methionine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.conf
trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Proline.conf
trunk/test/pdb/1XFF/1XFF.A.Proline.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Proline.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.conf
trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Serine.conf
trunk/test/pdb/1XFF/1XFF.A.Serine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Serine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Threonine.conf
trunk/test/pdb/1XFF/1XFF.A.Threonine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Threonine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Tryptophan.conf
trunk/test/pdb/1XFF/1XFF.A.Tryptophan.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Tryptophan.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Tyrosine.conf
trunk/test/pdb/1XFF/1XFF.A.Tyrosine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Tyrosine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.Valine.conf
trunk/test/pdb/1XFF/1XFF.A.Valine.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.Valine.dll.sol
trunk/test/pdb/1XFF/1XFF.A.arff
trunk/test/pdb/1XFF/1XFF.A.conf
trunk/test/pdb/1XFF/1XFF.A.conf.jamon.log.html
trunk/test/pdb/1XFF/1XFF.A.dll.sol
trunk/test/pdb/1XFF/1XFF.A.fasta
trunk/test/pdb/1XFF/1XFF.A.rdf
trunk/test/pdb/1XFF.rdf
trunk/test/pdb/Escherichia coli.pos
Removed Paths:
-------------
trunk/test/pdb/1BGP/
trunk/test/pdb/1BTK/
trunk/test/pdb/1BV1/
trunk/test/pdb/1CPC/
trunk/test/pdb/1DKZ/
trunk/test/pdb/1DOK/
trunk/test/pdb/1DOR/
trunk/test/pdb/1DOS/
trunk/test/pdb/1DUP/
trunk/test/pdb/1ECA/
trunk/test/pdb/1ECP/
trunk/test/pdb/1EDM/
trunk/test/pdb/1FMT/
trunk/test/pdb/1FNA/
trunk/test/pdb/1FUA/
trunk/test/pdb/1FUR/
trunk/test/pdb/1FVK/
trunk/test/pdb/1FWC/
trunk/test/pdb/1G3P/
trunk/test/pdb/1GIF/
trunk/test/pdb/1GOT/
trunk/test/pdb/1GSA/
trunk/test/pdb/1GVP/
trunk/test/pdb/1HA1/
trunk/test/pdb/1HAV/
trunk/test/pdb/1HCR/
trunk/test/pdb/1HGX/
trunk/test/pdb/1HSB/
trunk/test/pdb/1IAK/
trunk/test/pdb/1IDA/
trunk/test/pdb/1IIB/
trunk/test/pdb/1ISU/
trunk/test/pdb/1JET/
trunk/test/pdb/1JFR/
trunk/test/pdb/1KPT/
trunk/test/pdb/1KVE/
trunk/test/pdb/1KWA/
trunk/test/pdb/1LAT/
trunk/test/pdb/1LKK/
trunk/test/pdb/1LMB/
trunk/test/pdb/1LTS/
trunk/test/pdb/1LUC/
trunk/test/pdb/1MKA/
trunk/test/pdb/1MLD/
trunk/test/pdb/1MOL/
trunk/test/pdb/1MPG/
trunk/test/pdb/1MRP/
trunk/test/pdb/1MTY/
trunk/test/pdb/1MUC/
trunk/test/pdb/1MUG/
trunk/test/pdb/1NBA/
trunk/test/pdb/1NBC/
trunk/test/pdb/1NCI/
trunk/test/pdb/1NP1/
trunk/test/pdb/1ONR/
trunk/test/pdb/1PNK/
trunk/test/pdb/1POA/
trunk/test/pdb/1QBA/
trunk/test/pdb/1RYP/
trunk/test/pdb/1TCA/
trunk/test/pdb/1VWL/
trunk/test/pdb/1WBA/
trunk/test/pdb/1WPO/
trunk/test/pdb/2BAA/
trunk/test/pdb/2CYP/
trunk/test/pdb/2KIN/
trunk/test/pdb/3CLA/
trunk/test/pdb/3LQH/
trunk/test/pdb/5HPG/
trunk/test/pdb/5P21/
trunk/test/pdb/8ABP/
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-10-26 09:43:32 UTC (rev 3323)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-10-26 11:38:13 UTC (rev 3324)
@@ -17,14 +17,10 @@
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.PatternLayout;
-import org.dllearner.cli.Start;
import org.dllearner.core.ComponentInitException;
-import org.dllearner.core.ComponentManager;
import org.dllearner.core.LearningProblemUnsupportedException;
-import org.dllearner.core.ReasonerComponent;
-import org.dllearner.core.owl.Description;
-import org.dllearner.reasoning.FastInstanceChecker;
+
import com.hp.hpl.jena.rdf.model.NodeIterator;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.ResIterator;
@@ -32,8 +28,6 @@
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
-import com.dumontierlab.pdb2rdf.model.PdbRdfModel;
-
public class HelixRDFCreator {
private static Logger _logger = Logger.getLogger(HelixRDFCreator.class);
@@ -107,7 +101,6 @@
* load = true -> load alle .rdf, .conf and .arff Files that can be found within the directory dataDir
* load = false -> don't load anything
*/
- Boolean load = false;
Boolean dlLearn = true;
Boolean wekaLearn = true;
Added: trunk/test/pdb/1XFF/1XFF.A.Alanine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Alanine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Alanine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,26 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A13"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A55"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A57"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A58"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A113"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A128"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A144"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A148"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A195"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A6"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A8"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A31"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A34"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A38"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A70"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A75"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A85"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A155"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A171"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A172"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A190"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A212"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A227"
Added: trunk/test/pdb/1XFF/1XFF.A.Alanine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Alanine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Alanine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>124714.0</td><td>0.03969883092515676</td><td>4951.0</td><td>0.3026117352194724</td><td>0.0</td><td>0.0</td><td>45.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:32 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>25268.0</td><td>0.7957891404147538</td><td>20108.0</td><td>10.65673523811086</td><td>0.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:32 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Alanine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Alanine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Alanine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 39.13%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Alanine
+ accuracy: 39.13%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Histidine)
+ accuracy: 39.13%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 39.13%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 39.13%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Arginine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Arginine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Arginine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,23 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A21"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A22"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A26"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A108"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A142"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A147"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A10"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A44"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A46"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A47"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A73"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A114"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A153"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A164"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A173"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A201"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A202"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A216"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A217"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A231"
Added: trunk/test/pdb/1XFF/1XFF.A.Arginine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Arginine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Arginine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>68868.0</td><td>0.0421676250217808</td><td>2904.0</td><td>0.3445925586755652</td><td>0.0</td><td>0.0</td><td>45.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:15 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>13942.0</td><td>0.4589011619566777</td><td>6398.0</td><td>7.715718449680175</td><td>0.0</td><td>0.0</td><td>401.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:15 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Arginine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Arginine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Arginine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 30%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Arginine
+ accuracy: 30%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Histidine)
+ accuracy: 30%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 30%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 30%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Asparagine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Asparagine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Asparagine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,10 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A103"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A132"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A84"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A98"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A187"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A220"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A237"
Added: trunk/test/pdb/1XFF/1XFF.A.Asparagine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Asparagine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Asparagine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>488921.0</td><td>0.03930082774108701</td><td>19215.0</td><td>0.32167796497955703</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:35 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>106249.0</td><td>0.5368991708157254</td><td>57045.0</td><td>8.729401295659214</td><td>1.0</td><td>0.0</td><td>529.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:35 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Asparagine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Asparagine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Asparagine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 28.571%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Asparagine
+ accuracy: 28.571%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Histidine)
+ accuracy: 28.571%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 28.571%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 28.571%
+
Added: trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,13 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A123"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A192"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A11"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A29"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A37"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A162"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A167"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A210"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A223"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A233"
Added: trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>155838.0</td><td>0.03821917632413147</td><td>5956.0</td><td>0.31010794022520033</td><td>0.0</td><td>0.0</td><td>51.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:34 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>30686.0</td><td>0.6794303591214235</td><td>20849.0</td><td>9.799920449479227</td><td>1.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:34 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.AsparticAcid.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 20%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:AsparticAcid
+ accuracy: 20%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Histidine)
+ accuracy: 20%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 20%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 20%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Cysteine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Cysteine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Cysteine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,4 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A1"
Added: trunk/test/pdb/1XFF/1XFF.A.Cysteine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Cysteine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Cysteine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>369090.0</td><td>0.04132054512449538</td><td>15251.0</td><td>0.3512727089839151</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:15 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>80204.0</td><td>0.5631888683856167</td><td>45170.0</td><td>8.821118760656532</td><td>0.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:15 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Cysteine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Cysteine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Cysteine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: http://bio2rdf.org/pdb:Leucine
+ accuracy: 100%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Isoleucine
+ accuracy: 100%
+
+solution: 2
+ description: http://bio2rdf.org/pdb:Histidine
+ accuracy: 100%
+
+solution: 3
+ description: http://bio2rdf.org/pdb:Glycine
+ accuracy: 100%
+
+solution: 4
+ description: http://bio2rdf.org/pdb:Glutamine
+ accuracy: 100%
+
Added: trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,26 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A14"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A18"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A59"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A60"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A105"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A109"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A110"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A125"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A134"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A143"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A24"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A39"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A79"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A82"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A91"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A102"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A121"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A186"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A207"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A208"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A213"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A228"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A235"
Added: trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>421411.0</td><td>0.04067050931276118</td><td>17139.0</td><td>0.33925571539518223</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:19 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>90407.0</td><td>0.5150043691307089</td><td>46560.0</td><td>8.438411803116043</td><td>3.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:19 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.GlutamicAcid.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 43.478%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:GlutamicAcid
+ accuracy: 43.478%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Histidine)
+ accuracy: 43.478%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 43.478%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 43.478%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Glutamine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Glutamine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Glutamine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,10 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A52"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A56"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A151"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A193"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A9"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A137"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A232"
Added: trunk/test/pdb/1XFF/1XFF.A.Glutamine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Glutamine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Glutamine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>452706.0</td><td>0.03980508321073721</td><td>18020.0</td><td>0.33037844252946563</td><td>1.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:22 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>95853.0</td><td>0.4950497115374584</td><td>47452.0</td><td>8.269894442023512</td><td>1.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:22 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Glutamine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Glutamine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Glutamine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 57.143%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Glutamine
+ accuracy: 57.143%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Histidine)
+ accuracy: 57.143%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 57.143%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:GlutamicAcid)
+ accuracy: 57.143%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Glycine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Glycine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Glycine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,26 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A19"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A2"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A5"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A27"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A32"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A40"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A49"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A65"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A66"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A68"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A78"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A99"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A115"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A138"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A139"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A154"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A157"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A175"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A181"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A183"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A185"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A209"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A226"
Added: trunk/test/pdb/1XFF/1XFF.A.Glycine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Glycine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Glycine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>47346.0</td><td>0.04076373928103747</td><td>1930.0</td><td>0.3512518830942915</td><td>0.0</td><td>0.0</td><td>45.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:09 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>9850.0</td><td>0.1565482233502538</td><td>1542.0</td><td>4.7821948959769855</td><td>1.0</td><td>0.0</td><td>344.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:09 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Glycine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Glycine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Glycine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 4.348%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Glycine
+ accuracy: 4.348%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Histidine)
+ accuracy: 4.348%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 4.348%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:GlutamicAcid)
+ accuracy: 4.348%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Histidine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Histidine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Histidine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,15 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A104"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A129"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A41"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A61"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A64"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A71"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A77"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A86"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A88"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A92"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A97"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A165"
Added: trunk/test/pdb/1XFF/1XFF.A.Histidine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Histidine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Histidine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>303294.0</td><td>0.03681246579226757</td><td>11165.0</td><td>0.361941980809781</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:50 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>59175.0</td><td>0.4749302915082383</td><td>28104.0</td><td>7.9202651840828</td><td>16.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:50 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Histidine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Histidine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Histidine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 16.667%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Histidine
+ accuracy: 16.667%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 16.667%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 16.667%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:GlutamicAcid)
+ accuracy: 16.667%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Isoleucine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Isoleucine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Isoleucine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A15"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A127"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A3"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A7"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A69"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A93"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A100"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A101"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A149"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A160"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A180"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A189"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A204"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A211"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A214"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A221"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A234"
Added: trunk/test/pdb/1XFF/1XFF.A.Isoleucine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Isoleucine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Isoleucine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>274515.0</td><td>0.03695608618836858</td><td>10145.0</td><td>0.3604806609907787</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:47 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>54062.0</td><td>0.505438200584514</td><td>27325.0</td><td>8.158675793216828</td><td>4.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:47 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Isoleucine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Isoleucine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Isoleucine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 11.765%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Isoleucine
+ accuracy: 11.765%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 11.765%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 11.765%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:GlutamicAcid)
+ accuracy: 11.765%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Leucine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Leucine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Leucine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,28 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A16"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A17"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A20"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A23"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A54"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A107"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A111"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A130"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A135"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A141"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A146"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A194"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A33"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A45"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A48"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A63"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A152"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A169"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A170"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A178"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A182"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A196"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A197"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A206"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A238"
Added: trunk/test/pdb/1XFF/1XFF.A.Leucine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Leucine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Leucine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>335999.0</td><td>0.04201500599704166</td><td>14117.0</td><td>0.3615366327756158</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:11 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>70735.0</td><td>0.6197780448151552</td><td>43840.0</td><td>9.255043070818324</td><td>1.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:11 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Leucine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Leucine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Leucine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 48%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Leucine
+ accuracy: 48%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 48%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 48%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:GlutamicAcid)
+ accuracy: 48%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Lysine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Lysine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Lysine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,8 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A50"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A112"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A136"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A224"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A230"
Added: trunk/test/pdb/1XFF/1XFF.A.Lysine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Lysine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Lysine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>218715.0</td><td>0.03602862172233272</td><td>7880.0</td><td>0.33605550602578027</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:41 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>41743.0</td><td>0.5882902522578636</td><td>24557.0</td><td>8.94018147551723</td><td>0.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:41 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Lysine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Lysine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Lysine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 60%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Lysine
+ accuracy: 60%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 60%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 60%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:GlutamicAcid)
+ accuracy: 60%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Methionine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Methionine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Methionine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,7 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A53"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A42"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A161"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A184"
Added: trunk/test/pdb/1XFF/1XFF.A.Methionine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Methionine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Methionine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>396729.0</td><td>0.040392812221944956</td><td>16025.0</td><td>0.34172280900163604</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:17 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>85312.0</td><td>0.5383298949737434</td><td>45926.0</td><td>8.63622664710604</td><td>3.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:17 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Methionine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Methionine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Methionine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 25%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Methionine
+ accuracy: 25%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 25%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 25%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:GlutamicAcid)
+ accuracy: 25%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,8 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A118"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A188"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A203"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A205"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A222"
Added: trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>307702.0</td><td>0.03699033480445366</td><td>11382.0</td><td>0.36036509736687183</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:55 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>63808.0</td><td>0.5118793881644935</td><td>32662.0</td><td>8.281475452315586</td><td>0.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:56 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Phenylalanine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: http://bio2rdf.org/pdb:Isoleucine
+ accuracy: 100%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Histidine
+ accuracy: 100%
+
+solution: 2
+ description: http://bio2rdf.org/pdb:Glycine
+ accuracy: 100%
+
+solution: 3
+ description: http://bio2rdf.org/pdb:Glutamine
+ accuracy: 100%
+
+solution: 4
+ description: http://bio2rdf.org/pdb:GlutamicAcid
+ accuracy: 100%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Proline.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Proline.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Proline.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,11 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A106"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A150"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A62"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A80"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A87"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A166"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A177"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A198"
Added: trunk/test/pdb/1XFF/1XFF.A.Proline.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Proline.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Proline.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>23817.0</td><td>0.036108661880169625</td><td>860.0</td><td>0.3321170773327638</td><td>0.0</td><td>0.0</td><td>34.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:06 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>4967.0</td><td>0.16529092007247836</td><td>821.0</td><td>4.951543207510954</td><td>5.0</td><td>0.0</td><td>344.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:06 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Proline.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Proline.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Proline.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: 25%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Proline
+ accuracy: 25%
+
+solution: 2
+ description: (not http://bio2rdf.org/pdb:Glycine)
+ accuracy: 25%
+
+solution: 3
+ description: (not http://bio2rdf.org/pdb:Glutamine)
+ accuracy: 25%
+
+solution: 4
+ description: (not http://bio2rdf.org/pdb:GlutamicAcid)
+ accuracy: 25%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,3 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
Added: trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>220647.0</td><td>0.03596695173739049</td><td>7936.0</td><td>0.3349497294539293</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:43 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>43852.0</td><td>0.5909422603302016</td><td>25914.0</td><td>8.809421095120069</td><td>0.0</td><td>0.0</td><td>507.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:29:43 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Selenomethionine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: Thing
+ accuracy: �%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Histidine
+ accuracy: �%
+
+solution: 2
+ description: http://bio2rdf.org/pdb:Glycine
+ accuracy: �%
+
+solution: 3
+ description: http://bio2rdf.org/pdb:Glutamine
+ accuracy: �%
+
+solution: 4
+ description: http://bio2rdf.org/pdb:GlutamicAcid
+ accuracy: �%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Serine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Serine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Serine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,13 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A30"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A81"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A90"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A120"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A163"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A174"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A176"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A191"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A218"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A236"
Added: trunk/test/pdb/1XFF/1XFF.A.Serine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Serine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Serine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</th><th>Total</th><th>StdDev</th><th>LastValue</th><th>Min</th><th>Max</th><th>Active</th><th>AvgActive</th><th>MaxActive</th><th>FirstAccess</th><th>LastAccess</th><th>Enabled</th><th>Primary</th><th>HasListeners</th><th>Label</th>
+<tr><td>addNode, ms.</td><td>457211.0</td><td>0.04011933221204214</td><td>18343.0</td><td>0.3297577376588546</td><td>0.0</td><td>0.0</td><td>62.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:32 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>addNode, ms.</td></tr>
+<tr><td>refineNode, ms.</td><td>100732.0</td><td>0.5586407497121074</td><td>56273.0</td><td>8.925655045785778</td><td>0.0</td><td>0.0</td><td>529.0</td><td>0.0</td><td>1.0</td><td>1.0</td><td>Wed Oct 26 13:29:04 CEST 2011</td><td>Wed Oct 26 13:30:33 CEST 2011</td><td>true</td><td>false</td><td>false</td><td>refineNode, ms.</td></tr>
+</table>
\ No newline at end of file
Added: trunk/test/pdb/1XFF/1XFF.A.Serine.dll.sol
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Serine.dll.sol (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Serine.dll.sol 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,20 @@
+solution: 0
+ description: http://bio2rdf.org/pdb:Isoleucine
+ accuracy: 100%
+
+solution: 1
+ description: http://bio2rdf.org/pdb:Histidine
+ accuracy: 100%
+
+solution: 2
+ description: http://bio2rdf.org/pdb:Glycine
+ accuracy: 100%
+
+solution: 3
+ description: http://bio2rdf.org/pdb:Glutamine
+ accuracy: 100%
+
+solution: 4
+ description: http://bio2rdf.org/pdb:GlutamicAcid
+ accuracy: 100%
+
Added: trunk/test/pdb/1XFF/1XFF.A.Threonine.conf
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Threonine.conf (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Threonine.conf 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,16 @@
+import("../AA_properties.owl");
+import("1XFF.A.rdf");
+
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A124"
++"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A140"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A43"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A67"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A72"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A76"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A117"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A122"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A158"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A168"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A200"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A215"
+-"http://bio2rdf.org/pdb:1XFF/chemicalComponent_A225"
Added: trunk/test/pdb/1XFF/1XFF.A.Threonine.conf.jamon.log.html
===================================================================
--- trunk/test/pdb/1XFF/1XFF.A.Threonine.conf.jamon.log.html (rev 0)
+++ trunk/test/pdb/1XFF/1XFF.A.Threonine.conf.jamon.log.html 2011-10-26 11:38:13 UTC (rev 3324)
@@ -0,0 +1,6 @@
+
+<table border='1' rules='all'>
+<th>Label</th><th>Hits</th><th>Avg</...
[truncated message content] |
