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r546
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actionTools/ 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
graphAveraging/ 546 (11 years ago) by duarte: New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble Fixed bug in RIGEnsemble: was not working for cif files. Added a graph averaging output to main() in RIGEnsemble
ppi/ 539 (11 years ago) by stehr: some refactoring in TinkerRunner and related classes (moved forceConstant parameter from constructor to reconstruct method; made force field file type an enum)
proteinstructure/ 546 (11 years ago) by duarte: New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble Fixed bug in RIGEnsemble: was not working for cif files. Added a graph averaging output to main() in RIGEnsemble
sadp/ 501 (11 years ago) by duarte: Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
tinker/ 541 (11 years ago) by duarte: Added a FAST switch to reconstruct and a reconstructFast method in TinkerRunner: without simulated annealing tinker runs much faster.
tools/ 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
vecmath/ 524 (11 years ago) by duarte: Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files: - now reading (and requiring) TARGET record for CASP TS files - now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph. - in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100 - we allow PDB files without a HEADER, i.e. only ATOM lines New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
Manifest.txt 544 (11 years ago) by duarte: Updated version to 1.0-rc1
benchmarkGraphAlgorithm.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.
cnCoarseNbhood.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.
cnHashIterNbhood.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.
compareCMs.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.
dumpseq.java 535 (11 years ago) by duarte: Added option to output to standard output
genDbGraph.java 514 (11 years ago) by filippis: Latest scop and csa versions updated.
genGraph.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.
iterEvalNbhood.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.
iterateNbs.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.
iterateUpperNbs.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.
listInfoLoss.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
make-aglappe.sh 534 (11 years ago) by duarte: Now compiling also scripts in default package
makeNbhTbl.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.
minInfoGain.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
reconstruct.java 541 (11 years ago) by duarte: Added a FAST switch to reconstruct and a reconstructFast method in TinkerRunner: without simulated annealing tinker runs much faster.
rewriteNBHood.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.
scoreTargetMoves.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testClusterConnection.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.
testDeltaDistanceMap.java 517 (11 years ago) by duarte: Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps. Changed all other classes using Alignment to accommodate this. NOTE: graph averaging hasn't been tested after the change
testGetChains.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.
testGraphAverager.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testJUNGframework.java 542 (11 years ago) by duarte: Using Ca/Cg for testing as Ca/Cb is now allowed
testMySQLConnection.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.
testPyMol.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.
testResidueSelectionString.java 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.
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