[ViewVC] Revision 1392 of: owl

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Author:	jmduarteg
Date:	Thu May 19 14:27:50 2011 UTC (11 years 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
trunk/src/analyseHistone.java	modified , text changed
trunk/src/benchmarkGraphAlgorithm.java	modified , text changed
trunk/src/checkChirality.java	modified , text changed
trunk/src/dumpseq.java	modified , text changed
trunk/src/genDbGraph.java	modified , text changed
trunk/src/mapMutations.java	modified , text changed
trunk/src/owl/core/connections/CSAConnection.java	modified , text changed
trunk/src/owl/core/connections/ConsurfConnection.java	deleted
trunk/src/owl/core/runners/DaliRunner.java	modified , text changed
trunk/src/owl/core/runners/DsspRunner.java	modified , text changed
trunk/src/owl/core/runners/NaccessRunner.java	modified , text changed
trunk/src/owl/core/runners/tinker/ConstraintsMaker.java	modified , text changed
trunk/src/owl/core/sequence/Sequence.java	modified , text changed
trunk/src/owl/core/structure/AaResidue.java (Copied from trunk/src/owl/core/structure/Residue.java, r1387)	added , text changed
trunk/src/owl/core/structure/Asa.java	modified , text changed
trunk/src/owl/core/structure/Atom.java	modified , text changed
trunk/src/owl/core/structure/AtomLine.java	added
trunk/src/owl/core/structure/AtomLineList.java	added
trunk/src/owl/core/structure/AtomRadii.java	modified , text changed
trunk/src/owl/core/structure/AtomType.java	modified , text changed
trunk/src/owl/core/structure/ChainInterface.java	modified , text changed
trunk/src/owl/core/structure/CiffileParser.java	modified , text changed
trunk/src/owl/core/structure/HetResidue.java	added
trunk/src/owl/core/structure/InterfaceRimCore.java	modified , text changed
trunk/src/owl/core/structure/NucResidue.java	added
trunk/src/owl/core/structure/Nucleotide.java	modified , text changed
trunk/src/owl/core/structure/PdbAsymUnit.java	modified , text changed
trunk/src/owl/core/structure/PdbChain.java	modified , text changed
trunk/src/owl/core/structure/PdbUnitCell.java	modified , text changed
trunk/src/owl/core/structure/PdbaseParser.java	modified , text changed
trunk/src/owl/core/structure/PdbfileParser.java	modified , text changed
trunk/src/owl/core/structure/PdbxPolySeqGroup.java	added
trunk/src/owl/core/structure/PdbxPolySeqLine.java	added
trunk/src/owl/core/structure/PdbxPolySeqLineList.java	added
trunk/src/owl/core/structure/Residue.java	modified , text changed
trunk/src/owl/core/structure/SecStructureLine.java	added
trunk/src/owl/core/structure/features/SecStrucElement.java	modified , text changed
trunk/src/owl/core/structure/graphs/FileRIGraph.java	modified , text changed
trunk/src/owl/core/structure/graphs/RIGGeometry.java	modified , text changed
trunk/src/owl/decoyScoring/GeomScorer.java	modified , text changed
trunk/src/owl/decoyScoring/Scorer.java	modified , text changed
trunk/src/owl/embed/Embedder.java	modified , text changed
trunk/src/owl/gmbp/CMPdb_sphoxel.java	modified , text changed
trunk/src/owl/gmbp/CMPdb_sphoxel_greedy.java	modified , text changed
trunk/src/owl/gmbp/GmbpGeometry.java	modified , text changed
trunk/src/owl/gmbp/Gmbp_Geom.java	modified , text changed
trunk/src/owl/graphAveraging/PhiPsiAverager.java	modified , text changed
trunk/src/owl/mutanom/FoldXRunner.java	modified , text changed
trunk/src/owl/mutanom/MainAnalysis.java	modified , text changed
trunk/src/owl/mutanom/MutationSimulator.java	modified , text changed
trunk/src/owl/mutanom/MutationTools.java	modified , text changed
trunk/src/owl/mutanom/Sandbox.java	modified , text changed
trunk/src/owl/mutanom/core/Gene.java	modified , text changed
trunk/src/owl/mutanom/core/Mutation.java	modified , text changed
trunk/src/owl/mutanom/core/TargetList.java	modified , text changed
trunk/src/owl/mutanom/output/SvgGenerator.java	modified , text changed
trunk/src/owl/tests/core/runners/tinker/TinkerRunnerTest.java	modified , text changed
trunk/src/owl/tests/core/structure/PdbAsymUnitTest.java	modified , text changed
trunk/src/owl/tests/core/structure/PdbChainTest.java (Copied from trunk/src/owl/tests/core/structure/PdbTest.java, r1387)	added , text changed
trunk/src/owl/tests/core/structure/PdbParsersTest.java	modified , text changed
trunk/src/owl/tests/core/structure/PdbTest.java	deleted
trunk/src/owl/tests/core/structure/data/1tdrA.grades	deleted
trunk/src/owl/tests/core/structure/data/cullpdb_20	modified , text changed
trunk/src/scorePdbSet.java	modified , text changed