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r1576
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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/ 1576 (7 years ago) by jmduarteg: Another important optimisation: now bounds are translated and not recalculated from scratch after translation. Fixed a bug in bounds copying (wasn't copying the boundsProtOnly boolean)
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
computeEnergies.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
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
pairwiseSeqId.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.
alignSeq.java 1340 (8 years ago) by hstehr: Fixed bugs in method for reading from PIR file; added script to convert from PIR to Fasta
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.
dumpseq.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.
reconstruct.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,...)
averageGraph.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,...)
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.
enumerateAssemblies.java 1471 (7 years ago) by jmduarteg: Introduced some more experimental code for enumeration of assemblies. BEWARE many things are UNFINISHED, namely in InterfaceGraph class the code to find induced and symmetry related interfaces is just a draft. There are many fundamental issues not solved yet. Be careful especially with implementations of equals and hashCode methods in InterfaceGraph, SubunitId, InterfaceGraphEdge etc. They alter "quietly" the behaviour of everything.
genDbGraph.java 1472 (7 years ago) by jmduarteg: Fixed a couple of problems with ScopConnection. Added another atom type.
getPisaAssemblyPreds.java 1480 (7 years ago) by jmduarteg: Minor fix
enumerateInterfaces.java 1573 (7 years ago) by jmduarteg: IMPORTANT changes and fixes in interface calculation: - very important bug fix: BoundingBox was not always telling properly whether 2 boxes overlap. This not only fixes the important bug but also boosts the speed of interface calculation - optimisation of PdbChain.getAICGraph not to return an empty graph whenever no overlap of boxes is found (instead of generating empty distance matrix and checking its emptiness): this alone gives the biggest performance boost to interface calculation, around 5x faster thanks to this alone - fine optimisation of max/min calculation in BoundingBox - made sure that bounds caching is done properly - introduced the right solution for symmetry redundancy elimination: operators multiplication is the identity. Before we had an ad-hoc solution that wasn't comprehensive at all - in any case the symmetry redundancy elimination is right now almost turned off because we introduced new conditions to re-check equivalent operators to fix cases like 2gsg, 3ka0, 1vzi, 1g3p and 1eaq, where some interfaces are missed due to an equivalent operator making the molecule fall in a cell where there's no contacts All in all this totally changes the interface calculation: 1) by a massive boost in performance 2) by making it more correct, surely there were cases with missing interfaces, we were just lucky not to find them in testing
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