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r438
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actionTools/ 437 (12 years ago) by lpetzo: an abstract getter
proteinstructure/ 438 (12 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
sadp/ 426 (12 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
tinker/ 420 (12 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
tools/ 419 (12 years ago) by duarte: Re-branching for JUNG2 development
Manifest.txt 419 (12 years ago) by duarte: Re-branching for JUNG2 development
benchmarkGraphAlgorithm.java 424 (12 years ago) by duarte: Added last i/o method from old Graph (write to file in Ioannis network format) Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods Fixed the write_graph_to_file method name in executables in default package
calculateGridDensity.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
cnCoarseNbhood.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
cnEvalTargetNbhood.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
cnHashIterNbhood.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
cnex1.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
compareCMs.java 423 (12 years ago) by duarte: New methods in RIGraph copy() and compare(other) Basic testing of copy introduced on testJUNGframework
createGraphDb.sh 419 (12 years ago) by duarte: Re-branching for JUNG2 development
genDbGraph.java 438 (12 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
genGraph.java 431 (12 years ago) by duarte: Fixed bug: was not working with crossed contacts (with "/") because the "/" was not allowed in file names. Now replacing / with :
hashIterNbhood.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
iterEvalNbhood.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
iterateNbhood.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
iterateNbs.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
iterateUpperNbhood.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
iterateUpperNbs.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
listInfoGain.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
listInfoLoss.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
makeNbhTbl.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
maxInfoGain.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
minInfoGain.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
reconstruct.java 420 (12 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
rewriteNBHood.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
rewriteNBHood_parallel.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
runGenDbGraph.sh 419 (12 years ago) by duarte: Re-branching for JUNG2 development
scoreTargetMoves.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
testClusterConnection.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
testDeltaDistanceMap.java 420 (12 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
testGraph2Pml.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
testGraphAverager.java 424 (12 years ago) by duarte: Added last i/o method from old Graph (write to file in Ioannis network format) Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods Fixed the write_graph_to_file method name in executables in default package
testGraphClustering.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
testJUNGframework.java 430 (12 years ago) by duarte: Fixed tester after changes in getAllCommonNnhSizes
testMySQLConnection.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
testPdb.java 424 (12 years ago) by duarte: Added last i/o method from old Graph (write to file in Ioannis network format) Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods Fixed the write_graph_to_file method name in executables in default package
testPyMol.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
testPymolServer.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
testResidueSelectionString.java 422 (12 years ago) by duarte: Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
writeTargetMoves.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
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