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r804
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actionTools/ 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
embed/ 804 (10 years ago) by duarte: Made Bound[][] bounds a member, thus changing the signature of most methods. Refactored getBoundsAllPairs(bounds) to better name computeTriangleInequality: now it uses as input the bounds member variable and updates it as output.
graphAveraging/ 788 (10 years ago) by filippis: white TO talyn
litNet/ 788 (10 years ago) by filippis: white TO talyn
ppi/ 788 (10 years ago) by filippis: white TO talyn
proteinstructure/ 799 (10 years ago) by duarte: Fixed in BoundsSmoother: now the lower bound will be set to the triangle inequality value only if the newly found lower bound is bigger than the hard spheres bound. Now we also introduce contiguous CA distance constraints (3.8) In main now checking for violations to the full bounds matrix. New method in Pdb for getting distance matrix as Jama object
sadp/ 501 (11 years ago) by duarte: Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
sequence/ 801 (10 years ago) by duarte: Fixed bug: was not doing correctly the sanity checks in getAlignmentFullSeqs
tests/ 788 (10 years ago) by filippis: white TO talyn
tinker/ 795 (10 years ago) by duarte: Fixed bug (hopefully): was not closing drmaa session after every runParallelDistgeom, only in the shutdown hook. We need to close it always in case there is more than one run within the same instance of the JVM.
tools/ 788 (10 years ago) by filippis: white TO talyn
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 730 (11 years ago) by duarte: Updated version to 1.1.0
addSeq2Mcma.java 769 (10 years ago) by stehr: added methods and executables to calculate 3d superimpositions using PolyposeRunner
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.
benchmarkGraphAlgorithm.java 788 (10 years ago) by filippis: white TO talyn
calculateGridDensity.java 788 (10 years ago) by filippis: white TO talyn
compareAlignments.java 769 (10 years ago) by stehr: added methods and executables to calculate 3d superimpositions using PolyposeRunner
compareCMs.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
computeEnergies.java 573 (11 years ago) by duarte: Fixed script: was exiting after computing native energy!
createGraphDb.sh 790 (10 years ago) by filippis: white TO talyn
doClassifySingleModels.sh 789 (10 years ago) by filippis: white TO talyn
dumppdb.java 794 (10 years ago) by duarte: Got rid of hard coded mysql server references in scripts.
dumpseq.java 794 (10 years ago) by duarte: Got rid of hard coded mysql server references in scripts.
genDbGraph.java 794 (10 years ago) by duarte: Got rid of hard coded mysql server references in scripts.
genGraph.java 794 (10 years ago) by duarte: Got rid of hard coded mysql server references in scripts.
make-aglappe.sh 777 (10 years ago) by duarte: Added drmaa.jar to make file
pairwiseSeqId.java 774 (10 years ago) by stehr: updated output of pairwiseSeqId
reconstruct.java 784 (10 years ago) by duarte: Minor change in help string
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)
superimposeMult.java 771 (10 years ago) by stehr: now taking command line parameters
testClusterConnection.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testDbRIGraph.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
testGetChains.java 788 (10 years ago) by filippis: white TO talyn
testGraph2Pml.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testJUNGframework.java 660 (11 years ago) by duarte: Put another test: finding edges is independent of order of indices given for UNDIRECTED.
testMySQLConnection.java 792 (10 years ago) by duarte: Cleaned up and updated the mysql connection example
testPdb.java 793 (10 years ago) by duarte: Cleaned up and updated the testPdb example code.
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.
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