 ../
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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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tools/
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381
(16 years ago)
by lpetzo:
a generic pair class
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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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tinker/
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393
(16 years ago)
by duarte:
Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
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proteinstructure/
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402
(16 years ago)
by duarte:
Forgot CiffilePdb!: not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
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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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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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389
(16 years ago)
by stehr:
implemented tinker reconstruction of consensus graphs created with GraphAverager
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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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reconstruct.java
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393
(16 years ago)
by duarte:
Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
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runGenDbGraph.sh
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395
(16 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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genGraph.java
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396
(16 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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399
(16 years ago)
by stehr:
added class PairwiseSequenceAlignment
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