 ../
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tools/
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203
(17 years ago)
by duarte:
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
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tinker/
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333
(17 years ago)
by duarte:
Now does correct atom mapping for any atom of any residue ONLY for amber prm files
createConstraints does not work yet with multi atom contact types
Got rid of all the commented out mapAtoms code + some refactoring
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sadp/
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316
(17 years ago)
by lpetzo:
initial version of sadp
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proteinstructure/
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332
(17 years ago)
by stehr:
added constructor for trivial alignment, renamed getSequence to getAlignedSequence
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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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testPymolServer.java
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203
(17 years ago)
by duarte:
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
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testPyMol.java
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114
(18 years ago)
by duarte:
Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server
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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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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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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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testDeltaDistanceMap.java
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327
(17 years ago)
by stehr:
fixed missing references to constants in class AA
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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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scoreTargetMoves.java
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312
(17 years ago)
by lappe:
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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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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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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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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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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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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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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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iterateUpperNbs.java
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268
(17 years ago)
by lappe:
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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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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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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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iterEvalNbhood.java
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269
(17 years ago)
by lappe:
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hashIterNbhood.java
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267
(17 years ago)
by lappe:
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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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genDbGraph.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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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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cnex1.java
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265
(17 years ago)
by lappe:
final version
incl. pessimistic tie-break
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cnHashIterNbhood.java
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266
(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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cnCoarseNbhood.java
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272
(17 years ago)
by lappe:
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calculateGridDensity.java
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303
(17 years ago)
by stehr:
added writeResultsToFile()
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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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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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