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Author: jmduarteg
Date: Wed Mar 30 09:55:49 2011 UTC (8 years, 7 months ago)
Log Message:
MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.

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Directorytrunk/src/analyseHistone.java modified , text changed
Directorytrunk/src/averageGraph.java modified , text changed
Directorytrunk/src/benchmarkGraphAlgorithm.java modified , text changed
Directorytrunk/src/calcVolsAndSurfs.java modified , text changed
Directorytrunk/src/calculateGridDensity.java modified , text changed
Directorytrunk/src/checkChirality.java modified , text changed
Directorytrunk/src/compareCMs.java modified , text changed
Directorytrunk/src/dumppdb.java modified , text changed
Directorytrunk/src/dumpseq.java modified , text changed
Directorytrunk/src/examples/ContactMapOverDir.java deleted
Directorytrunk/src/examples/HelloAGLappe.java deleted
Directorytrunk/src/examples/helloRank.java deleted
Directorytrunk/src/examples/testMySQLConnection.java
(Copied from trunk/src/testMySQLConnection.java, r1347)
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Directorytrunk/src/examples/testPdb.java
(Copied from trunk/src/testPdb.java, r1347)
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Directorytrunk/src/genDbGraph.java modified , text changed
Directorytrunk/src/genGraph.java modified , text changed
Directorytrunk/src/mapMutations.java modified , text changed
Directorytrunk/src/mirrorIt.java modified , text changed
Directorytrunk/src/owl/casp/benchmarking/Benchmarking.java modified , text changed
Directorytrunk/src/owl/casp/benchmarking/scoreAllModelsWithRanks.java modified , text changed
Directorytrunk/src/owl/casp/benchmarking/updateTargetTable.java modified , text changed
Directorytrunk/src/owl/casp/pipeline/RunAll.java modified , text changed
Directorytrunk/src/owl/casp/pipeline/TemplateSelection.java modified , text changed
Directorytrunk/src/owl/casp/tools/MapStru2Seq.java modified , text changed
Directorytrunk/src/owl/cccp/ConsensusPredictor.java modified , text changed
Directorytrunk/src/owl/cccp/benchmarkCCCP.java modified , text changed
Directorytrunk/src/owl/cccp/rankModels.java modified , text changed
Directorytrunk/src/owl/cccp/testGraphAverager.java modified , text changed
Directorytrunk/src/owl/core/connections/CSAConnection.java modified , text changed
Directorytrunk/src/owl/core/connections/ConsurfConnection.java modified , text changed
Directorytrunk/src/owl/core/connections/ECConnection.java modified , text changed
Directorytrunk/src/owl/core/connections/GTGHit.java modified , text changed
Directorytrunk/src/owl/core/connections/ScopConnection.java modified , text changed
Directorytrunk/src/owl/core/connections/pisa/PisaInterface.java modified , text changed
Directorytrunk/src/owl/core/connections/pisa/PisaMolecule.java modified , text changed
Directorytrunk/src/owl/core/features/InvalidFeatureCoordinatesException.java modified , text changed
Directorytrunk/src/owl/core/runners/CalcSurfVolRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/DaliRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/DsspRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/NaccessRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/PolyposeRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/PymolRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/blast/BlastUtils.java modified , text changed
Directorytrunk/src/owl/core/runners/tinker/ConstraintsMaker.java modified , text changed
Directorytrunk/src/owl/core/runners/tinker/TinkerRunner.java modified , text changed
Directorytrunk/src/owl/core/sequence/alignment/MultipleSequenceAlignment.java modified , text changed
Directorytrunk/src/owl/core/structure/Asa.java modified , text changed
Directorytrunk/src/owl/core/structure/ChainInterface.java modified , text changed
Directorytrunk/src/owl/core/structure/CiffileParser.java
(Copied from trunk/src/owl/core/structure/CiffilePdb.java, r1367)
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Directorytrunk/src/owl/core/structure/CiffilePdb.java deleted
Directorytrunk/src/owl/core/structure/Pdb.java deleted
Directorytrunk/src/owl/core/structure/PdbAsymUnit.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbChain.java
(Copied from trunk/src/owl/core/structure/Pdb.java, r1367)
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Directorytrunk/src/owl/core/structure/PdbChainSet.java
(Copied from trunk/src/owl/core/structure/PdbSet.java, r1367)
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Directorytrunk/src/owl/core/structure/PdbSet.java deleted
Directorytrunk/src/owl/core/structure/PdbUnitCell.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbaseParser.java
(Copied from trunk/src/owl/core/structure/PdbasePdb.java, r1367)
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Directorytrunk/src/owl/core/structure/PdbasePdb.java deleted
Directorytrunk/src/owl/core/structure/PdbfileParser.java
(Copied from trunk/src/owl/core/structure/PdbfilePdb.java, r1367)
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Directorytrunk/src/owl/core/structure/PdbfilePdb.java deleted
Directorytrunk/src/owl/core/structure/Residue.java modified , text changed
Directorytrunk/src/owl/core/structure/Template.java modified , text changed
Directorytrunk/src/owl/core/structure/TemplateList.java modified , text changed
Directorytrunk/src/owl/core/structure/alignment/PaulStructAligner.java modified , text changed
Directorytrunk/src/owl/core/structure/alignment/StructAligner.java modified , text changed
Directorytrunk/src/owl/core/structure/alignment/StructureAlignmentEvaluator.java modified , text changed
Directorytrunk/src/owl/core/structure/features/SecondaryStructure.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/AICGraph.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/CaspRRFileRIGraph.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/DbRIGraph.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/FileRIGraph.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/GraphIOGDLFile.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/ProtStructGraph.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/RIGEnsemble.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/RIGMatrix.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/RIGraph.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/RIGraphMinSpanningTree.java modified , text changed
Directorytrunk/src/owl/core/structure/scoring/DRToThree.java modified , text changed
Directorytrunk/src/owl/core/structure/scoring/HydrophobicPotential.java modified , text changed
Directorytrunk/src/owl/core/structure/scoring/ResidueContactScoringFunction.java modified , text changed
Directorytrunk/src/owl/core/util/BoundingBox.java modified , text changed
Directorytrunk/src/owl/core/util/FileTypeGuesser.java modified , text changed
Directorytrunk/src/owl/core/util/GridCell.java modified , text changed
Directorytrunk/src/owl/decoyScoring/AtomCombinedScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/AtomCountScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/AtomTripletScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/AtomTypeScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/DistanceScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/GeomScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/ResCombinedScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/ResCountScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/ResTripletScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/ResTypeScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/Scorer.java modified , text changed
Directorytrunk/src/owl/embed/ConePeeler.java modified , text changed
Directorytrunk/src/owl/embed/Distiller.java modified , text changed
Directorytrunk/src/owl/embed/Embedder.java modified , text changed
Directorytrunk/src/owl/embed/Reconstructer.java modified , text changed
Directorytrunk/src/owl/embed/Scorer.java modified , text changed
Directorytrunk/src/owl/embed/SetScore.java modified , text changed