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r407
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actionTools/ 369 (11 years ago) by lpetzo: This package provides a set of very basic abstract classes serving as interfaces to very basic tasks such as: 1. condition checkings (class Checker), 2. data retrieval (class Retriever) and 3. pure workers that perform any kind of actions that do not depend on any kind of input data (class Doer). Each of these classes is a subclass of class Action which only purpose is to store the object affected by the subclasses action method.
tools/ 381 (11 years ago) by lpetzo: a generic pair class
sadp/ 386 (11 years ago) by lpetzo: MODIFICATIONS ------------- class SADP: - added exception handling stuff for exceptions thrown by class Alignment
tinker/ 393 (11 years ago) by duarte: Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
proteinstructure/ 407 (11 years ago) by filippis: contactTypes.dat -SC_CAGLY contact type added SecStrucElement.java -getSheetSerial method is now public Pdb.java -writeToDbFast added Graph.java -write_graph_to_db_fast -expBB,CW,CT,CR,w,d are now taken into account in a correct way -node_id, sssid, sheetSerial and turn are now also filled in DbGraph.java -expBB,CW,CT,CR,w,d are now taken into account in a correct way -directionality is also taken into account now when reading edges genDbGraph.java -sequence separation added as option createGraphDb.java added
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:
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
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 389 (11 years ago) by stehr: implemented tinker reconstruction of consensus graphs created with GraphAverager
scoreTargetMoves.java 390 (11 years ago) by duarte: Not creating anymore the score table
reconstruct.java 393 (11 years ago) by duarte: Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
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)
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,...)
genDbGraph.java 407 (11 years ago) by filippis: contactTypes.dat -SC_CAGLY contact type added SecStrucElement.java -getSheetSerial method is now public Pdb.java -writeToDbFast added Graph.java -write_graph_to_db_fast -expBB,CW,CT,CR,w,d are now taken into account in a correct way -node_id, sssid, sheetSerial and turn are now also filled in DbGraph.java -expBB,CW,CT,CR,w,d are now taken into account in a correct way -directionality is also taken into account now when reading edges genDbGraph.java -sequence separation added as option createGraphDb.java added
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