 ../
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tools/
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983
(12 years ago)
by hstehr:
adding some convenience methods to IntervalSet
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tinker/
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996
(12 years ago)
by matt4077:
reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.
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tests/
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988
(12 years ago)
by jmduarteg:
Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.
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sequence/
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951
(12 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.
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sadp/
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958
(12 years ago)
by duarte:
Moved Interval* and IntPair* classes to tools package
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runners/
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996
(12 years ago)
by matt4077:
reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.
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proteinstructure/
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996
(12 years ago)
by matt4077:
reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.
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ppi/
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951
(12 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.
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litNet/
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951
(12 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.
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graphAveraging/
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988
(12 years ago)
by jmduarteg:
Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.
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features/
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981
(12 years ago)
by hstehr:
Introducing new StructuralDomainFeature for structural domains as defined by SCOP, CATH, DomainParser etc.
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embed/
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964
(12 years ago)
by gmueller:
new class for sparse double matrices
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deltaRank/
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996
(12 years ago)
by matt4077:
reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.
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connections/
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987
(12 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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casp/
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973
(12 years ago)
by duarte:
Moving the CASP project into OWL as the casp package.
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actionTools/
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951
(12 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.
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writeSASAtoBFactor.java
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987
(12 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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writePerAtomDistancesToBFactor.java
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951
(12 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.
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testPymolServer.java
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951
(12 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.
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testPyMol.java
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951
(12 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.
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testPdb.java
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953
(12 years ago)
by duarte:
Refactoring of inconsistently named methods in RIGraph
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testMySQLConnection.java
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951
(12 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.
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testJUNGframework.java
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951
(12 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.
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testDbRIGraph.java
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953
(12 years ago)
by duarte:
Refactoring of inconsistently named methods in RIGraph
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testClusterConnection.java
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995
(12 years ago)
by jmduarteg:
Removed the executable property
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superimposeMult.java
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951
(12 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.
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scorePdbSet.java
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960
(12 years ago)
by duarte:
New executable class from my workspace.
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scoreDecoys.java
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951
(12 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.
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runMD.java
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951
(12 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.
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reconstruct.java
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996
(12 years ago)
by matt4077:
reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.
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pairwiseSeqId.java
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951
(12 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.
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mirrorIt.java
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951
(12 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.
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mapMutations.java
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988
(12 years ago)
by jmduarteg:
Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.
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genGraph.java
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953
(12 years ago)
by duarte:
Refactoring of inconsistently named methods in RIGraph
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genDbGraph.java
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988
(12 years ago)
by jmduarteg:
Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.
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dumpseq.java
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951
(12 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.
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dumppdb.java
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951
(12 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.
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computeEnergies.java
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951
(12 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.
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compareCMs.java
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953
(12 years ago)
by duarte:
Refactoring of inconsistently named methods in RIGraph
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compareAlignments.java
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951
(12 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.
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checkChirality.java
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957
(12 years ago)
by duarte:
Added some useful tools to the default package from my workspace. More clean up.
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calculateGridDensity.java
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951
(12 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.
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calcVolsAndSurfs.java
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957
(12 years ago)
by duarte:
Added some useful tools to the default package from my workspace. More clean up.
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benchmarkGraphAlgorithm.java
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953
(12 years ago)
by duarte:
Refactoring of inconsistently named methods in RIGraph
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averageGraph.java
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953
(12 years ago)
by duarte:
Refactoring of inconsistently named methods in RIGraph
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analyseHistone.java
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961
(12 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
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alignSeq.java
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951
(12 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.
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addSeq2Mcma.java
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951
(12 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.
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