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examples/ 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
owl/ 1329 (11 years ago) by jmduarteg: Important change: now the PDB file reader will try to read and fix the numbering of PDB files. Whenever the alignment is wrong it will realign and renumber using the jaligner package. The result of reading original PDB files now will be the same as that of reading CIF files, including proper mapping of classical PDB numbers to SEQRES residue serials (as in CIF). There is one change of behaviour in comparison to before: when no SEQRES present the sequence is taken to be that of ATOM lines instead of padding it with Xs. Still in this version the re-alignment is not perfect as there are some times when ambiguities occur and they are not solved (e.g. in 2nwr where alignment in an unobserved loop can be at two possible places for a GLY). That is anyway a rather minor problem (coordinates are still fine, just the chain is not ordered correctly at 1 or 2 points) and rare (~1% of files)
addSeq2Mcma.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
alignSeq.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
analyseHistone.java 1005 (12 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
averageGraph.java 1009 (12 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
benchmarkGraphAlgorithm.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
calcVolsAndSurfs.java 1032 (12 years ago) by jmduarteg: Extracted the calc-vol and calc-surf runner code to its own Runner class.
calculateGridDensity.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
checkChirality.java 1005 (12 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
compareAlignments.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
compareCMs.java 1009 (12 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
computeEnergies.java 1009 (12 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
dumppdb.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
dumpseq.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
enumerateInterfaces.java 1280 (11 years ago) by jmduarteg: Now enumerateInterfaces takes file from local cif file PDB repo. Fixed some docs.
genDbGraph.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
genGraph.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
mapMutations.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
mirrorIt.java 1005 (12 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
pairwiseSeqId.java 1009 (12 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
reconstruct.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
runMD.java 1009 (12 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
scoreDecoys.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
scoreGeomOfPdbs.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
scorePdbSet.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
superimposeMult.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
testAICGraph.java 1192 (11 years ago) by jmduarteg: Committing test class for AICGraph
testClusterConnection.java 1005 (12 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
testDbRIGraph.java 1009 (12 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
testJUNGframework.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
testMySQLConnection.java 1005 (12 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
testPdb.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
testPyMol.java 1005 (12 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
testPymolServer.java 951 (12 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.
unitCellVol.java 1181 (11 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.
writePerAtomDistancesToBFactor.java 1005 (12 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
writeSASAtoBFactor.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
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