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r938
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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
litNet/ 788 (10 years ago) by filippis: white TO talyn
graphAveraging/ 811 (10 years ago) by duarte: New options -e and -i in reconstruct (for forcing angle constraints)
sequence/ 883 (10 years ago) by stehr: some cosmetic changes
tools/ 917 (9 years ago) by stehr: bugfix for last checkin (null pointer exception)
tests/ 919 (9 years ago) by duarte: Fixed bug: was not handling correctly sequences with 'X' in reconstruction Fixed bug: Pdb.getPhi/Psi were failing because hasCoordinates(int,String) was NullPointing for unobserved residues. Added test case for getAllPhiPsi
proteinstructure/ 925 (9 years ago) by winkelma: merged tinker changes into trunk
actionTools/ 925 (9 years ago) by winkelma: merged tinker changes into trunk
tinker/ 925 (9 years ago) by winkelma: merged tinker changes into trunk
embed/ 937 (9 years ago) by gmueller:
features/ 938 (9 years ago) by stehr: fixed bugs in getDescription()
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.
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.
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)
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.
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.
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
reconstruct.java 834 (10 years ago) by duarte: Now using file name as id for reports when reconstructing from cm files.
mapMutations.java 839 (10 years ago) by stehr: added option to keep pymol script
mirrorIt.java 844 (10 years ago) by duarte: New script to mirror a pdb
alignSeq.java 847 (10 years ago) by stehr: new executable for pairwise (global) sequence alignment
analyseHistone.java 866 (10 years ago) by duarte: Refactored Residue->PolResidue. Now Residue will be the proper implementation of a residue as part of a Pdb
Manifest.txt 882 (10 years ago) by stehr: updated version to 1.2.0 (forgot to change version number in last tag)
writePerAtomDistancesToBFactor.java 887 (10 years ago) by stehr: rewrote method getPerAtomDistances such that atom serials do not need to match between the two structures (matching corresponding atoms based in resser)
scoreDecoys.java 904 (10 years ago) by duarte: Moved all decoy scoring stuff to its own package. Split CombinedScorer into two classes AtomCombinedScorer and ResCombinedScorer. Made combined scorer more efficient: now loading only once the graphs.
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