 ../
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examples/
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1198
(9 years ago)
by cvehlow:
classes moved
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owl/
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1248
(9 years ago)
by jmduarteg:
Now using our own ASA calculation instead of NACCESS for the interface areas calculation. We are slower than NACCESS but at least don't depend on it anymore, old NACCESS methods can still be used.
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testPymolServer.java
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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.
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testClusterConnection.java
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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
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testMySQLConnection.java
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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
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checkChirality.java
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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
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mirrorIt.java
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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
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writeSASAtoBFactor.java
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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
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testPyMol.java
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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
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dumppdb.java
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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
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analyseHistone.java
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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
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dumpseq.java
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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
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writePerAtomDistancesToBFactor.java
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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
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scorePdbSet.java
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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
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computeEnergies.java
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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
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superimposeMult.java
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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
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testPdb.java
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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
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addSeq2Mcma.java
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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
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compareAlignments.java
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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
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averageGraph.java
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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
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testDbRIGraph.java
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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
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testJUNGframework.java
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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
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scoreDecoys.java
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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
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runMD.java
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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
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alignSeq.java
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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
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pairwiseSeqId.java
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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
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compareCMs.java
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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
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calcVolsAndSurfs.java
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1032
(9 years ago)
by jmduarteg:
Extracted the calc-vol and calc-surf runner code to its own Runner class.
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mapMutations.java
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1033
(9 years ago)
by jmduarteg:
Extracted the CSA parsing code to its own connection class.
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genDbGraph.java
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1035
(9 years ago)
by jmduarteg:
Extracted the EC data parsing code to its own connection class.
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genGraph.java
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1080
(9 years ago)
by jmduarteg:
Undoing some stuff commited by error in last commit
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reconstruct.java
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1099
(9 years ago)
by jmduarteg:
Some fixes to the help string
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unitCellVol.java
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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.
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benchmarkGraphAlgorithm.java
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1189
(9 years ago)
by jmduarteg:
Implemented inter-chain contact calculation (using same hashing algorithm as in intra-chain).
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calculateGridDensity.java
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1191
(9 years ago)
by jmduarteg:
Considerable clean up of Pdb. Now the algorithm for calculating atom contacts is all under new class Grid (also refactored Box to GridCell). Tests for graph calculations passed.
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testAICGraph.java
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1192
(9 years ago)
by jmduarteg:
Committing test class for AICGraph
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scoreGeomOfPdbs.java
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1208
(9 years ago)
by cvehlow:
Scoring:KendallsTau-method added to Statistics
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enumerateInterfaces.java
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1246
(9 years ago)
by jmduarteg:
Some minor improvements: now populating ids of ChainInterfaces, now interface area is half to match pisa's.
Fixed bug in getAllInterfaces tester, wasn't comparing properly in small values.
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