 ../
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examples/
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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owl/
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1349
(11 years ago)
by hstehr:
moving info about reduced alphabets from main() to printReducedAlphabetInfo()
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addSeq2Mcma.java
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1342
(11 years ago)
by hstehr:
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alignSeq.java
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1340
(11 years ago)
by hstehr:
Fixed bugs in method for reading from PIR file; added script to convert from PIR to Fasta
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analyseHistone.java
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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
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averageGraph.java
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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
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benchmarkGraphAlgorithm.java
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1341
(11 years ago)
by jmduarteg:
Now parsing pdb titles in PDB, CIF and pdbase. Tests pass.
Moved some constants from Pdb to PdbAsymUnit
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calcVolsAndSurfs.java
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1032
(12 years ago)
by jmduarteg:
Extracted the calc-vol and calc-surf runner code to its own Runner class.
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calculateGridDensity.java
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1341
(11 years ago)
by jmduarteg:
Now parsing pdb titles in PDB, CIF and pdbase. Tests pass.
Moved some constants from Pdb to PdbAsymUnit
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checkChirality.java
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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
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clustal2fasta.java
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1344
(11 years ago)
by hstehr:
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compareAlignments.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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compareCMs.java
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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
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computeEnergies.java
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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
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dumppdb.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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dumpseq.java
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1351
(11 years ago)
by hstehr:
unnecessary codes removed
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enumerateInterfaces.java
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1345
(11 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)
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genDbGraph.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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genGraph.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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mapMutations.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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mirrorIt.java
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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
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pairwiseSeqId.java
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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
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pir2fasta.java
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1343
(11 years ago)
by hstehr:
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reconstruct.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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runMD.java
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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
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scoreDecoys.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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scoreGeomOfPdbs.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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scorePdbSet.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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superimposeMult.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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testAICGraph.java
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1192
(11 years ago)
by jmduarteg:
Committing test class for AICGraph
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testClusterConnection.java
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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
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testDbRIGraph.java
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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
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testJUNGframework.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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testMySQLConnection.java
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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
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testPdb.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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testPyMol.java
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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
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testPymolServer.java
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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.
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unitCellVol.java
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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.
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writePerAtomDistancesToBFactor.java
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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
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writeSASAtoBFactor.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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