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r916
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tools/ 916 (9 years ago) by stehr: New convenience methods in MySQLConnection for simple retrieval of String, Integer and Double arrays from an SQL query. Some documentation clean-up.
tinker/ 885 (10 years ago) by duarte: Major change: now hydrogens are read in Pdb and subclasses New getChirality method in Residue. Added some more unit tests.
tests/ 885 (10 years ago) by duarte: Major change: now hydrogens are read in Pdb and subclasses New getChirality method in Residue. Added some more unit tests.
sequence/ 883 (10 years ago) by stehr: some cosmetic changes
sadp/ 501 (11 years ago) by duarte: Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
proteinstructure/ 916 (9 years ago) by stehr: New convenience methods in MySQLConnection for simple retrieval of String, Integer and Double arrays from an SQL query. Some documentation clean-up.
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)
features/ 915 (9 years ago) by stehr: fixed an interesting bug where a recursive function call would lead to a stack overflow exception
embed/ 884 (10 years ago) by duarte: Major commit: - change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors - added many tests and test files for Pdb (and merged some already existing tests from the default package) - removed obsolete classes related to msd - bug fix: PdbfilePdb now properly reads files with alt codes - all tests passed
actionTools/ 877 (10 years ago) by stehr: Testing package-info.java for adding javadoc comment at the package level
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
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)
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 793 (10 years ago) by duarte: Cleaned up and updated the testPdb example code.
testMySQLConnection.java 792 (10 years ago) by duarte: Cleaned up and updated the mysql connection example
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.
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 (10 years ago) by stehr: now taking command line parameters
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.
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 834 (10 years ago) by duarte: Now using file name as id for reports when reconstructing from cm files.
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
mirrorIt.java 844 (10 years ago) by duarte: New script to mirror a pdb
mapMutations.java 839 (10 years ago) by stehr: added option to keep pymol script
make-aglappe.sh 777 (10 years ago) by duarte: Added drmaa.jar to make file
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.
dumpseq.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.
doClassifySingleModels.sh 789 (10 years ago) by filippis: white TO talyn
createGraphDb.sh 790 (10 years ago) by filippis: white TO talyn
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 (10 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.
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
alignSeq.java 847 (10 years ago) by stehr: new executable for pairwise (global) sequence alignment
addSeq2Mcma.java 769 (10 years ago) by stehr: added methods and executables to calculate 3d superimpositions using PolyposeRunner
Manifest.txt 882 (10 years ago) by stehr: updated version to 1.2.0 (forgot to change version number in last tag)
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