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r1683
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examples/ 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,...)
owl/ 1683 (6 years ago) by jmduarteg: Important change: now interface search goes up to 6th shell of neighbouring cells. This solves bug CRK-101 where no interfaces were found for 1was. It also solves the case of many PDB entries that need 3rd shell (e.g. 24 entries in a test of ~2000 pdbs) and rare but occurring cases that need 5th shell (e.g. 2 entries in test of ~2000 pdbs). It seems that PISA uses 3rd shell and thus they miss interfaces occurring at >3 neighbours. Tested that this doesn't add any overhead at all to the runtime (the overlap check is very fast).
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
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
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
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
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.
compareAlignments.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
addSeq2Mcma.java 1342 (8 years ago) by hstehr:
pir2fasta.java 1343 (8 years ago) by hstehr:
clustal2fasta.java 1344 (8 years ago) by hstehr:
genGraph.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.
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.
calcVolsAndSurfs.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.
scoreGeomOfPdbs.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.
mirrorIt.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.
testAICGraph.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.
testJUNGframework.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.
dumppdb.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.
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.
calculateGridDensity.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.
compareCMs.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 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.
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.
benchmarkGraphAlgorithm.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.
writeSASAtoBFactor.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,...)
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,...)
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,...)
calcMass.java 1407 (8 years ago) by jmduarteg: New methods and script to calculate mass of a protein/chain.
genDbGraph.java 1472 (8 years ago) by jmduarteg: Fixed a couple of problems with ScopConnection. Added another atom type.
getPisaAssemblyPreds.java 1480 (8 years ago) by jmduarteg: Minor fix
alignSeq.java 1594 (7 years ago) by jmduarteg: Now will also take uniprot codes as input
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
reconstruct.java 1678 (6 years ago) by jmduarteg: Moved geometry related calculations to the GeometryTools class: rmsd, screw component, axis type, axis-angle etc. Like that the calculations can be used from anywhere. Introduced the OptSuperposition class as output of the rmsd calculation. Improved the rmsd calculation in PdbChain (and corrected some bugs). Also improved a lot the rmsd unit testing. All tests in PdbChainTest are now done with cif files and not anymore with pdbase. Implemented an optimal superposition method in ChainInterface and some output for that in enumerateInterfaces with the intention of finding the pseudo-symmetric relationship between NCS related chains in an interface. All tests passed.
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.
averageGraph.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.
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.
dumpseq.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.
enumerateInterfaces.java 1681 (6 years ago) by jmduarteg: Now interface list can be cut to a minimal area cutoff, with all interfaces below discarded
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