 ../
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proteinstructure/
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355
(13 years ago)
by duarte:
FIXED BUG: now doesn't fail with records that are delimited with \n; ;\n
Method tokeniseFields is now completely rewritten: is what does all the magic of parsing all the oddities of the mmcif format
Using RandomAccessFile to open the file only once and then seek to the positions we need to scan at each point. Might be slower due to the RandomAccessFile that does no buffering. Also maybe because the new tokenisation is not very optimal
Now parseCifFile does the whole parsing calling also the submethods instead of calling them in the constructor
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sadp/
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316
(13 years ago)
by lpetzo:
initial version of sadp
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tinker/
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347
(13 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
(13 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
(13 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
(13 years ago)
by duarte:
Also writing graph to file
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calculateGridDensity.java
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303
(13 years ago)
by stehr:
added writeResultsToFile()
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cnCoarseNbhood.java
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272
(13 years ago)
by lappe:
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cnEvalTargetNbhood.java
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271
(13 years ago)
by lappe:
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cnHashIterNbhood.java
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266
(13 years ago)
by lappe:
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cnex1.java
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265
(13 years ago)
by lappe:
final version
incl. pessimistic tie-break
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compareCMs.java
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215
(13 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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285
(13 years ago)
by duarte:
Fixed a few bugs in reading of list file
Better output and error messages
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genGraph.java
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285
(13 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
(13 years ago)
by lappe:
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iterEvalNbhood.java
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269
(13 years ago)
by lappe:
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iterateNbhood.java
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202
(13 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
(13 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
(13 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
(13 years ago)
by lappe:
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listInfoGain.java
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202
(13 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
(13 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
(15 years ago)
by stehr:
moved executables (classes with main function) to root directory
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maxInfoGain.java
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202
(13 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
(13 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
(13 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
(13 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
(13 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
(13 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
(13 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
(13 years ago)
by stehr:
fixed missing references to constants in class AA
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testGraph2Pml.java
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116
(14 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
(13 years ago)
by stehr:
added some test programs to default package
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testGraphClustering.java
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351
(13 years ago)
by stehr:
added some test programs to default package
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testMySQLConnection.java
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202
(13 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
(13 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
(14 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
(13 years ago)
by duarte:
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
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testResidueSelectionString.java
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351
(13 years ago)
by stehr:
added some test programs to default package
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writeTargetMoves.java
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313
(13 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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