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r1351
File Last Change
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examples/ 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
owl/ 1349 (8 years ago) by hstehr: moving info about reduced alphabets from main() to printReducedAlphabetInfo()
addSeq2Mcma.java 1342 (8 years ago) by hstehr:
alignSeq.java 1340 (8 years ago) by hstehr: Fixed bugs in method for reading from PIR file; added script to convert from PIR to Fasta
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
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
benchmarkGraphAlgorithm.java 1341 (8 years ago) by jmduarteg: Now parsing pdb titles in PDB, CIF and pdbase. Tests pass. Moved some constants from Pdb to PdbAsymUnit
calcVolsAndSurfs.java 1032 (9 years ago) by jmduarteg: Extracted the calc-vol and calc-surf runner code to its own Runner class.
calculateGridDensity.java 1341 (8 years ago) by jmduarteg: Now parsing pdb titles in PDB, CIF and pdbase. Tests pass. Moved some constants from Pdb to PdbAsymUnit
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
clustal2fasta.java 1344 (8 years ago) by hstehr:
compareAlignments.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
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
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
dumppdb.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
dumpseq.java 1351 (8 years ago) by hstehr: unnecessary codes removed
enumerateInterfaces.java 1345 (8 years ago) by jmduarteg: Now the colors of chains of pymol generated images are consistent with the letter codes (given a chain letter code the color will always be the same for it for all images generated)
genDbGraph.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.
mapMutations.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
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
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
pir2fasta.java 1343 (8 years ago) by hstehr:
reconstruct.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
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
scoreDecoys.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.
scorePdbSet.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.
testAICGraph.java 1192 (9 years ago) by jmduarteg: Committing test class for AICGraph
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
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
testJUNGframework.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
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
testPdb.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
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
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.
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.
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
writeSASAtoBFactor.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
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