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[DL-Learner SVN] SF.net SVN: dl-learner:[2801] trunk
|
From: <km...@us...> - 2011-05-13 07:51:18
|
Revision: 2801
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2801&view=rev
Author: kmpf
Date: 2011-05-13 07:51:11 +0000 (Fri, 13 May 2011)
Log Message:
-----------
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
trunk/test/pdb/bt426.list
trunk/test/pdb/plp273.list
trunk/test/pdb/plp364.list
trunk/test/pdb/plp399.list
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-05-12 17:05:26 UTC (rev 2800)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-05-13 07:51:11 UTC (rev 2801)
@@ -31,6 +31,8 @@
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.model.NodeIterator;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.ResIterator;
@@ -38,6 +40,7 @@
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
+import com.hp.hpl.jena.vocabulary.RDFS;
import com.dumontierlab.pdb2rdf.model.PdbRdfModel;
import com.dumontierlab.pdb2rdf.parser.PdbXmlParser;
@@ -178,7 +181,9 @@
trainmodel.removeAll();
trainmodel.add(getRdfModelForIds(trainSet.getTrainset()[i].getPdbID(), trainSet.getTrainset()[i].getChainID()));
+ System.out.println(getSpecies(trainmodel, trainSet.getTrainset()[i].getPdbID()));
+
/*
* as we have sometimes to handle several amino acid chains we need the first
@@ -464,6 +469,28 @@
qe.close();
return construct;
}
+
+ private static String getSpecies( PdbRdfModel model, String pdbID) {
+ String queryString ;
+ queryString =
+ "PREFIX pdb: <http://bio2rdf.org/pdb:> " +
+ "PREFIX dcterms: <http://purl.org/dc/terms/> " +
+ "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> " +
+ "PREFIX fn: <http://www.w3.org/2005/xpath-functions#> " +
+ "SELECT * " +
+ "WHERE { ?s ?p ?o .}"; //FILTER (str(?xxx) = fn:concat(str(?x4), '/extraction/source/gene/organism')) . }";
+
+ System.out.println(queryString);
+ Query query = QueryFactory.create(queryString);
+ QueryExecution qe = QueryExecutionFactory.create(query, model);
+ ResultSet results = qe.execSelect();
+ qe.close();
+ ResultSetFormatter.out (System.out, results, query);
+ return ResultSetFormatter.asText(results);
+ }
+
+
private static ResIterator getFirstAA( PdbRdfModel model) {
PdbRdfModel construct = new PdbRdfModel();
Modified: trunk/test/pdb/bt426.list
===================================================================
--- trunk/test/pdb/bt426.list 2011-05-12 17:05:26 UTC (rev 2800)
+++ trunk/test/pdb/bt426.list 2011-05-13 07:51:11 UTC (rev 2801)
@@ -1,426 +1,426 @@
-1LMB.3
-8ABP
-1MRP
-1G3P
-1GVP
-1AT0
-1AOP
-1AMP
-1AK0
-1BGP
-2CYP
-1LAT.B
-1LUC.B
-1MTY.B
-1NBA.B
-1NCI.B
-1KVE.B
-1KWA.B
-1EDM.B
-1FMT.B
-1GOT.B
-1ATZ.B
-1APY.B
-1AQZ.B
-1A28.B
-1BDM.B
-1BEN.B
-1BTK.B
-1CPC.B
-1VWL.B
-1WPO.B
-1PNK.B
-1RYP.2
-5P21
-1HA1
-1ECA
-1FUA
-1FNA
-1GSA
-1A6Q
-1AK1
-1ABA
-1BV1
-1BA1
-1TCA
-1WBA
-1POA
-1QBA
-2BAA
-3CLA
-2KIN.B
-5HPG.A
-1LKK.A
-1LTS.A
-1MLD.A
-1MOL.A
-1MKA.A
-1MUG.A
-1MUC.A
-1MPG.A
-1NBC.A
-1NP1.A
-1ONR.A
-1HGX.A
-1HAV.A
-1HCR.A
-1HSB.A
-1IIB.A
-1IDA.A
-1IAK.A
-1ISU.A
-1JET.A
-1JFR.A
-1KVE.A
-1KPT.A
-1DOR.A
-1DOS.A
-1DOK.A
-1DKZ.A
-1DUP.A
-1ECP.A
-1FUR.A
-1FVK.A
-1FWC.A
-1GIF.A
-1GDO.A
-1GAR.A
-1GUQ.A
-1ALV.A
-1ALI.A
-1AMU.A
-1AOZ.A
-1AOQ.A
-1AOH.A
-1AOC.A
-1AJS.A
-1ADO.A
-1AFW.A
-1AGJ.A
-1AT1.A
-1AVM.A
-1AWS.A
-1AQ6.A
-1AQ0.A
-1A7T.A
-1A2Z.A
-1A2Y.A
-1A2P.A
-1A34.A
-1BKR.A
-1BEB.A
-1BFT.A
-1BBP.A
-1CHM.A
-1CKA.A
-1CYD.A
-1XIK.A
-1XGS.A
-1YTB.A
-1TVX.A
-1VCA.A
-1PHN.A
-1RGE.A
-1SLT.A
-1SLU.A
-1SPU.A
-5ICB
-1NAR
-1JER
-1KNB
-1FDR
-1A62
-1ARB
-1AQB
-1AJ2
-1AD2
-1BYB
-1C52
-1CFB
-1YER
-1WAB
-2POR
-3CYR
-3SEB
-3SDH.A
-2HMZ.A
-2ARC.A
-2PSP.A
-8RXN.A
-1HTR.P
-1LIS
-1MSC
-1NLS
-1ORC
-1HFC
-1IFC
-1JPC
-1FUS
-1FDS
-1A9S
-1AL3
-1AAC
-1BGC
-1C1C
-1YCC
-1TYS
-1VCC
-1POC
-1PGS
-1RHS
-2CTC
-2PLC
-2SNS
-2SN3
-3TSS
-1MTY.G
-1GOT.G
-1LIT
-1MBD
-1OPD
-1IGD
-1KID
-1DAD
-1EDT
-1FIT
-1GND
-1AWD
-1BRT
-1BFD
-1CHD
-1VSD
-1VID
-1PUD
-1POT
-1SMD
-2LBD
-2HFT
-2END
-1RYP.F
-1LBU
-1MWE
-1NEU
-1HOE
-1KVU
-1EDE
-1A8E
-1ALU
-1TFE
-1UAE
-1PHE
-1RIE
-1CSE.E
-1NIF
-1KPF
-1ERV
-1ARV
-1ANF
-1BKF
-1CNV
-1THV
-1QNF
-1LT5.D
-1MTY.D
-1AGQ.D
-1JDW
-1EDG
-1AH7
-1AF7
-1BFG
-1RMG
-2HBG
-1NOX
-1IXH
-1KUH
-1A68
-1A1X
-1AMX
-1CSH
-1CEX
-1THX
-1VHH
-2AYH
-3COX
-1RYP.J
-1LKI
-1MSI
-1MAI
-1OPY
-1DXY
-1GKY
-1GAI
-1A8I
-1ALY
-1UBI
-1R69
-2DRI
-1FLE.I
-1CEW.I
-1CSE.I
-1YVE.I
-1RYP.I
-1MRJ
-1AJJ
-1AKZ
-1CTJ
-8RUC.I
-1MSK
-1NPK
-1IDK
-2BBK.H
-1GD1.O
-1LML
-1LCL
-1MML
-1ECL
-1AYL
-1AOL
-153L
-119L
-2SIL
-1LAM
-1MZM
-1EZM
-1AMM
-1CEM
-2MCM
-2GDM
-1NFN
-1HXN
-1DUN
-1AXN
-1BTN
-1CSN
-1CBN
-1ISO
-1IDO
-1AZO
-1ALO
-1AKO
-1AHO
-1BDO
-1CPO
-1CEO
-1XJO
-1PDO
-1YAI.C
-1TAD.C
-1TSP
-1WHT.B
-7RSA
-1PTQ
-1PDA
-2FHA
-2CBA
-2WEA
-2PIA
-5CSM.A
-4PGA.A
-7AHL.A
-6GSV.A
-1XYZ.A
-1YAS.A
-1TRK.A
-1URN.A
-1VPS.A
-1PCF.A
-1RYP.1
-1RVA.A
-1SVP.A
-2I1B
-2A0B
-2KIN.A
-2FIV.A
-2CHS.A
-2CCY.A
-2SCP.A
-4XIS
-1ONC
-1OIS
-1VLS
-1VJS
-3B5C
-1PNE
-3PTE
-1REQ.D
-1UXY
-1V39
-1WHI
-1PTY
-1PMI
-2ACY
-2PHY
-2PII
-3CHY
-1REG.Y
-1SGP.I
-1SKZ
-2SIC.I
-2ILK
-2ABK
-2SAK
-1TML
-3NUL
-2FDN
-3PCG.M
-1WHO
-5PTP
-1PHP
-1SFP
-1SBP
-1NUL.B
-1PRX.B
-1SFT.B
-1SRA
-2MSB.B
-2VHB.B
-2RSP.B
-1NWP.A
-1OVA.A
-1XSO.A
-1UNK.A
-1WDC.A
-1STM.A
-4MT2
-1NXB
-1XNB
-1TIB
-1WER
-1SVB
-2RN2
-3VUB
-3DAA.A
-2NAC.A
-2HPD.A
-2BOP.A
-2TYS.A
-256B.A
-1OYC
-1PLC
-1RSS
-1REC
-2HTS
-3GRS
-1PPT
-2PGD
-3LZT
-1TIF
-1VIF
-1RCF
-2ENG
-1UCH
-2PTH
-5PTI
-1PII
-1RSY
-1RA9
-2TGI
-1OSP.O
-4BCL
-6CEL
-2ERL
-1ZIN
-1VIN
-1PPN
-1RRO
+1LMB.3.
+8ABP.
+1MRP.
+1G3P.
+1GVP.
+1AT0.
+1AOP.
+1AMP.
+1AK0.
+1BGP.
+2CYP.
+1LAT.B.
+1LUC.B.
+1MTY.B.
+1NBA.B.
+1NCI.B.
+1KVE.B.
+1KWA.B.
+1EDM.B.
+1FMT.B.
+1GOT.B.
+1ATZ.B.
+1APY.B.
+1AQZ.B.
+1A28.B.
+1BDM.B.
+1BEN.B.
+1BTK.B.
+1CPC.B.
+1VWL.B.
+1WPO.B.
+1PNK.B.
+1RYP.2.
+5P21.
+1HA1.
+1ECA.
+1FUA.
+1FNA.
+1GSA.
+1A6Q.
+1AK1.
+1ABA.
+1BV1.
+1BA1.
+1TCA.
+1WBA.
+1POA.
+1QBA.
+2BAA.
+3CLA.
+2KIN.B.
+5HPG.A.
+1LKK.A.
+1LTS.A.
+1MLD.A.
+1MOL.A.
+1MKA.A.
+1MUG.A.
+1MUC.A.
+1MPG.A.
+1NBC.A.
+1NP1.A.
+1ONR.A.
+1HGX.A.
+1HAV.A.
+1HCR.A.
+1HSB.A.
+1IIB.A.
+1IDA.A.
+1IAK.A.
+1ISU.A.
+1JET.A.
+1JFR.A.
+1KVE.A.
+1KPT.A.
+1DOR.A.
+1DOS.A.
+1DOK.A.
+1DKZ.A.
+1DUP.A.
+1ECP.A.
+1FUR.A.
+1FVK.A.
+1FWC.A.
+1GIF.A.
+1GDO.A.
+1GAR.A.
+1GUQ.A.
+1ALV.A.
+1ALI.A.
+1AMU.A.
+1AOZ.A.
+1AOQ.A.
+1AOH.A.
+1AOC.A.
+1AJS.A.
+1ADO.A.
+1AFW.A.
+1AGJ.A.
+1AT1.A.
+1AVM.A.
+1AWS.A.
+1AQ6.A.
+1AQ0.A.
+1A7T.A.
+1A2Z.A.
+1A2Y.A.
+1A2P.A.
+1A34.A.
+1BKR.A.
+1BEB.A.
+1BFT.A.
+1BBP.A.
+1CHM.A.
+1CKA.A.
+1CYD.A.
+1XIK.A.
+1XGS.A.
+1YTB.A.
+1TVX.A.
+1VCA.A.
+1PHN.A.
+1RGE.A.
+1SLT.A.
+1SLU.A.
+1SPU.A.
+5ICB.
+1NAR.
+1JER.
+1KNB.
+1FDR.
+1A62.
+1ARB.
+1AQB.
+1AJ2.
+1AD2.
+1BYB.
+1C52.
+1CFB.
+1YER.
+1WAB.
+2POR.
+3CYR.
+3SEB.
+3SDH.A.
+2HMZ.A.
+2ARC.A.
+2PSP.A.
+8RXN.A.
+1HTR.P.
+1LIS.
+1MSC.
+1NLS.
+1ORC.
+1HFC.
+1IFC.
+1JPC.
+1FUS.
+1FDS.
+1A9S.
+1AL3.
+1AAC.
+1BGC.
+1C1C.
+1YCC.
+1TYS.
+1VCC.
+1POC.
+1PGS.
+1RHS.
+2CTC.
+2PLC.
+2SNS.
+2SN3.
+3TSS.
+1MTY.G.
+1GOT.G.
+1LIT.
+1MBD.
+1OPD.
+1IGD.
+1KID.
+1DAD.
+1EDT.
+1FIT.
+1GND.
+1AWD.
+1BRT.
+1BFD.
+1CHD.
+1VSD.
+1VID.
+1PUD.
+1POT.
+1SMD.
+2LBD.
+2HFT.
+2END.
+1RYP.F.
+1LBU.
+1MWE.
+1NEU.
+1HOE.
+1KVU.
+1EDE.
+1A8E.
+1ALU.
+1TFE.
+1UAE.
+1PHE.
+1RIE.
+1CSE.E.
+1NIF.
+1KPF.
+1ERV.
+1ARV.
+1ANF.
+1BKF.
+1CNV.
+1THV.
+1QNF.
+1LT5.D.
+1MTY.D.
+1AGQ.D.
+1JDW.
+1EDG.
+1AH7.
+1AF7.
+1BFG.
+1RMG.
+2HBG.
+1NOX.
+1IXH.
+1KUH.
+1A68.
+1A1X.
+1AMX.
+1CSH.
+1CEX.
+1THX.
+1VHH.
+2AYH.
+3COX.
+1RYP.J.
+1LKI.
+1MSI.
+1MAI.
+1OPY.
+1DXY.
+1GKY.
+1GAI.
+1A8I.
+1ALY.
+1UBI.
+1R69.
+2DRI.
+1FLE.I.
+1CEW.I.
+1CSE.I.
+1YVE.I.
+1RYP.I.
+1MRJ.
+1AJJ.
+1AKZ.
+1CTJ.
+8RUC.I.
+1MSK.
+1NPK.
+1IDK.
+2BBK.H.
+1GD1.O.
+1LML.
+1LCL.
+1MML.
+1ECL.
+1AYL.
+1AOL.
+153L.
+119L.
+2SIL.
+1LAM.
+1MZM.
+1EZM.
+1AMM.
+1CEM.
+2MCM.
+2GDM.
+1NFN.
+1HXN.
+1DUN.
+1AXN.
+1BTN.
+1CSN.
+1CBN.
+1ISO.
+1IDO.
+1AZO.
+1ALO.
+1AKO.
+1AHO.
+1BDO.
+1CPO.
+1CEO.
+1XJO.
+1PDO.
+1YAI.C.
+1TAD.C.
+1TSP.
+1WHT.B.
+7RSA.
+1PTQ.
+1PDA.
+2FHA.
+2CBA.
+2WEA.
+2PIA.
+5CSM.A.
+4PGA.A.
+7AHL.A.
+6GSV.A.
+1XYZ.A.
+1YAS.A.
+1TRK.A.
+1URN.A.
+1VPS.A.
+1PCF.A.
+1RYP.1.
+1RVA.A.
+1SVP.A.
+2I1B.
+2A0B.
+2KIN.A.
+2FIV.A.
+2CHS.A.
+2CCY.A.
+2SCP.A.
+4XIS.
+1ONC.
+1OIS.
+1VLS.
+1VJS.
+3B5C.
+1PNE.
+3PTE.
+1REQ.D.
+1UXY.
+1V39.
+1WHI.
+1PTY.
+1PMI.
+2ACY.
+2PHY.
+2PII.
+3CHY.
+1REG.Y.
+1SGP.I.
+1SKZ.
+2SIC.I.
+2ILK.
+2ABK.
+2SAK.
+1TML.
+3NUL.
+2FDN.
+3PCG.M.
+1WHO.
+5PTP.
+1PHP.
+1SFP.
+1SBP.
+1NUL.B.
+1PRX.B.
+1SFT.B.
+1SRA.
+2MSB.B.
+2VHB.B.
+2RSP.B.
+1NWP.A.
+1OVA.A.
+1XSO.A.
+1UNK.A.
+1WDC.A.
+1STM.A.
+4MT2.
+1NXB.
+1XNB.
+1TIB.
+1WER.
+1SVB.
+2RN2.
+3VUB.
+3DAA.A.
+2NAC.A.
+2HPD.A.
+2BOP.A.
+2TYS.A.
+256B.A.
+1OYC.
+1PLC.
+1RSS.
+1REC.
+2HTS.
+3GRS.
+1PPT.
+2PGD.
+3LZT.
+1TIF.
+1VIF.
+1RCF.
+2ENG.
+1UCH.
+2PTH.
+5PTI.
+1PII.
+1RSY.
+1RA9.
+2TGI.
+1OSP.O.
+4BCL.
+6CEL.
+2ERL.
+1ZIN.
+1VIN.
+1PPN.
+1RRO.
2BBK.L
Modified: trunk/test/pdb/plp273.list
===================================================================
--- trunk/test/pdb/plp273.list 2011-05-12 17:05:26 UTC (rev 2800)
+++ trunk/test/pdb/plp273.list 2011-05-13 07:51:11 UTC (rev 2801)
@@ -1,273 +1,273 @@
-2W8X.A
-2W9Y.A
-2WCJ.A
-2WCR.A
-2WFB.A
-2WFO.A
-2WJ5.A
-2WJ9.A
-2WJR.A
-2WL1.A
-2WNF.A
-2WPV.B
-2WQF.A
-2WTP.A
-2WUJ.A
-2WUU.A
-2WUX.A
-2WVX.A
-2WY3.B
-2WZO.A
-2ZXY.A
-3A0Z.A
-3A4R.A
-3A57.A
-3A5P.A
-3AAP.A
-3FOT.A
-3FOV.A
-3FQG.A
-3FRR.A
-3FSO.A
-3FSS.A
-3FWK.A
-3FWZ.A
-3FX7.A
-3FYB.A
-3FYM.A
-3G02.A
-3G0M.A
-3G1J.A
-3G21.A
-3G2B.A
-3G2S.A
-3G36.A
-3G3T.A
-3G5B.A
-3G7G.A
-3GA3.A
-3GA4.A
-3GAE.A
-3GBW.A
-3GBY.A
-3GDW.A
-3GE3.E
-3GFP.A
-3GI7.A
-3GIX.A
-3GKJ.A
-3GMG.A
-3GN6.A
-3GNE.A
-3GNZ.P
-3GOE.A
-3GP4.A
-3GP6.A
-3GQQ.A
-3GWH.A
-3GWN.A
-3GXW.A
-3GY9.A
-3GZB.A
-3H05.A
-3H0W.A
-3H20.A
-3H3L.A
-3H51.A
-3H5J.A
-3H6P.C
-3H6R.A
-3H7H.B
-3H8T.A
-3H96.A
-3H9W.A
-3HA2.A
-3HE5.B
-3HFO.A
-3HH1.A
-3HL1.A
-3HN0.A
-3HN5.A
-3HO6.A
-3HOI.A
-3HPC.X
-3HR0.A
-3HRL.A
-3HRR.A
-3HSH.A
-3HTV.A
-3HVS.A
-3HWP.A
-3HWU.A
-3HX8.A
-3HXL.A
-3HYN.A
-3HZP.A
-3I0W.A
-3I1A.A
-3I2V.A
-3I4O.A
-3I7M.A
-3I84.A
-3IBM.A
-3IC3.A
-3ID1.A
-3IDF.A
-3IDU.A
-3IE4.A
-3IEE.A
-3IG9.A
-3IHT.A
-3IJM.A
-3IKB.A
-3IKW.A
-3ILW.A
-3IM3.A
-3IMK.A
-3IP4.C
-3IPF.A
-3IPJ.A
-3IR4.A
-3IT5.A
-3IU6.A
-3IUF.A
-3IUO.A
-3IUW.A
-3IVV.A
-3IWF.A
-3IX3.A
-3JQY.A
-3JRN.A
-3JSZ.A
-3JTW.A
-3JU0.A
-3JUD.A
-3JXO.A
-3JYG.A
-3JYZ.A
-3JZ9.A
-3K0X.A
-3K0Z.A
-3K2O.A
-3K5J.A
-3K69.A
-3K6O.A
-3K7X.A
-3KD3.A
-3KDE.C
-3KDF.A
-3KDF.B
-3KDG.A
-3KE7.A
-3KG9.A
-3KGK.A
-3KK4.A
-3KKF.A
-3KKG.A
-3KLQ.A
-3KMI.A
-3KOG.A
-3KOS.A
-3KPE.A
-3KUC.B
-3KWS.A
-3KXT.A
-3KYZ.A
-3KZ5.A
-3KZD.A
-3KZP.A
-3L0Q.B
-3L15.A
-3L23.A
-3L29.A
-3L3E.A
-3L4H.A
-3L51.B
-3L6T.A
-3L7H.A
-2X2S.A
-2X2U.A
-2X32.A
-2X3G.A
-2X4J.A
-2X4K.A
-2X4W.A
-2X55.A
-2X5N.A
-2XCJ.A
-2XDG.A
-2XDH.A
-2XF7.A
-2XFV.A
-2XG5.B
-2XLG.A
-2XMJ.A
-3AG3.D
-3L9A.X
-3LAX.A
-3LDC.A
-3LDU.A
-3LE4.A
-3LFR.A
-3LGB.A
-3LHE.A
-3LHO.A
-3LHR.A
-3LLO.A
-3LM3.A
-3LQ9.A
-3LR2.A
-3LR4.A
-3LS0.A
-3LUC.A
-3LUM.A
-3LUR.A
-3LUU.A
-3LWC.A
-3LWG.A
-3LXR.F
-3LYD.A
-3LYG.A
-3LYH.A
-3LYY.A
-3M1T.A
-3M66.A
-3M6J.A
-3M7K.A
-3M7O.A
-3M8J.A
-3M9Q.A
-3MAB.A
-3MAL.A
-3MCB.A
-3MCB.B
-3MCQ.A
-3MDP.A
-3MG1.A
-3MHS.B
-3MR0.A
-3MSW.A
-3MT0.A
-3MW8.A
-3MWZ.A
-3MZO.A
-3N0R.A
-3N1E.A
-3N6Y.A
-3N9B.A
-3NE8.A
-3NFT.A
-3NKE.A
-3NKG.A
-3NKL.A
-3NO2.A
-3NOH.A
-3NPD.A
-3NQI.A
-3NRF.A
-3NRW.A
-3NS2.A
-3NY3.A
-3NZN.A
-3O6C.A
+2W8X.A.
+2W9Y.A.
+2WCJ.A.
+2WCR.A.
+2WFB.A.
+2WFO.A.
+2WJ5.A.
+2WJ9.A.
+2WJR.A.
+2WL1.A.
+2WNF.A.
+2WPV.B.
+2WQF.A.
+2WTP.A.
+2WUJ.A.
+2WUU.A.
+2WUX.A.
+2WVX.A.
+2WY3.B.
+2WZO.A.
+2ZXY.A.
+3A0Z.A.
+3A4R.A.
+3A57.A.
+3A5P.A.
+3AAP.A.
+3FOT.A.
+3FOV.A.
+3FQG.A.
+3FRR.A.
+3FSO.A.
+3FSS.A.
+3FWK.A.
+3FWZ.A.
+3FX7.A.
+3FYB.A.
+3FYM.A.
+3G02.A.
+3G0M.A.
+3G1J.A.
+3G21.A.
+3G2B.A.
+3G2S.A.
+3G36.A.
+3G3T.A.
+3G5B.A.
+3G7G.A.
+3GA3.A.
+3GA4.A.
+3GAE.A.
+3GBW.A.
+3GBY.A.
+3GDW.A.
+3GE3.E.
+3GFP.A.
+3GI7.A.
+3GIX.A.
+3GKJ.A.
+3GMG.A.
+3GN6.A.
+3GNE.A.
+3GNZ.P.
+3GOE.A.
+3GP4.A.
+3GP6.A.
+3GQQ.A.
+3GWH.A.
+3GWN.A.
+3GXW.A.
+3GY9.A.
+3GZB.A.
+3H05.A.
+3H0W.A.
+3H20.A.
+3H3L.A.
+3H51.A.
+3H5J.A.
+3H6P.C.
+3H6R.A.
+3H7H.B.
+3H8T.A.
+3H96.A.
+3H9W.A.
+3HA2.A.
+3HE5.B.
+3HFO.A.
+3HH1.A.
+3HL1.A.
+3HN0.A.
+3HN5.A.
+3HO6.A.
+3HOI.A.
+3HPC.X.
+3HR0.A.
+3HRL.A.
+3HRR.A.
+3HSH.A.
+3HTV.A.
+3HVS.A.
+3HWP.A.
+3HWU.A.
+3HX8.A.
+3HXL.A.
+3HYN.A.
+3HZP.A.
+3I0W.A.
+3I1A.A.
+3I2V.A.
+3I4O.A.
+3I7M.A.
+3I84.A.
+3IBM.A.
+3IC3.A.
+3ID1.A.
+3IDF.A.
+3IDU.A.
+3IE4.A.
+3IEE.A.
+3IG9.A.
+3IHT.A.
+3IJM.A.
+3IKB.A.
+3IKW.A.
+3ILW.A.
+3IM3.A.
+3IMK.A.
+3IP4.C.
+3IPF.A.
+3IPJ.A.
+3IR4.A.
+3IT5.A.
+3IU6.A.
+3IUF.A.
+3IUO.A.
+3IUW.A.
+3IVV.A.
+3IWF.A.
+3IX3.A.
+3JQY.A.
+3JRN.A.
+3JSZ.A.
+3JTW.A.
+3JU0.A.
+3JUD.A.
+3JXO.A.
+3JYG.A.
+3JYZ.A.
+3JZ9.A.
+3K0X.A.
+3K0Z.A.
+3K2O.A.
+3K5J.A.
+3K69.A.
+3K6O.A.
+3K7X.A.
+3KD3.A.
+3KDE.C.
+3KDF.A.
+3KDF.B.
+3KDG.A.
+3KE7.A.
+3KG9.A.
+3KGK.A.
+3KK4.A.
+3KKF.A.
+3KKG.A.
+3KLQ.A.
+3KMI.A.
+3KOG.A.
+3KOS.A.
+3KPE.A.
+3KUC.B.
+3KWS.A.
+3KXT.A.
+3KYZ.A.
+3KZ5.A.
+3KZD.A.
+3KZP.A.
+3L0Q.B.
+3L15.A.
+3L23.A.
+3L29.A.
+3L3E.A.
+3L4H.A.
+3L51.B.
+3L6T.A.
+3L7H.A.
+2X2S.A.
+2X2U.A.
+2X32.A.
+2X3G.A.
+2X4J.A.
+2X4K.A.
+2X4W.A.
+2X55.A.
+2X5N.A.
+2XCJ.A.
+2XDG.A.
+2XDH.A.
+2XF7.A.
+2XFV.A.
+2XG5.B.
+2XLG.A.
+2XMJ.A.
+3AG3.D.
+3L9A.X.
+3LAX.A.
+3LDC.A.
+3LDU.A.
+3LE4.A.
+3LFR.A.
+3LGB.A.
+3LHE.A.
+3LHO.A.
+3LHR.A.
+3LLO.A.
+3LM3.A.
+3LQ9.A.
+3LR2.A.
+3LR4.A.
+3LS0.A.
+3LUC.A.
+3LUM.A.
+3LUR.A.
+3LUU.A.
+3LWC.A.
+3LWG.A.
+3LXR.F.
+3LYD.A.
+3LYG.A.
+3LYH.A.
+3LYY.A.
+3M1T.A.
+3M66.A.
+3M6J.A.
+3M7K.A.
+3M7O.A.
+3M8J.A.
+3M9Q.A.
+3MAB.A.
+3MAL.A.
+3MCB.A.
+3MCB.B.
+3MCQ.A.
+3MDP.A.
+3MG1.A.
+3MHS.B.
+3MR0.A.
+3MSW.A.
+3MT0.A.
+3MW8.A.
+3MWZ.A.
+3MZO.A.
+3N0R.A.
+3N1E.A.
+3N6Y.A.
+3N9B.A.
+3NE8.A.
+3NFT.A.
+3NKE.A.
+3NKG.A.
+3NKL.A.
+3NO2.A.
+3NOH.A.
+3NPD.A.
+3NQI.A.
+3NRF.A.
+3NRW.A.
+3NS2.A.
+3NY3.A.
+3NZN.A.
+3O6C.A.
3OAJ.A
Modified: trunk/test/pdb/plp364.list
===================================================================
--- trunk/test/pdb/plp364.list 2011-05-12 17:05:26 UTC (rev 2800)
+++ trunk/test/pdb/plp364.list 2011-05-13 07:51:11 UTC (rev 2801)
@@ -1,364 +1,364 @@
-2JK9.A
-2V4X.A
-2VQ4.A
-2VTC.A
-2VV6.A
-2VXT.I
-2VXZ.A
-2VZC.A
-2W2R.A
-2W61.A
-2W6A.A
-2W7A.A
-2W7N.A
-2ZK9.X
-2ZNR.A
-2ZQ5.A
-2ZQE.A
-2ZSI.B
-2ZX0.A
-3BYP.A
-3BYQ.A
-3C1Q.A
-3C7T.A
-3C8L.A
-3C8W.A
-3CHM.A
-3CKK.A
-3CNY.A
-3CP7.A
-3CT6.A
-3CZ6.A
-3D1R.A
-3D2Q.A
-3D34.A
-3D3B.J
-3D59.A
-3D85.C
-3DAN.A
-3DD7.A
-3DS2.A
-3DSB.A
-3E7H.A
-3E7U.X
-3E8O.A
-3E8T.A
-3EBT.A
-3ECF.A
-3ECH.A
-3EDO.A
-3EEH.A
-3EER.A
-3EF8.A
-3EHG.A
-3EHM.A
-3EKI.A
-3EMF.A
-3EMI.A
-3ENU.A
-3EO6.A
-3ER7.A
-3ES4.A
-3EYT.A
-3EZI.A
-3F0P.A
-3F2E.A
-3F40.A
-3F4M.A
-3F62.A
-3F7E.A
-3F7Q.A
-3F8X.A
-3F95.A
-3F9S.A
-3FAU.A
-3FB9.A
-3FBL.A
-3FCN.A
-3FF2.A
-3FF5.A
-3FFV.A
-3FG9.A
-3FGR.B
-3FGV.A
-3FH1.A
-3FIA.A
-3FID.A
-3FJU.B
-3FK8.A
-3FKA.A
-3FM2.A
-3FMY.A
-2W8X.A
-2W9Y.A
-2WCJ.A
-2WCR.A
-2WFB.A
-2WFO.A
-2WJ5.A
-2WJ9.A
-2WJR.A
-2WL1.A
-2WNF.A
-2WPV.B
-2WQF.A
-2WTP.A
-2WUJ.A
-2WUU.A
-2WUX.A
-2WVX.A
-2WY3.B
-2WZO.A
-2ZXY.A
-3A0Z.A
-3A4R.A
-3A57.A
-3A5P.A
-3AAP.A
-3FOT.A
-3FOV.A
-3FQG.A
-3FRR.A
-3FSO.A
-3FSS.A
-3FWK.A
-3FWZ.A
-3FX7.A
-3FYB.A
-3FYM.A
-3G02.A
-3G0M.A
-3G1J.A
-3G21.A
-3G2B.A
-3G2S.A
-3G36.A
-3G3T.A
-3G5B.A
-3G7G.A
-3GA3.A
-3GA4.A
-3GAE.A
-3GBW.A
-3GBY.A
-3GDW.A
-3GE3.E
-3GFP.A
-3GI7.A
-3GIX.A
-3GKJ.A
-3GMG.A
-3GN6.A
-3GNE.A
-3GNZ.P
-3GOE.A
-3GP4.A
-3GP6.A
-3GQQ.A
-3GWH.A
-3GWN.A
-3GXW.A
-3GY9.A
-3GZB.A
-3H05.A
-3H0W.A
-3H20.A
-3H3L.A
-3H51.A
-3H5J.A
-3H6P.C
-3H6R.A
-3H7H.B
-3H8T.A
-3H96.A
-3H9W.A
-3HA2.A
-3HE5.B
-3HFO.A
-3HH1.A
-3HL1.A
-3HN0.A
-3HN5.A
-3HO6.A
-3HOI.A
-3HPC.X
-3HR0.A
-3HRL.A
-3HRR.A
-3HSH.A
-3HTV.A
-3HVS.A
-3HWP.A
-3HWU.A
-3HX8.A
-3HXL.A
-3HYN.A
-3HZP.A
-3I0W.A
-3I1A.A
-3I2V.A
-3I4O.A
-3I7M.A
-3I84.A
-3IBM.A
-3IC3.A
-3ID1.A
-3IDF.A
-3IDU.A
-3IE4.A
-3IEE.A
-3IG9.A
-3IHT.A
-3IJM.A
-3IKB.A
-3IKW.A
-3ILW.A
-3IM3.A
-3IMK.A
-3IP4.C
-3IPF.A
-3IPJ.A
-3IR4.A
-3IT5.A
-3IU6.A
-3IUF.A
-3IUO.A
-3IUW.A
-3IVV.A
-3IWF.A
-3IX3.A
-3JQY.A
-3JRN.A
-3JSZ.A
-3JTW.A
-3JU0.A
-3JUD.A
-3JXO.A
-3JYG.A
-3JYZ.A
-3JZ9.A
-3K0X.A
-3K0Z.A
-3K2O.A
-3K5J.A
-3K69.A
-3K6O.A
-3K7X.A
-3KD3.A
-3KDE.C
-3KDF.A
-3KDF.B
-3KDG.A
-3KE7.A
-3KG9.A
-3KGK.A
-3KK4.A
-3KKF.A
-3KKG.A
-3KLQ.A
-3KMI.A
-3KOG.A
-3KOS.A
-3KPE.A
-3KUC.B
-3KWS.A
-3KXT.A
-3KYZ.A
-3KZ5.A
-3KZD.A
-3KZP.A
-3L0Q.B
-3L15.A
-3L23.A
-3L29.A
-3L3E.A
-3L4H.A
-3L51.B
-3L6T.A
-3L7H.A
-2X2S.A
-2X2U.A
-2X32.A
-2X3G.A
-2X4J.A
-2X4K.A
-2X4W.A
-2X55.A
-2X5N.A
-2XCJ.A
-2XDG.A
-2XDH.A
-2XF7.A
-2XFV.A
-2XG5.B
-2XLG.A
-2XMJ.A
-3AG3.D
-3L9A.X
-3LAX.A
-3LDC.A
-3LDU.A
-3LE4.A
-3LFR.A
-3LGB.A
-3LHE.A
-3LHO.A
-3LHR.A
-3LLO.A
-3LM3.A
-3LQ9.A
-3LR2.A
-3LR4.A
-3LS0.A
-3LUC.A
-3LUM.A
-3LUR.A
-3LUU.A
-3LWC.A
-3LWG.A
-3LXR.F
-3LYD.A
-3LYG.A
-3LYH.A
-3LYY.A
-3M1T.A
-3M66.A
-3M6J.A
-3M7K.A
-3M7O.A
-3M8J.A
-3M9Q.A
-3MAB.A
-3MAL.A
-3MCB.A
-3MCB.B
-3MCQ.A
-3MDP.A
-3MG1.A
-3MHS.B
-3MR0.A
-3MSW.A
-3MT0.A
-3MW8.A
-3MWZ.A
-3MZO.A
-3N0R.A
-3N1E.A
-3N6Y.A
-3N9B.A
-3NE8.A
-3NFT.A
-3NKE.A
-3NKG.A
-3NKL.A
-3NO2.A
-3NOH.A
-3NPD.A
-3NQI.A
-3NRF.A
-3NRW.A
-3NS2.A
-3NY3.A
-3NZN.A
-3O6C.A
+2JK9.A.
+2V4X.A.
+2VQ4.A.
+2VTC.A.
+2VV6.A.
+2VXT.I.
+2VXZ.A.
+2VZC.A.
+2W2R.A.
+2W61.A.
+2W6A.A.
+2W7A.A.
+2W7N.A.
+2ZK9.X.
+2ZNR.A.
+2ZQ5.A.
+2ZQE.A.
+2ZSI.B.
+2ZX0.A.
+3BYP.A.
+3BYQ.A.
+3C1Q.A.
+3C7T.A.
+3C8L.A.
+3C8W.A.
+3CHM.A.
+3CKK.A.
+3CNY.A.
+3CP7.A.
+3CT6.A.
+3CZ6.A.
+3D1R.A.
+3D2Q.A.
+3D34.A.
+3D3B.J.
+3D59.A.
+3D85.C.
+3DAN.A.
+3DD7.A.
+3DS2.A.
+3DSB.A.
+3E7H.A.
+3E7U.X.
+3E8O.A.
+3E8T.A.
+3EBT.A.
+3ECF.A.
+3ECH.A.
+3EDO.A.
+3EEH.A.
+3EER.A.
+3EF8.A.
+3EHG.A.
+3EHM.A.
+3EKI.A.
+3EMF.A.
+3EMI.A.
+3ENU.A.
+3EO6.A.
+3ER7.A.
+3ES4.A.
+3EYT.A.
+3EZI.A.
+3F0P.A.
+3F2E.A.
+3F40.A.
+3F4M.A.
+3F62.A.
+3F7E.A.
+3F7Q.A.
+3F8X.A.
+3F95.A.
+3F9S.A.
+3FAU.A.
+3FB9.A.
+3FBL.A.
+3FCN.A.
+3FF2.A.
+3FF5.A.
+3FFV.A.
+3FG9.A.
+3FGR.B.
+3FGV.A.
+3FH1.A.
+3FIA.A.
+3FID.A.
+3FJU.B.
+3FK8.A.
+3FKA.A.
+3FM2.A.
+3FMY.A.
+2W8X.A.
+2W9Y.A.
+2WCJ.A.
+2WCR.A.
+2WFB.A.
+2WFO.A.
+2WJ5.A.
+2WJ9.A.
+2WJR.A.
+2WL1.A.
+2WNF.A.
+2WPV.B.
+2WQF.A.
+2WTP.A.
+2WUJ.A.
+2WUU.A.
+2WUX.A.
+2WVX.A.
+2WY3.B.
+2WZO.A.
+2ZXY.A.
+3A0Z.A.
+3A4R.A.
+3A57.A.
+3A5P.A.
+3AAP.A.
+3FOT.A.
+3FOV.A.
+3FQG.A.
+3FRR.A.
+3FSO.A.
+3FSS.A.
+3FWK.A.
+3FWZ.A.
+3FX7.A.
+3FYB.A.
+3FYM.A.
+3G02.A.
+3G0M.A.
+3G1J.A.
+3G21.A.
+3G2B.A.
+3G2S.A.
+3G36.A.
+3G3T.A.
+3G5B.A.
+3G7G.A.
+3GA3.A.
+3GA4.A.
+3GAE.A.
+3GBW.A.
+3GBY.A.
+3GDW.A.
+3GE3.E.
+3GFP.A.
+3GI7.A.
+3GIX.A.
+3GKJ.A.
+3GMG.A.
+3GN6.A.
+3GNE.A.
+3GNZ.P.
+3GOE.A.
+3GP4.A.
+3GP6.A.
+3GQQ.A.
+3GWH.A.
+3GWN.A.
+3GXW.A.
+3GY9.A.
+3GZB.A.
+3H05.A.
+3H0W.A.
+3H20.A.
+3H3L.A.
+3H51.A.
+3H5J.A.
+3H6P.C.
+3H6R.A.
+3H7H.B.
+3H8T.A.
+3H96.A.
+3H9W.A.
+3HA2.A.
+3HE5.B.
+3HFO.A.
+3HH1.A.
+3HL1.A.
+3HN0.A.
+3HN5.A.
+3HO6.A.
+3HOI.A.
+3HPC.X.
+3HR0.A.
+3HRL.A.
+3HRR.A.
+3HSH.A.
+3HTV.A.
+3HVS.A.
+3HWP.A.
+3HWU.A.
+3HX8.A.
+3HXL.A.
+3HYN.A.
+3HZP.A.
+3I0W.A.
+3I1A.A.
+3I2V.A.
+3I4O.A.
+3I7M.A.
+3I84.A.
+3IBM.A.
+3IC3.A.
+3ID1.A.
+3IDF.A.
+3IDU.A.
+3IE4.A.
+3IEE.A.
+3IG9.A.
+3IHT.A.
+3IJM.A.
+3IKB.A.
+3IKW.A.
+3ILW.A.
+3IM3.A.
+3IMK.A.
+3IP4.C.
+3IPF.A.
+3IPJ.A.
+3IR4.A.
+3IT5.A.
+3IU6.A.
+3IUF.A.
+3IUO.A.
+3IUW.A.
+3IVV.A.
+3IWF.A.
+3IX3.A.
+3JQY.A.
+3JRN.A.
+3JSZ.A.
+3JTW.A.
+3JU0.A.
+3JUD.A.
+3JXO.A.
+3JYG.A.
+3JYZ.A.
+3JZ9.A.
+3K0X.A.
+3K0Z.A.
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+3K69.A.
+3K6O.A.
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+3KDE.C.
+3KDF.A.
+3KDF.B.
+3KDG.A.
+3KE7.A.
+3KG9.A.
+3KGK.A.
+3KK4.A.
+3KKF.A.
+3KKG.A.
+3KLQ.A.
+3KMI.A.
+3KOG.A.
+3KOS.A.
+3KPE.A.
+3KUC.B.
+3KWS.A.
+3KXT.A.
+3KYZ.A.
+3KZ5.A.
+3KZD.A.
+3KZP.A.
+3L0Q.B.
+3L15.A.
+3L23.A.
+3L29.A.
+3L3E.A.
+3L4H.A.
+3L51.B.
+3L6T.A.
+3L7H.A.
+2X2S.A.
+2X2U.A.
+2X32.A.
+2X3G.A.
+2X4J.A.
+2X4K.A.
+2X4W.A.
+2X55.A.
+2X5N.A.
+2XCJ.A.
+2XDG.A.
+2XDH.A.
+2XF7.A.
+2XFV.A.
+2XG5.B.
+2XLG.A.
+2XMJ.A.
+3AG3.D.
+3L9A.X.
+3LAX.A.
+3LDC.A.
+3LDU.A.
+3LE4.A.
+3LFR.A.
+3LGB.A.
+3LHE.A.
+3LHO.A.
+3LHR.A.
+3LLO.A.
+3LM3.A.
+3LQ9.A.
+3LR2.A.
+3LR4.A.
+3LS0.A.
+3LUC.A.
+3LUM.A.
+3LUR.A.
+3LUU.A.
+3LWC.A.
+3LWG.A.
+3LXR.F.
+3LYD.A.
+3LYG.A.
+3LYH.A.
+3LYY.A.
+3M1T.A.
+3M66.A.
+3M6J.A.
+3M7K.A.
+3M7O.A.
+3M8J.A.
+3M9Q.A.
+3MAB.A.
+3MAL.A.
+3MCB.A.
+3MCB.B.
+3MCQ.A.
+3MDP.A.
+3MG1.A.
+3MHS.B.
+3MR0.A.
+3MSW.A.
+3MT0.A.
+3MW8.A.
+3MWZ.A.
+3MZO.A.
+3N0R.A.
+3N1E.A.
+3N6Y.A.
+3N9B.A.
+3NE8.A.
+3NFT.A.
+3NKE.A.
+3NKG.A.
+3NKL.A.
+3NO2.A.
+3NOH.A.
+3NPD.A.
+3NQI.A.
+3NRF.A.
+3NRW.A.
+3NS2.A.
+3NY3.A.
+3NZN.A.
+3O6C.A.
3OAJ.A
Modified: trunk/test/pdb/plp399.list
===================================================================
--- trunk/test/pdb/plp399.list 2011-05-12 17:05:26 UTC (rev 2800)
+++ trunk/test/pdb/plp399.list 2011-05-13 07:51:11 UTC (rev 2801)
@@ -1,399 +1,399 @@
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-3JUD.A
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-2AQ6.A
-3KLQ.A
-3L15.A
-3N9B.A
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-3NOH.A
-3KDF.A
-3KDF.B
-3KDE.C
-3KDG.A
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+3HWU.A.
+3HWP.A.
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+3GNZ.P.
+3OAJ.A.
+3I0W.A.
+3C1Q.A.
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+3CZ6.A.
+3EYT.A.
+2WZO.A.
+2VZC.A.
+3FF2.A.
+3FFV.A.
+3FF5.A.
+3NQI.A.
+2XG5.B.
+3HH1.A.
+2VE8.A.
+3D2Q.A.
+3NS2.A.
+3E7U.X.
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+3GIX.A.
+3KWS.A.
+3IP4.C.
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+2AQ6.A.
+3KLQ.A.
+3L15.A.
+3N9B.A.
+3NO2.A.
+3NOH.A.
+3KDF.A.
+3KDF.B.
+3KDE.C.
+3KDG.A.
+3KD3.A.
+3CT6.A.
+3IG9.A.
+3L9A.X.
+3LDC.A.
+3LDU.A.
+3FWK.A.
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+3BFQ.G.
+3GE3.E.
+3LUM.A.
+3LUU.A.
+3LUC.A.
+3LUR.A.
+3IU6.A.
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+3LHO.A.
+3ER7.A.
+2QZQ.A.
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+3LQ9.A.
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+3M8J.A.
+2ZCA.A.
+3F7Q.A.
+3F7E.A.
+3MHS.C.
+3HSH.A.
+3KKG.A.
+3KK4.A.
+3KKF.A.
+3NRF.A.
+3NRW.A.
+3HYN.A.
+3EMF.A.
+3EMI.A.
+3C8L.A.
+3C8W.A.
+3IR4.A.
+3L23.A.
+3L29.A.
+3BO6.A.
+2P1M.A.
+2ZF9.A.
+2X32.A.
+2X3G.A.
+2QPX.A.
+3G5B.A.
+2ZK9.X.
+3M66.A.
+3M6J.A.
+3E8O.A.
+3E8T.A.
+3ILW.A.
+2ILR.A.
+3BCY.A.
+3LWG.A.
+3LWC.A.
+3H7H.B.
+2W9Y.A.
+2JK9.A.
+3NPD.A.
+3H8T.A.
+3M7K.A.
+3M7O.A.
+3L6T.A.
+3JXO.A.
+2WUU.A.
+2WUJ.A.
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+3L51.B.
+3FAU.A.
+3L0Q.B.
+3D85.C.
+3MCQ.A.
+3MCB.A.
+3MCB.B.
+2R2A.A.
+3DD7.A.
+3L3E.A.
+3N6Y.A.
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