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r788
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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()
tools/ 788 (10 years ago) by filippis: white TO talyn
tinker/ 786 (10 years ago) by duarte: Implemented a more robust approach to failure of jobs in parallel distgeom. Now we send 1.1*n jobs and require that only n of them finish successfully. These solves many issues: even if 0.1*n jobs fail the whole thing will be successful, if a jobs hangs forever we will not wait for it to finish.
tests/ 788 (10 years ago) by filippis: white TO talyn
sequence/ 788 (10 years ago) by filippis: white TO talyn
sadp/ 501 (11 years ago) by duarte: Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
proteinstructure/ 788 (10 years ago) by filippis: white TO talyn
ppi/ 788 (10 years ago) by filippis: white TO talyn
litNet/ 788 (10 years ago) by filippis: white TO talyn
graphAveraging/ 788 (10 years ago) by filippis: white TO talyn
embed/ 787 (10 years ago) by duarte: First implementation of the embedding part of the EMBED algorithm by Havel: from an exact complete distance matrix gives 3d coordinates for the embedding.
actionTools/ 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 788 (10 years ago) by filippis: white TO talyn
testJUNGframework.java 660 (11 years ago) by duarte: Put another test: finding edges is independent of order of indices given for UNDIRECTED.
testGraph2Pml.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testGetChains.java 788 (10 years ago) by filippis: white TO talyn
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
testDbRIGraph.java 788 (10 years ago) by filippis: white TO talyn
testClusterConnection.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
superimposeMult.java 771 (11 years ago) by stehr: now taking command line parameters
runMD.java 715 (11 years ago) by duarte: New option -s to do split output. Now converting final gro file to pdb Fixed bugs: - now flushing correctly the gromacs.log (by closing log) - now properly cleaning up temp files (the ones written to /tmp)
reconstruct.java 784 (10 years ago) by duarte: Minor change in help string
pairwiseSeqId.java 774 (11 years ago) by stehr: updated output of pairwiseSeqId
make-aglappe.sh 777 (11 years ago) by duarte: Added drmaa.jar to make file
genGraph.java 788 (10 years ago) by filippis: white TO talyn
genDbGraph.java 788 (10 years ago) by filippis: white TO talyn
dumpseq.java 788 (10 years ago) by filippis: white TO talyn
dumppdb.java 788 (10 years ago) by filippis: white TO talyn
doClassifySingleModels.sh 580 (11 years ago) by filippis: createGraphDb: -the node_id in the single_model_node table changed to AUTO_INCREMENT doClassifySingleModels: -the interSS for CR added RIGraph: -write_graph_to_db methods treat the node_id field in the single_model_node table as AUTO_INCREMENT -write_graph_to_motiffile method added
createGraphDb.sh 580 (11 years ago) by filippis: createGraphDb: -the node_id in the single_model_node table changed to AUTO_INCREMENT doClassifySingleModels: -the interSS for CR added RIGraph: -write_graph_to_db methods treat the node_id field in the single_model_node table as AUTO_INCREMENT -write_graph_to_motiffile method added
computeEnergies.java 573 (11 years ago) by duarte: Fixed script: was exiting after computing native energy!
compareCMs.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
compareAlignments.java 769 (11 years ago) by stehr: added methods and executables to calculate 3d superimpositions using PolyposeRunner
calculateGridDensity.java 788 (10 years ago) by filippis: white TO talyn
benchmarkGraphAlgorithm.java 788 (10 years ago) by filippis: white TO talyn
averageGraph.java 782 (10 years ago) by duarte: New constructor with no arguments for MySQLConnection, it reads connection parameters from ~/.my.cnf. Modified accordingly the executable classes reconstruct and averageGraph. Now they will only work if user has a .my.cnf.
addSeq2Mcma.java 769 (11 years ago) by stehr: added methods and executables to calculate 3d superimpositions using PolyposeRunner
Manifest.txt 730 (11 years ago) by duarte: Updated version to 1.1.0
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