 ../
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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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tinker/
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368
(16 years ago)
by duarte:
Now parsing tinker's error function value, changed report file format (again!!)
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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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sadp/
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371
(16 years ago)
by lpetzo:
Class ContactMap:
- Exception ContactMapConstructionError is thrown if the construction of a contact map from a Graph object fails.
- changed method to determine the number of nodes of a graph object.
- changed method to iterate through the set of edges of the graph (though the previous version seemed to be much more efficient ...)
Class SADP:
- added some new members controlling to input order of the contact maps (preservedInputOrder)
- the progress status of the run() method is send to a Retriever object
- added getters and setter for all data member.
- implemented methods to compute the sequence alignment and the node matching
- a couple of changes in method main
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proteinstructure/
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374
(16 years ago)
by duarte:
Fixed bug: getContacts was not copying weights
Got rid of useless copyKeepingNodes(), made main Graph constructor public. Some new setters and getters
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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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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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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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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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testPymolServer.java
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203
(17 years ago)
by duarte:
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
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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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benchmarkGraphAlgorithm.java
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254
(17 years ago)
by duarte:
Also writing graph to file
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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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hashIterNbhood.java
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267
(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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iterEvalNbhood.java
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269
(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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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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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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calculateGridDensity.java
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303
(17 years ago)
by stehr:
added writeResultsToFile()
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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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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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testDeltaDistanceMap.java
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327
(17 years ago)
by stehr:
fixed missing references to constants in class AA
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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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testGraphAverager.java
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351
(16 years ago)
by stehr:
added some test programs to default package
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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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reconstruct.java
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373
(16 years ago)
by duarte:
Fixed (yet again) the report output, now also outputting size (number of residues) of protein
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scoreTargetMoves.java
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375
(16 years ago)
by duarte:
Cleaned up. More command line parameters
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