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r429
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actionTools/ 417 (11 years ago) by lpetzo: abstract class implementing the Runnable interface
proteinstructure/ 429 (11 years ago) by filippis: DbGraph-fix bug
sadp/ 416 (11 years ago) by lpetzo: - changed the identation mode - added some comments
tinker/ 393 (11 years ago) by duarte: Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
tools/ 381 (11 years ago) by lpetzo: a generic pair class
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
createGraphDb.sh 413 (11 years ago) by filippis: createGraphDb.sh -pchain_code is now modified to VARCHAR(2) from CHAR(1) due to pdbase_chain_code -index for pdb_residue_info table added
genDbGraph.java 412 (11 years ago) by filippis: Changes in Pdb -checkConsurfHssp: in the mistakes calculated I add now at the end the difference between the number of residues and the number of consurf scores -writeAtomLines has now a boolean argument called pdbCompatible: if pdbCompatible is true, then only the first character of chainCode and not the 'whole' chainCode is exported to the file. -another WriteAtomLines has also been added without this extra argument for backwards compatibility: default value for pdbCompatible is false -dump2pdbfile has also been changed in similar way -runDssp and runNaccess now call the above methods with true pdbCompatible Changes in genDbGraph -1 summary output line has been added to provide info about csa, naccess, scop, ec, dssp, ... -DSSP is run with 3state
genGraph.java 396 (11 years ago) by filippis: Added mode option in genDbGraph whether to find and store info for the residues (SCOP,NACCESS,EC,CSA,...)
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 393 (11 years ago) by duarte: Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
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
runGenDbGraph.sh 395 (11 years ago) by duarte: Initial commit. Provisional script to use the genDbGraph program when iterating through loads of structures, because of the "memory leak" problem is not possible to use directly genDbGraph to iterate over many structures (~1000)
scoreTargetMoves.java 390 (11 years ago) by duarte: Not creating anymore the score table
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 389 (11 years ago) by stehr: implemented tinker reconstruction of consensus graphs created with GraphAverager
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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