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r329
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proteinstructure/ 329 (11 years ago) by duarte: Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now Added method evaluatePrediction to Graph Some refactoring in Alignment and better javadocs
sadp/ 316 (11 years ago) by lpetzo: initial version of sadp
tinker/ 328 (11 years ago) by duarte: First commit of ConstraintsMaker (and PRMInfo needed for it) Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb) Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran Thus the PRMInfo class was needed, at the moment can read only amber prm files Some new methods and better javadoc in Pdb. Some new methods in AAinfo
tools/ 203 (11 years ago) by duarte: Using apache xmlrpc version 3.0 in PyMolServerOutputStream
Manifest.txt 321 (11 years ago) by stehr: added test program for difference distance maps, updated Manifest to v0.8.5
benchmarkGraphAlgorithm.java 254 (11 years ago) by duarte: Also writing graph to file
calculateGridDensity.java 303 (11 years ago) by stehr: added writeResultsToFile()
cnCoarseNbhood.java 272 (11 years ago) by lappe:
cnEvalTargetNbhood.java 271 (11 years ago) by lappe:
cnHashIterNbhood.java 266 (11 years ago) by lappe:
cnex1.java 265 (11 years ago) by lappe: final version incl. pessimistic tie-break
compareCMs.java 215 (11 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 285 (11 years ago) by duarte: Fixed a few bugs in reading of list file Better output and error messages
genGraph.java 285 (11 years ago) by duarte: Fixed a few bugs in reading of list file Better output and error messages
hashIterNbhood.java 267 (11 years ago) by lappe:
iterEvalNbhood.java 269 (11 years ago) by lappe:
iterateNbhood.java 202 (11 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 (11 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 (11 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 (11 years ago) by lappe:
listInfoGain.java 202 (11 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 (11 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 (12 years ago) by stehr: moved executables (classes with main function) to root directory
maxInfoGain.java 202 (11 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 (11 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
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
rewriteNBHood_parallel.java 291 (11 years ago) by lappe: 1st version scoring with pdb_reps_graph_4_2 and full nbhood string
scoreTargetMoves.java 312 (11 years ago) by lappe:
testClusterConnection.java 202 (11 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 (11 years ago) by filippis: testGraph2Pml.java fixed according to changes made in Msdsd2Pdb.java
testMySQLConnection.java 202 (11 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 (11 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 (11 years ago) by duarte: Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server
testPymolServer.java 203 (11 years ago) by duarte: Using apache xmlrpc version 3.0 in PyMolServerOutputStream
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 ?
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