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r506
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tools/ 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
tinker/ 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
sadp/ 501 (11 years ago) by duarte: Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
proteinstructure/ 506 (11 years ago) by duarte: New method to convert secondary structure
graphAveraging/ 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
actionTools/ 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
writeTargetMoves.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testResidueSelectionString.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testPymolServer.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testPyMol.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testPdb.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testMySQLConnection.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testJUNGframework.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testGraphAverager.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testGraph2Pml.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testGetChains.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testDeltaDistanceMap.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testDbRIGraph.java 503 (11 years ago) by filippis: createGraphDb: -scop_graph table added -!!!!residue serial fields (num, i_num, j_num) are changed to unsigned !!!!ProtStructGraph: -interSSE variable added -getResidueSerial abstract method added -restrictContactsBetweenSs method added !!!!AIGraph: -getResidueSerial method added RIGraph: -!!!!getResidueSerial method added -scop graphs are written to db correctly -interSSE variable taken into account for CR db field DbRIgraph: -changes made so to be able to read from db using a scop id -interSSE and minSeqSep are set now in get_db_graph_info() -!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs. testDbRIGraph added: It reads one graph from a source db based either -on pdbcode, chaincode and graph properties or -on scop id and graph properties or -on a graph id and it writes the graph to a destination db. Pdb: -unused scop regions are now removed in restrictToScopDomain -unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet -!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence CatalSiteSet: - removeCatalSiteRes(int resser) method added CatalyticSite: -remRes(int resser) method added Scop: -remove(ScopRegion e) method added genDbGraph:Comments only added to demonstrate new functionality. -comment added to show how to use restrictContactsBetweenSs -comment added to show how to use restrictToScopDomain -runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results -runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
testClusterConnection.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
scoreTargetMoves.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
rewriteNBHood_parallel.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
rewriteNBHood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
reconstruct.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
minInfoGain.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
maxInfoGain.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
makeNbhTbl.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
make-aglappe.sh 496 (11 years ago) by duarte: Rescued the make-aglappe.sh script from the old trunk
listInfoLoss.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
listInfoGain.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
iterateUpperNbs.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
iterateUpperNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
iterateNbs.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
iterateNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
iterEvalNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
hashIterNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
genGraph.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
genDbGraph.java 503 (11 years ago) by filippis: createGraphDb: -scop_graph table added -!!!!residue serial fields (num, i_num, j_num) are changed to unsigned !!!!ProtStructGraph: -interSSE variable added -getResidueSerial abstract method added -restrictContactsBetweenSs method added !!!!AIGraph: -getResidueSerial method added RIGraph: -!!!!getResidueSerial method added -scop graphs are written to db correctly -interSSE variable taken into account for CR db field DbRIgraph: -changes made so to be able to read from db using a scop id -interSSE and minSeqSep are set now in get_db_graph_info() -!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs. testDbRIGraph added: It reads one graph from a source db based either -on pdbcode, chaincode and graph properties or -on scop id and graph properties or -on a graph id and it writes the graph to a destination db. Pdb: -unused scop regions are now removed in restrictToScopDomain -unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet -!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence CatalSiteSet: - removeCatalSiteRes(int resser) method added CatalyticSite: -remRes(int resser) method added Scop: -remove(ScopRegion e) method added genDbGraph:Comments only added to demonstrate new functionality. -comment added to show how to use restrictContactsBetweenSs -comment added to show how to use restrictToScopDomain -runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results -runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
dumpseq.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
createGraphDb.sh 503 (11 years ago) by filippis: createGraphDb: -scop_graph table added -!!!!residue serial fields (num, i_num, j_num) are changed to unsigned !!!!ProtStructGraph: -interSSE variable added -getResidueSerial abstract method added -restrictContactsBetweenSs method added !!!!AIGraph: -getResidueSerial method added RIGraph: -!!!!getResidueSerial method added -scop graphs are written to db correctly -interSSE variable taken into account for CR db field DbRIgraph: -changes made so to be able to read from db using a scop id -interSSE and minSeqSep are set now in get_db_graph_info() -!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs. testDbRIGraph added: It reads one graph from a source db based either -on pdbcode, chaincode and graph properties or -on scop id and graph properties or -on a graph id and it writes the graph to a destination db. Pdb: -unused scop regions are now removed in restrictToScopDomain -unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet -!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence CatalSiteSet: - removeCatalSiteRes(int resser) method added CatalyticSite: -remRes(int resser) method added Scop: -remove(ScopRegion e) method added genDbGraph:Comments only added to demonstrate new functionality. -comment added to show how to use restrictContactsBetweenSs -comment added to show how to use restrictToScopDomain -runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results -runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
compareCMs.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
cnex1.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
cnHashIterNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
cnEvalTargetNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
cnCoarseNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
calculateGridDensity.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
benchmarkGraphAlgorithm.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
Manifest.txt 493 (11 years ago) by stehr: Changed version number to 0.9
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