 ../
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tools/
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381
(14 years ago)
by lpetzo:
a generic pair class
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tinker/
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393
(14 years ago)
by duarte:
Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
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sadp/
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416
(14 years ago)
by lpetzo:
- changed the identation mode
- added some comments
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proteinstructure/
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425
(14 years ago)
by duarte:
Fixed bug in Graph constructor from sadp's ContactMap
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actionTools/
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417
(14 years ago)
by lpetzo:
abstract class implementing the Runnable interface
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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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testResidueSelectionString.java
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351
(14 years ago)
by stehr:
added some test programs to default package
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testPymolServer.java
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203
(15 years ago)
by duarte:
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
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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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testPdb.java
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215
(15 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
(15 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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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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389
(14 years ago)
by stehr:
implemented tinker reconstruction of consensus graphs created with GraphAverager
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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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testDeltaDistanceMap.java
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327
(14 years ago)
by stehr:
fixed missing references to constants in class AA
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testClusterConnection.java
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202
(15 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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390
(14 years ago)
by duarte:
Not creating anymore the score table
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runGenDbGraph.sh
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395
(14 years ago)
by duarte:
Initial commit. Provisional script to use the genDbGraph program when iterating through loads of structures, because of the "memory leak" problem is not possible to use directly genDbGraph to iterate over many structures (~1000)
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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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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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reconstruct.java
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393
(14 years ago)
by duarte:
Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
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minInfoGain.java
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202
(15 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
(15 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
(16 years ago)
by stehr:
moved executables (classes with main function) to root directory
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listInfoLoss.java
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202
(15 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
(15 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
(14 years ago)
by lappe:
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iterateUpperNbhood.java
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202
(15 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
(15 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
(15 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
(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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genGraph.java
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396
(14 years ago)
by filippis:
Added mode option in genDbGraph whether to find and store info for the residues (SCOP,NACCESS,EC,CSA,...)
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genDbGraph.java
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412
(14 years ago)
by filippis:
Changes in Pdb
-checkConsurfHssp: in the mistakes calculated I add now at the end the difference between the number of residues and the number of consurf scores
-writeAtomLines has now a boolean argument called pdbCompatible: if pdbCompatible is true, then only the first character of chainCode and not the 'whole' chainCode is exported to the file.
-another WriteAtomLines has also been added without this extra argument for backwards compatibility: default value for pdbCompatible is false
-dump2pdbfile has also been changed in similar way
-runDssp and runNaccess now call the above methods with true pdbCompatible
Changes in genDbGraph
-1 summary output line has been added to provide info about csa, naccess, scop, ec, dssp, ...
-DSSP is run with 3state
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createGraphDb.sh
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413
(14 years ago)
by filippis:
createGraphDb.sh
-pchain_code is now modified to VARCHAR(2) from CHAR(1) due to pdbase_chain_code
-index for pdb_residue_info table added
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compareCMs.java
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215
(15 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
(14 years ago)
by lappe:
final version
incl. pessimistic tie-break
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cnHashIterNbhood.java
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266
(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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cnCoarseNbhood.java
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272
(14 years ago)
by lappe:
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calculateGridDensity.java
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303
(14 years ago)
by stehr:
added writeResultsToFile()
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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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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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