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r1331
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examples/ 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
owl/ 1331 (8 years ago) by jmduarteg: Another improvement to PdbfilePdb parsing: now we can also detect some ambiguous cases in alignments by checking the contiguity of the 3D chain. This fixes 2 cases from our test data set: 1dki and 2ofz. Now only 2 warnings for the whole dataset (both because of ambiguous assignment in HIS tags, safe to ignore. Could even be that CIF got them wrong)
testPymolServer.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
testClusterConnection.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
testMySQLConnection.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
checkChirality.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
mirrorIt.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
testPyMol.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
analyseHistone.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
writePerAtomDistancesToBFactor.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
computeEnergies.java 1009 (9 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
averageGraph.java 1009 (9 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
testDbRIGraph.java 1009 (9 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
runMD.java 1009 (9 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
pairwiseSeqId.java 1009 (9 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
compareCMs.java 1009 (9 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
calcVolsAndSurfs.java 1032 (9 years ago) by jmduarteg: Extracted the calc-vol and calc-surf runner code to its own Runner class.
unitCellVol.java 1181 (9 years ago) by jmduarteg: Now parsing the unit cell and crystal space group info when reading PDB sources. New simple script for unit cell volume.
testAICGraph.java 1192 (9 years ago) by jmduarteg: Committing test class for AICGraph
enumerateInterfaces.java 1280 (8 years ago) by jmduarteg: Now enumerateInterfaces takes file from local cif file PDB repo. Fixed some docs.
scorePdbSet.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
reconstruct.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
genGraph.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
superimposeMult.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
benchmarkGraphAlgorithm.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
testPdb.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
scoreGeomOfPdbs.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
addSeq2Mcma.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
genDbGraph.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
compareAlignments.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
writeSASAtoBFactor.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
mapMutations.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
testJUNGframework.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
dumppdb.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
scoreDecoys.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
alignSeq.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
calculateGridDensity.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
dumpseq.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
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