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r1004
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actionTools/ 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
casp/ 973 (9 years ago) by duarte: Moving the CASP project into OWL as the casp package.
connections/ 998 (9 years ago) by jmduarteg: Minor refactoring and comment fixes
deltaRank/ 996 (9 years ago) by matt4077: reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.
embed/ 1002 (9 years ago) by gmueller: latest version of gabriel (embed.contactmaps)
features/ 998 (9 years ago) by jmduarteg: Minor refactoring and comment fixes
graphAveraging/ 1000 (9 years ago) by jmduarteg: Now DsspRunner is purely static (makes more sense)
litNet/ 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
owl/ 1004 (9 years ago) by hstehr: starting refactoring: first creating packages owl and owl.core
ppi/ 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
proteinstructure/ 999 (9 years ago) by jmduarteg: Fixed the dsspRunner call (now it's static).
runners/ 1000 (9 years ago) by jmduarteg: Now DsspRunner is purely static (makes more sense)
sadp/ 958 (9 years ago) by duarte: Moved Interval* and IntPair* classes to tools package
sequence/ 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
tests/ 1000 (9 years ago) by jmduarteg: Now DsspRunner is purely static (makes more sense)
tinker/ 996 (9 years ago) by matt4077: reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.
tools/ 983 (9 years ago) by hstehr: adding some convenience methods to IntervalSet
addSeq2Mcma.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
alignSeq.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
analyseHistone.java 961 (9 years ago) by duarte: Now analyseHistone will output the coordinates of the side chains of ARGs (NH1 atom) and LYSs (NZ atom) instead of the CA atoms. Some new methods in Pdb
averageGraph.java 953 (9 years ago) by duarte: Refactoring of inconsistently named methods in RIGraph
benchmarkGraphAlgorithm.java 953 (9 years ago) by duarte: Refactoring of inconsistently named methods in RIGraph
calcVolsAndSurfs.java 957 (9 years ago) by duarte: Added some useful tools to the default package from my workspace. More clean up.
calculateGridDensity.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
checkChirality.java 957 (9 years ago) by duarte: Added some useful tools to the default package from my workspace. More clean up.
compareAlignments.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
compareCMs.java 953 (9 years ago) by duarte: Refactoring of inconsistently named methods in RIGraph
computeEnergies.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
dumppdb.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
dumpseq.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
genDbGraph.java 1000 (9 years ago) by jmduarteg: Now DsspRunner is purely static (makes more sense)
genGraph.java 953 (9 years ago) by duarte: Refactoring of inconsistently named methods in RIGraph
mapMutations.java 1000 (9 years ago) by jmduarteg: Now DsspRunner is purely static (makes more sense)
mirrorIt.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
pairwiseSeqId.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
reconstruct.java 996 (9 years ago) by matt4077: reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.
runMD.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
scoreDecoys.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
scorePdbSet.java 960 (9 years ago) by duarte: New executable class from my workspace.
superimposeMult.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
testClusterConnection.java 995 (9 years ago) by jmduarteg: Removed the executable property
testDbRIGraph.java 953 (9 years ago) by duarte: Refactoring of inconsistently named methods in RIGraph
testJUNGframework.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
testMySQLConnection.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
testPdb.java 953 (9 years ago) by duarte: Refactoring of inconsistently named methods in RIGraph
testPyMol.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
testPymolServer.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
writePerAtomDistancesToBFactor.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
writeSASAtoBFactor.java 987 (9 years ago) by jmduarteg: New package runners for Runner classes. At the moment only contains the new class NaccessRunner (moved out of Pdb class) Introduced a config file for tests so that one can set externally the executable paths and any other necessary data to run tests (at the moment only implemented in PdbTest.java). PdbTest now should run anywhere (if you have a local pdbase installation!) Moved the consurf parser out of Pdb to its own class ConsurfConnection in the connection package.
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