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r892
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tools/ 889 (10 years ago) by duarte: New spearman method
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/ 892 (10 years ago) by duarte: Added isAllAtom to Pdb and getNumHeavyAtoms to Pdb and Residue. Fixed some docs that were still not properly clarifying about hydrogens. Added complete main methods to AtomTypeScorer and ResTypeScorer with command line options and defaults.
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/ 879 (10 years ago) by stehr: moving all classes in proteinstructure.features to features
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
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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