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Author: jmduarteg
Date: Thu May 19 14:27:50 2011 UTC (8 years, 5 months ago)
Log Message:
MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.

Changed paths

Path Details
Directorytrunk/src/analyseHistone.java modified , text changed
Directorytrunk/src/benchmarkGraphAlgorithm.java modified , text changed
Directorytrunk/src/checkChirality.java modified , text changed
Directorytrunk/src/dumpseq.java modified , text changed
Directorytrunk/src/genDbGraph.java modified , text changed
Directorytrunk/src/mapMutations.java modified , text changed
Directorytrunk/src/owl/core/connections/CSAConnection.java modified , text changed
Directorytrunk/src/owl/core/connections/ConsurfConnection.java deleted
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/tinker/ConstraintsMaker.java modified , text changed
Directorytrunk/src/owl/core/sequence/Sequence.java modified , text changed
Directorytrunk/src/owl/core/structure/AaResidue.java
(Copied from trunk/src/owl/core/structure/Residue.java, r1387)
added , text changed
Directorytrunk/src/owl/core/structure/Asa.java modified , text changed
Directorytrunk/src/owl/core/structure/Atom.java modified , text changed
Directorytrunk/src/owl/core/structure/AtomLine.java added
Directorytrunk/src/owl/core/structure/AtomLineList.java added
Directorytrunk/src/owl/core/structure/AtomRadii.java modified , text changed
Directorytrunk/src/owl/core/structure/AtomType.java modified , text changed
Directorytrunk/src/owl/core/structure/ChainInterface.java modified , text changed
Directorytrunk/src/owl/core/structure/CiffileParser.java modified , text changed
Directorytrunk/src/owl/core/structure/HetResidue.java added
Directorytrunk/src/owl/core/structure/InterfaceRimCore.java modified , text changed
Directorytrunk/src/owl/core/structure/NucResidue.java added
Directorytrunk/src/owl/core/structure/Nucleotide.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbAsymUnit.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbChain.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbUnitCell.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbaseParser.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbfileParser.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbxPolySeqGroup.java added
Directorytrunk/src/owl/core/structure/PdbxPolySeqLine.java added
Directorytrunk/src/owl/core/structure/PdbxPolySeqLineList.java added
Directorytrunk/src/owl/core/structure/Residue.java modified , text changed
Directorytrunk/src/owl/core/structure/SecStructureLine.java added
Directorytrunk/src/owl/core/structure/features/SecStrucElement.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/FileRIGraph.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/RIGGeometry.java modified , text changed
Directorytrunk/src/owl/decoyScoring/GeomScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/Scorer.java modified , text changed
Directorytrunk/src/owl/embed/Embedder.java modified , text changed
Directorytrunk/src/owl/gmbp/CMPdb_sphoxel.java modified , text changed
Directorytrunk/src/owl/gmbp/CMPdb_sphoxel_greedy.java modified , text changed
Directorytrunk/src/owl/gmbp/GmbpGeometry.java modified , text changed
Directorytrunk/src/owl/gmbp/Gmbp_Geom.java modified , text changed
Directorytrunk/src/owl/graphAveraging/PhiPsiAverager.java modified , text changed
Directorytrunk/src/owl/mutanom/FoldXRunner.java modified , text changed
Directorytrunk/src/owl/mutanom/MainAnalysis.java modified , text changed
Directorytrunk/src/owl/mutanom/MutationSimulator.java modified , text changed
Directorytrunk/src/owl/mutanom/MutationTools.java modified , text changed
Directorytrunk/src/owl/mutanom/Sandbox.java modified , text changed
Directorytrunk/src/owl/mutanom/core/Gene.java modified , text changed
Directorytrunk/src/owl/mutanom/core/Mutation.java modified , text changed
Directorytrunk/src/owl/mutanom/core/TargetList.java modified , text changed
Directorytrunk/src/owl/mutanom/output/SvgGenerator.java modified , text changed
Directorytrunk/src/owl/tests/core/runners/tinker/TinkerRunnerTest.java modified , text changed
Directorytrunk/src/owl/tests/core/structure/PdbAsymUnitTest.java modified , text changed
Directorytrunk/src/owl/tests/core/structure/PdbChainTest.java
(Copied from trunk/src/owl/tests/core/structure/PdbTest.java, r1387)
added , text changed
Directorytrunk/src/owl/tests/core/structure/PdbParsersTest.java modified , text changed
Directorytrunk/src/owl/tests/core/structure/PdbTest.java deleted
Directorytrunk/src/owl/tests/core/structure/data/1tdrA.grades deleted
Directorytrunk/src/owl/tests/core/structure/data/cullpdb_20 modified , text changed
Directorytrunk/src/scorePdbSet.java modified , text changed