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r365
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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
sadp/ 316 (12 years ago) by lpetzo: initial version of sadp
tinker/ 347 (11 years ago) by duarte: Writing report to file instead of standard output Catching unknown errors in runDistgeom (all other non-zero exit values)
tools/ 350 (11 years ago) by stehr: Machine: added main and some other methods; MySQLConnection: added explicit handling of some exceptions
Manifest.txt 321 (12 years ago) by stehr: added test program for difference distance maps, updated Manifest to v0.8.5
benchmarkGraphAlgorithm.java 254 (12 years ago) by duarte: Also writing graph to file
calculateGridDensity.java 303 (12 years ago) by stehr: added writeResultsToFile()
cnCoarseNbhood.java 272 (12 years ago) by lappe:
cnEvalTargetNbhood.java 271 (12 years ago) by lappe:
cnHashIterNbhood.java 266 (12 years ago) by lappe:
cnex1.java 265 (12 years ago) by lappe: final version incl. pessimistic tie-break
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
genDbGraph.java 359 (11 years ago) by duarte: Now can do multiple contact types/cutoffs per pdb structure
genGraph.java 285 (12 years ago) by duarte: Fixed a few bugs in reading of list file Better output and error messages
hashIterNbhood.java 267 (12 years ago) by lappe:
iterEvalNbhood.java 269 (12 years ago) by lappe:
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
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
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
iterateUpperNbs.java 268 (12 years ago) by lappe:
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
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
makeNbhTbl.java 24 (13 years ago) by stehr: moved executables (classes with main function) to root directory
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
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
reconstruct.java 349 (11 years ago) by duarte: Now writing also original pdb file Fixed output of rmsd: now only few decimal figures output
rewriteNBHood.java 299 (12 years ago) by lappe: only one out of both BB/SC insertion per moves based on sc/bb domin. out of temp shell
rewriteNBHood_parallel.java 291 (12 years ago) by lappe: 1st version scoring with pdb_reps_graph_4_2 and full nbhood string
scoreTargetMoves.java 354 (11 years ago) by duarte: Fixed bug: was outputing an empty column before the 'total' column
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
testDeltaDistanceMap.java 327 (11 years ago) by stehr: fixed missing references to constants in class AA
testGraph2Pml.java 116 (12 years ago) by filippis: testGraph2Pml.java fixed according to changes made in Msdsd2Pdb.java
testGraphAverager.java 351 (11 years ago) by stehr: added some test programs to default package
testGraphClustering.java 351 (11 years ago) by stehr: added some test programs to default package
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
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
testPyMol.java 114 (12 years ago) by duarte: Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server
testPymolServer.java 203 (12 years ago) by duarte: Using apache xmlrpc version 3.0 in PyMolServerOutputStream
testResidueSelectionString.java 351 (11 years ago) by stehr: added some test programs to default package
writeTargetMoves.java 313 (12 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 ?
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