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r355
File Last Change
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sadp/ 316 (12 years ago) by lpetzo: initial version of sadp
tinker/ 347 (12 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 (12 years ago) by stehr: Machine: added main and some other methods; MySQLConnection: added explicit handling of some exceptions
proteinstructure/ 355 (12 years ago) by duarte: FIXED BUG: now doesn't fail with records that are delimited with \n; ;\n Method tokeniseFields is now completely rewritten: is what does all the magic of parsing all the oddities of the mmcif format Using RandomAccessFile to open the file only once and then seek to the positions we need to scan at each point. Might be slower due to the RandomAccessFile that does no buffering. Also maybe because the new tokenisation is not very optimal Now parseCifFile does the whole parsing calling also the submethods instead of calling them in the constructor
makeNbhTbl.java 24 (13 years ago) by stehr: moved executables (classes with main function) to root directory
testPyMol.java 114 (12 years ago) by duarte: Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server
testGraph2Pml.java 116 (12 years ago) by filippis: testGraph2Pml.java fixed according to changes made in Msdsd2Pdb.java
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
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
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
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
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
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
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
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
testPymolServer.java 203 (12 years ago) by duarte: Using apache xmlrpc version 3.0 in PyMolServerOutputStream
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
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
benchmarkGraphAlgorithm.java 254 (12 years ago) by duarte: Also writing graph to file
cnex1.java 265 (12 years ago) by lappe: final version incl. pessimistic tie-break
cnHashIterNbhood.java 266 (12 years ago) by lappe:
hashIterNbhood.java 267 (12 years ago) by lappe:
iterateUpperNbs.java 268 (12 years ago) by lappe:
iterEvalNbhood.java 269 (12 years ago) by lappe:
cnEvalTargetNbhood.java 271 (12 years ago) by lappe:
cnCoarseNbhood.java 272 (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 285 (12 years ago) by duarte: Fixed a few bugs in reading of list file Better output and error messages
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 (12 years ago) by lappe: only one out of both BB/SC insertion per moves based on sc/bb domin. out of temp shell
calculateGridDensity.java 303 (12 years ago) by stehr: added writeResultsToFile()
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 ?
Manifest.txt 321 (12 years ago) by stehr: added test program for difference distance maps, updated Manifest to v0.8.5
testDeltaDistanceMap.java 327 (12 years ago) by stehr: fixed missing references to constants in class AA
reconstruct.java 349 (12 years ago) by duarte: Now writing also original pdb file Fixed output of rmsd: now only few decimal figures output
testResidueSelectionString.java 351 (12 years ago) by stehr: added some test programs to default package
testGraphClustering.java 351 (12 years ago) by stehr: added some test programs to default package
testGraphAverager.java 351 (12 years ago) by stehr: added some test programs to default package
scoreTargetMoves.java 354 (12 years ago) by duarte: Fixed bug: was outputing an empty column before the 'total' column
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