 ../
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proteinstructure/
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391
(16 years ago)
by stehr:
started implementing a wrapper for the Maxcluster application (some related code is now in SimilarityGraph but should be moved to MaxClusterRunner in the future)
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sadp/
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386
(16 years ago)
by lpetzo:
MODIFICATIONS
-------------
class SADP:
- added exception handling stuff for exceptions thrown by class Alignment
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tools/
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381
(16 years ago)
by lpetzo:
a generic pair class
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tinker/
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379
(16 years ago)
by stehr:
redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object;
updated reconstruct.java to make use of the new TinkerRunner method;
updated GraphAverager: now assigning edgetype and cutoff to consensus graph
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actionTools/
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369
(16 years ago)
by lpetzo:
This package provides a set of very basic abstract classes serving as interfaces to very basic tasks such as:
1. condition checkings (class Checker),
2. data retrieval (class Retriever) and
3. pure workers that perform any kind of actions that do not depend on any kind of input data (class Doer).
Each of these classes is a subclass of class Action which only purpose is to store the object affected by the subclasses action method.
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scoreTargetMoves.java
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390
(16 years ago)
by duarte:
Not creating anymore the score table
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testGraphAverager.java
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389
(16 years ago)
by stehr:
implemented tinker reconstruction of consensus graphs created with GraphAverager
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reconstruct.java
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379
(16 years ago)
by stehr:
redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object;
updated reconstruct.java to make use of the new TinkerRunner method;
updated GraphAverager: now assigning edgetype and cutoff to consensus graph
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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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testResidueSelectionString.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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testDeltaDistanceMap.java
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327
(17 years ago)
by stehr:
fixed missing references to constants in class AA
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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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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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calculateGridDensity.java
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303
(17 years ago)
by stehr:
added writeResultsToFile()
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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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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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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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iterEvalNbhood.java
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269
(17 years ago)
by lappe:
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iterateUpperNbs.java
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268
(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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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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benchmarkGraphAlgorithm.java
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254
(17 years ago)
by duarte:
Also writing graph to file
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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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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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testPymolServer.java
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203
(17 years ago)
by duarte:
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
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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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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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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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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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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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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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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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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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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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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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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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