 ../
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proteinstructure/
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357
(16 years ago)
by duarte:
Fixed bug: now does correctly quoting for any of the 3 cases: "", '' or ;;. Does also correctly multiline parsing of ;; quoted fields. Passed testing on cullpdb 90 (more than 9000 pdb entries)
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sadp/
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316
(17 years ago)
by lpetzo:
initial version of sadp
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tinker/
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347
(16 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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tools/
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350
(16 years ago)
by stehr:
Machine: added main and some other methods; MySQLConnection: added explicit handling of some exceptions
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Manifest.txt
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321
(17 years ago)
by stehr:
added test program for difference distance maps, updated Manifest to v0.8.5
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benchmarkGraphAlgorithm.java
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254
(17 years ago)
by duarte:
Also writing graph to file
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calculateGridDensity.java
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303
(17 years ago)
by stehr:
added writeResultsToFile()
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cnCoarseNbhood.java
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272
(17 years ago)
by lappe:
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cnEvalTargetNbhood.java
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271
(17 years ago)
by lappe:
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cnHashIterNbhood.java
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266
(17 years ago)
by lappe:
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cnex1.java
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265
(17 years ago)
by lappe:
final version
incl. pessimistic tie-break
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compareCMs.java
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215
(17 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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genDbGraph.java
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359
(16 years ago)
by duarte:
Now can do multiple contact types/cutoffs per pdb structure
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genGraph.java
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285
(17 years ago)
by duarte:
Fixed a few bugs in reading of list file
Better output and error messages
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hashIterNbhood.java
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267
(17 years ago)
by lappe:
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iterEvalNbhood.java
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269
(17 years ago)
by lappe:
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iterateNbhood.java
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202
(17 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
(17 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
(17 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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iterateUpperNbs.java
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268
(17 years ago)
by lappe:
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listInfoGain.java
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202
(17 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
(17 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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makeNbhTbl.java
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24
(18 years ago)
by stehr:
moved executables (classes with main function) to root directory
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maxInfoGain.java
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202
(17 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
(17 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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reconstruct.java
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349
(16 years ago)
by duarte:
Now writing also original pdb file
Fixed output of rmsd: now only few decimal figures output
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rewriteNBHood.java
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299
(17 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
(17 years ago)
by lappe:
1st version scoring with pdb_reps_graph_4_2 and full nbhood string
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scoreTargetMoves.java
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354
(16 years ago)
by duarte:
Fixed bug: was outputing an empty column before the 'total' column
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testClusterConnection.java
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202
(17 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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testDeltaDistanceMap.java
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327
(17 years ago)
by stehr:
fixed missing references to constants in class AA
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testGraph2Pml.java
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116
(17 years ago)
by filippis:
testGraph2Pml.java fixed according to changes made in Msdsd2Pdb.java
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testGraphAverager.java
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351
(16 years ago)
by stehr:
added some test programs to default package
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testGraphClustering.java
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351
(16 years ago)
by stehr:
added some test programs to default package
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testMySQLConnection.java
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202
(17 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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testPdb.java
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215
(17 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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testPyMol.java
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114
(17 years ago)
by duarte:
Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server
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testPymolServer.java
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203
(17 years ago)
by duarte:
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
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testResidueSelectionString.java
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351
(16 years ago)
by stehr:
added some test programs to default package
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writeTargetMoves.java
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313
(17 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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