 ../
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proteinstructure/
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352
(14 years ago)
by stehr:
Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
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tools/
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350
(14 years ago)
by stehr:
Machine: added main and some other methods; MySQLConnection: added explicit handling of some exceptions
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tinker/
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347
(14 years ago)
by duarte:
Writing report to file instead of standard output
Catching unknown errors in runDistgeom (all other non-zero exit values)
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sadp/
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316
(14 years ago)
by lpetzo:
initial version of sadp
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testResidueSelectionString.java
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351
(14 years ago)
by stehr:
added some test programs to default package
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testGraphClustering.java
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351
(14 years ago)
by stehr:
added some test programs to default package
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testGraphAverager.java
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351
(14 years ago)
by stehr:
added some test programs to default package
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reconstruct.java
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349
(14 years ago)
by duarte:
Now writing also original pdb file
Fixed output of rmsd: now only few decimal figures output
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scoreTargetMoves.java
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339
(14 years ago)
by duarte:
Now much faster thanks to hashing on pairs (separate script create the hash tables)
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testDeltaDistanceMap.java
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327
(14 years ago)
by stehr:
fixed missing references to constants in class AA
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Manifest.txt
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321
(14 years ago)
by stehr:
added test program for difference distance maps, updated Manifest to v0.8.5
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writeTargetMoves.java
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313
(14 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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calculateGridDensity.java
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303
(14 years ago)
by stehr:
added writeResultsToFile()
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rewriteNBHood.java
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299
(14 years ago)
by lappe:
only one out of both BB/SC insertion per moves based
on sc/bb domin. out of temp shell
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rewriteNBHood_parallel.java
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291
(14 years ago)
by lappe:
1st version scoring with pdb_reps_graph_4_2 and full nbhood string
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genGraph.java
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285
(14 years ago)
by duarte:
Fixed a few bugs in reading of list file
Better output and error messages
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genDbGraph.java
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285
(14 years ago)
by duarte:
Fixed a few bugs in reading of list file
Better output and error messages
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cnCoarseNbhood.java
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272
(14 years ago)
by lappe:
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cnEvalTargetNbhood.java
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271
(14 years ago)
by lappe:
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iterEvalNbhood.java
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269
(14 years ago)
by lappe:
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iterateUpperNbs.java
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268
(14 years ago)
by lappe:
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hashIterNbhood.java
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267
(14 years ago)
by lappe:
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cnHashIterNbhood.java
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266
(14 years ago)
by lappe:
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cnex1.java
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265
(14 years ago)
by lappe:
final version
incl. pessimistic tie-break
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benchmarkGraphAlgorithm.java
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254
(14 years ago)
by duarte:
Also writing graph to file
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testPdb.java
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215
(14 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
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compareCMs.java
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215
(14 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
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testPymolServer.java
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203
(14 years ago)
by duarte:
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
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iterateNbhood.java
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202
(14 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
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testClusterConnection.java
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202
(14 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
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testMySQLConnection.java
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202
(14 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
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listInfoGain.java
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202
(14 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
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iterateUpperNbhood.java
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202
(14 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
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listInfoLoss.java
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202
(14 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
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maxInfoGain.java
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202
(14 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
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minInfoGain.java
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202
(14 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
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iterateNbs.java
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202
(14 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
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testGraph2Pml.java
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116
(15 years ago)
by filippis:
testGraph2Pml.java fixed according to changes made in Msdsd2Pdb.java
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testPyMol.java
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114
(15 years ago)
by duarte:
Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server
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makeNbhTbl.java
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24
(16 years ago)
by stehr:
moved executables (classes with main function) to root directory
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