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r822
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actionTools/ 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
ppi/ 788 (10 years ago) by filippis: white TO talyn
tools/ 788 (10 years ago) by filippis: white TO talyn
litNet/ 788 (10 years ago) by filippis: white TO talyn
sequence/ 806 (10 years ago) by duarte: New method contains().
tinker/ 809 (10 years ago) by duarte: Introduced some more checks for validity of contact types.
graphAveraging/ 811 (10 years ago) by duarte: New options -e and -i in reconstruct (for forcing angle constraints)
tests/ 813 (10 years ago) by duarte: Fixed runNaccess to use unique file names and documented it. Wrote also a junit test case for it.
proteinstructure/ 822 (10 years ago) by duarte: Now Reconstructer can also take RIGraphs with "unobserved" residues (i.e. with missing nodes). Model pdb files that Reconstructer creates now contain strictly only CA atoms.
embed/ 822 (10 years ago) by duarte: Now Reconstructer can also take RIGraphs with "unobserved" residues (i.e. with missing nodes). Model pdb files that Reconstructer creates now contain strictly only CA atoms.
testPymolServer.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.
testResidueSelectionString.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.
testPyMol.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.
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
computeEnergies.java 573 (11 years ago) by duarte: Fixed script: was exiting after computing native energy!
testJUNGframework.java 660 (11 years ago) by duarte: Put another test: finding edges is independent of order of indices given for UNDIRECTED.
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)
Manifest.txt 730 (11 years ago) by duarte: Updated version to 1.1.0
addSeq2Mcma.java 769 (11 years ago) by stehr: added methods and executables to calculate 3d superimpositions using PolyposeRunner
compareAlignments.java 769 (11 years ago) by stehr: added methods and executables to calculate 3d superimpositions using PolyposeRunner
superimposeMult.java 771 (11 years ago) by stehr: now taking command line parameters
make-aglappe.sh 777 (11 years ago) by duarte: Added drmaa.jar to make file
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.
testGetChains.java 788 (10 years ago) by filippis: white TO talyn
benchmarkGraphAlgorithm.java 788 (10 years ago) by filippis: white TO talyn
testDbRIGraph.java 788 (10 years ago) by filippis: white TO talyn
calculateGridDensity.java 788 (10 years ago) by filippis: white TO talyn
doClassifySingleModels.sh 789 (10 years ago) by filippis: white TO talyn
createGraphDb.sh 790 (10 years ago) by filippis: white TO talyn
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.
genGraph.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.
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.
reconstruct.java 812 (10 years ago) by duarte: Fixed bug: in check of input of intervals wasn't checking ig intervals was null.
pairwiseSeqId.java 815 (10 years ago) by stehr: new executables for pairwise all-against-all sequence alignments (pairwiseSeqId) and for calculating surface accessibilities and writing them to the b-factor column
writeSASAtoBFactor.java 819 (10 years ago) by stehr: new command line tools for visualizing surface accessibility and for printing information about a mutated site in a protein structure
mapMutations.java 819 (10 years ago) by stehr: new command line tools for visualizing surface accessibility and for printing information about a mutated site in a protein structure
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