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r368
File (rev) Last Change
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tools/ 350 (11 years ago) by stehr: Machine: added main and some other methods; MySQLConnection: added explicit handling of some exceptions
tinker/ 368 (11 years ago) by duarte: Now parsing tinker's error function value, changed report file format (again!!)
sadp/ 316 (11 years ago) by lpetzo: initial version of sadp
proteinstructure/ 365 (11 years ago) by duarte: New method getEdge in EdgeSet, necessary since we introduced weights in the Edge class. To retrieve them we first need to retrieve the actual Edge object
writeTargetMoves.java 313 (11 years ago) by lappe: short form to compress nbstrings = condense multiple occurence of a symbol in the nbhstring to 1. Still a bitz buggy. sometimes 2 symbols are left in ?
testResidueSelectionString.java 351 (11 years ago) by stehr: added some test programs to default package
testPymolServer.java 203 (12 years ago) by duarte: Using apache xmlrpc version 3.0 in PyMolServerOutputStream
testPyMol.java 114 (12 years ago) by duarte: Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server
testPdb.java 215 (12 years ago) by stehr: some clean up of exceptions in Pdb and Graph classes: merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError, created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead
testMySQLConnection.java 202 (12 years ago) by duarte: MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
testGraphClustering.java 351 (11 years ago) by stehr: added some test programs to default package
testGraphAverager.java 351 (11 years ago) by stehr: added some test programs to default package
testGraph2Pml.java 116 (12 years ago) by filippis: testGraph2Pml.java fixed according to changes made in Msdsd2Pdb.java
testDeltaDistanceMap.java 327 (11 years ago) by stehr: fixed missing references to constants in class AA
testClusterConnection.java 202 (12 years ago) by duarte: MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
scoreTargetMoves.java 366 (11 years ago) by duarte: Now throwing all exceptions
rewriteNBHood_parallel.java 291 (12 years ago) by lappe: 1st version scoring with pdb_reps_graph_4_2 and full nbhood string
rewriteNBHood.java 299 (11 years ago) by lappe: only one out of both BB/SC insertion per moves based on sc/bb domin. out of temp shell
reconstruct.java 368 (11 years ago) by duarte: Now parsing tinker's error function value, changed report file format (again!!)
minInfoGain.java 202 (12 years ago) by duarte: MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
maxInfoGain.java 202 (12 years ago) by duarte: MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
makeNbhTbl.java 24 (13 years ago) by stehr: moved executables (classes with main function) to root directory
listInfoLoss.java 202 (12 years ago) by duarte: MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
listInfoGain.java 202 (12 years ago) by duarte: MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
iterateUpperNbs.java 268 (12 years ago) by lappe:
iterateUpperNbhood.java 202 (12 years ago) by duarte: MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
iterateNbs.java 202 (12 years ago) by duarte: MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
iterateNbhood.java 202 (12 years ago) by duarte: MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
iterEvalNbhood.java 269 (12 years ago) by lappe:
hashIterNbhood.java 267 (12 years ago) by lappe:
genGraph.java 285 (12 years ago) by duarte: Fixed a few bugs in reading of list file Better output and error messages
genDbGraph.java 359 (11 years ago) by duarte: Now can do multiple contact types/cutoffs per pdb structure
compareCMs.java 215 (12 years ago) by stehr: some clean up of exceptions in Pdb and Graph classes: merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError, created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead
cnex1.java 265 (12 years ago) by lappe: final version incl. pessimistic tie-break
cnHashIterNbhood.java 266 (12 years ago) by lappe:
cnEvalTargetNbhood.java 271 (12 years ago) by lappe:
cnCoarseNbhood.java 272 (12 years ago) by lappe:
calculateGridDensity.java 303 (11 years ago) by stehr: added writeResultsToFile()
benchmarkGraphAlgorithm.java 254 (12 years ago) by duarte: Also writing graph to file
Manifest.txt 321 (11 years ago) by stehr: added test program for difference distance maps, updated Manifest to v0.8.5
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