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r1704
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owl/ 1704 (5 years ago) by jmduarteg: Fixed bug in cif file parsing: was not tokenising correctly loop elements that had more multi-line quoting mixed with normal quoted fields and several records. Added one more test case for that.
examples/ 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
writeSASAtoBFactor.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
writePerAtomDistancesToBFactor.java 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
unitCellVol.java 1181 (9 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.
testPyMol.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
testJUNGframework.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
testDbRIGraph.java 1009 (9 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
testClusterConnection.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
testAICGraph.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
superimposeMult.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
scorePdbSet.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
scoreGeomOfPdbs.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
scoreDecoys.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
runMD.java 1009 (9 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
reconstruct.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
pir2fasta.java 1343 (8 years ago) by hstehr:
pairwiseSeqId.java 1679 (6 years ago) by jmduarteg: Moved to core.structure.io the classes that belong there (except for the parsers themselves, we can't move them yet because there are some protected methods needed in core.structure). Removed some warnings from other files.
mirrorIt.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
mapMutations.java 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
getPisaAssemblyPreds.java 1480 (8 years ago) by jmduarteg: Minor fix
genGraph.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
genDbGraph.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
enumerateInterfaces.java 1690 (5 years ago) by jmduarteg: Introducing chain clusters and interface clusters. We group chains in the same way as before (based on 100% seq identity) but now we have a more flexible scheme where we could introduce chain clustering based on seq-alignment/rmsd when reading from PDB file (not implemented yet). Interface clustering is implemented based on rmsd of superposition of both interface sides.
enumerateAssemblies.java 1668 (6 years ago) by jmduarteg: Some clean up and rationalisation: removing methods related to "parallel" interfaces. Now we call them more consistently "infinite" interfaces
dumpseq.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
dumppdb.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
computeEnergies.java 1679 (6 years ago) by jmduarteg: Moved to core.structure.io the classes that belong there (except for the parsers themselves, we can't move them yet because there are some protected methods needed in core.structure). Removed some warnings from other files.
compareCMs.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
compareAlignments.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
clustal2fasta.java 1344 (8 years ago) by hstehr:
checkChirality.java 1392 (8 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
calculateGridDensity.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
calcVolsAndSurfs.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
calcMass.java 1407 (8 years ago) by jmduarteg: New methods and script to calculate mass of a protein/chain.
benchmarkGraphAlgorithm.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
averageGraph.java 1698 (5 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
alignSeq.java 1594 (6 years ago) by jmduarteg: Now will also take uniprot codes as input
addSeq2Mcma.java 1342 (8 years ago) by hstehr:
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