../
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actionTools/
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447
(16 years ago)
by lpetzo:
class Getter:
- function get() is now throwing GetterError exception
class GetterError:
- wrapper exception for all type of exceptions thrown in the get() function of class Getter
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proteinstructure/
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444
(16 years ago)
by filippis:
Pdb.java:
-calc_atom_dist_matrix method added
-calc_dist_matrix works also for multi atom contact types by choosing the min distance
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sadp/
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426
(16 years ago)
by duarte:
Now PairWiseAlignmentConverter and PairwiseAlignmentGraphConverter work in the new JUNG framework.
New class IntPairComparator
Now sorting output in RIGraph.write_graph_to_file
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tinker/
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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tools/
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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Manifest.txt
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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benchmarkGraphAlgorithm.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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calculateGridDensity.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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cnCoarseNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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cnEvalTargetNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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cnHashIterNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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cnex1.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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compareCMs.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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createGraphDb.sh
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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genDbGraph.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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genGraph.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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hashIterNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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iterEvalNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateNbs.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateUpperNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateUpperNbs.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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listInfoGain.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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listInfoLoss.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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makeNbhTbl.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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maxInfoGain.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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minInfoGain.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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reconstruct.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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rewriteNBHood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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rewriteNBHood_parallel.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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scoreTargetMoves.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testClusterConnection.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testDeltaDistanceMap.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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testGetChains.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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testGraph2Pml.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testGraphAverager.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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testGraphClustering.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testJUNGframework.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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testMySQLConnection.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testPdb.java
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441
(16 years ago)
by duarte:
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
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testPyMol.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testPymolServer.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testResidueSelectionString.java
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422
(16 years ago)
by duarte:
Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
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writeTargetMoves.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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