 ../
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examples/
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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owl/
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1330
(11 years ago)
by jmduarteg:
Now the re-numbering of residue serials in PDB files has been improved. Instead of aligning the sequences whenever the serials don't match SEQRES, we first try to see if there is a shift in the serials with respect to SEQRES (happens in many cases). Only if we can't find a shift that fully matches SEQRES we proceed to re-aligning. We also treat properly now the ins codes. Mapping is as close to CIF as possible. The parsers test passes for the whole cullpdb20. For some entries like 2ofz the mapping does not coincide 100% with CIF as there are ambiguities in the alignment.
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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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testClusterConnection.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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testMySQLConnection.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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checkChirality.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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mirrorIt.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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testPyMol.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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analyseHistone.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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writePerAtomDistancesToBFactor.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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computeEnergies.java
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1009
(12 years ago)
by hstehr:
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
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averageGraph.java
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1009
(12 years ago)
by hstehr:
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
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testDbRIGraph.java
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1009
(12 years ago)
by hstehr:
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
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runMD.java
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1009
(12 years ago)
by hstehr:
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
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pairwiseSeqId.java
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1009
(12 years ago)
by hstehr:
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
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compareCMs.java
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1009
(12 years ago)
by hstehr:
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
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calcVolsAndSurfs.java
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1032
(12 years ago)
by jmduarteg:
Extracted the calc-vol and calc-surf runner code to its own Runner class.
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unitCellVol.java
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1181
(11 years ago)
by jmduarteg:
Now parsing the unit cell and crystal space group info when reading PDB sources. New simple script for unit cell volume.
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testAICGraph.java
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1192
(11 years ago)
by jmduarteg:
Committing test class for AICGraph
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enumerateInterfaces.java
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1280
(11 years ago)
by jmduarteg:
Now enumerateInterfaces takes file from local cif file PDB repo. Fixed some docs.
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scorePdbSet.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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reconstruct.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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genGraph.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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superimposeMult.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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benchmarkGraphAlgorithm.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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testPdb.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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scoreGeomOfPdbs.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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addSeq2Mcma.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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genDbGraph.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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compareAlignments.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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writeSASAtoBFactor.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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mapMutations.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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testJUNGframework.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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dumppdb.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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scoreDecoys.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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alignSeq.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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calculateGridDensity.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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dumpseq.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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