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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.
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.
deltaRank/ 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.
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.
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.
sadp/ 958 (9 years ago) by duarte: Moved Interval* and IntPair* classes to tools package
tinker/ 958 (9 years ago) by duarte: Moved Interval* and IntPair* classes to tools package
embed/ 964 (9 years ago) by gmueller: new class for sparse double matrices
casp/ 973 (9 years ago) by duarte: Moving the CASP project into OWL as the casp package.
features/ 981 (9 years ago) by hstehr: Introducing new StructuralDomainFeature for structural domains as defined by SCOP, CATH, DomainParser etc.
tools/ 983 (9 years ago) by hstehr: adding some convenience methods to IntervalSet
connections/ 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.
graphAveraging/ 988 (9 years ago) by jmduarteg: Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.
tests/ 988 (9 years ago) by jmduarteg: Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.
runners/ 988 (9 years ago) by jmduarteg: Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.
proteinstructure/ 989 (9 years ago) by hstehr: adding a method RIGraph.getOrderedNeighbors(Node) because the default method getNeighbors(Node) returns the neighbours in non-deterministic order(!) which caused me lots of trouble
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.
testClusterConnection.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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
genGraph.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
testPdb.java 953 (9 years ago) by duarte: Refactoring of inconsistently named methods in RIGraph
averageGraph.java 953 (9 years ago) by duarte: Refactoring of inconsistently named methods in RIGraph
testDbRIGraph.java 953 (9 years ago) by duarte: Refactoring of inconsistently named methods in RIGraph
compareCMs.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.
checkChirality.java 957 (9 years ago) by duarte: Added some useful tools to the default package from my workspace. More clean up.
scorePdbSet.java 960 (9 years ago) by duarte: New executable class from my workspace.
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
reconstruct.java 977 (9 years ago) by duarte: Better error message for no tinker paths set up
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.
genDbGraph.java 988 (9 years ago) by jmduarteg: Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.
mapMutations.java 988 (9 years ago) by jmduarteg: Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.
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