ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/src/owl/core/util
r1647
File Last Change
 ../
actionTools/ 1006 (12 years ago) by hstehr: refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker
BoundingBox.java 1577 (9 years ago) by jmduarteg: Important change in interface calculation: - another massive gain in run-time and memory usage: we first use the bounding boxes translations to see if it is worth translating the whole unit cells - thanks to that we now go to 2nd neighbors! (still performance is better than before with only 1st neighbors!). With that we fixed the long-standing bug by which we miss interfaces beyond the 1st neighbor - included a few examples of 2nd neighbor problem in test - re-done the symmetry redundancy elimination, it is there but it has a very little effect on overall performance. Now we only don't use an operator when we are very sure its partner was in the right place. In effect we could get rid of it because it wouldn't really affect the performance, we rather keep it as it is good to remember that there is a lot of symmetry redundancy
ClusterConnection.java 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
ColoredStrings.java 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
CombinationsGenerator.java 1431 (10 years ago) by jmduarteg: Changed behaviour of getId() in ChainInterfaceList, now uses the same ids as the interfaces, i.e. starts counting from 1 and not from 0. New graph classes for storing interface topology
DataDistributer.java 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
DataDistribution.java 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
FileFormatException.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
FileTypeGuesser.java 1617 (9 years ago) by jmduarteg: Adding more possible start for a PDB file
FloatPairSet.java 1023 (12 years ago) by cvehlow: FloatPairSet first commit
GEExitStatus.java 1524 (10 years ago) by jmduarteg: New classes for Grid Engine job querying
GEUtil.java 1524 (10 years ago) by jmduarteg: New classes for Grid Engine job querying
GeometryTools.java 1394 (11 years ago) by jmduarteg: Removed obsolete classes to analyse histone. Moved some useful methods for inertia moment calculation to GeometryTools
Goodies.java 1630 (9 years ago) by jmduarteg: New feature: now blast xml parser can read either raw xml or gzipped xml files. Also HomologList will use xml.gz files only as cache files
Graph2Pml.java 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
Grid.java 1573 (9 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
GridCell.java 1372 (11 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.
HashGrid.java 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
InertiaMomentAndAxis.java 1394 (11 years ago) by jmduarteg: Removed obsolete classes to analyse histone. Moved some useful methods for inertia moment calculation to GeometryTools
IntPairComparator.java 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
IntPairSet.java 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
Interval.java 1497 (10 years ago) by jmduarteg: New feature: now can specify a subinterval in UniprotHomologList
IntervalSet.java 1042 (12 years ago) by jmduarteg: New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)
KendallsTau.java 1207 (11 years ago) by cvehlow: Scoring:KendallsTau-method added to Statistics
Machine.java 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
MultiOutputStream.java 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
MySQLConnection.java 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
MySQLConnectionCheck.java 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
Pair.java 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
PyMol.java 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
PymolServerOutputStream.java 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
QueryThread.java 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
RegexFileFilter.java 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
Statistics.java 1208 (11 years ago) by cvehlow: Scoring:KendallsTau-method added to Statistics
StreamGobbler.java 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
SystemCmd.java 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
TableSorter.java 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
Triplet.java 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
utils4DB.java 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
utils4lh.java 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
         39 files shown