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r891
File (rev) Last Change
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contactTypes.dat 885 (10 years ago) by duarte: Major change: now hydrogens are read in Pdb and subclasses New getChirality method in Residue. Added some more unit tests.
aapairsBounds.dat 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
TypeScorer.java 891 (10 years ago) by duarte: New classes for scoring protein structures based on residue/atom type empirical potentials.
TemplateList.java 756 (11 years ago) by duarte: New static method in BlastHit to get subjectId from templateId New member source in TemplateList
Template.java 753 (11 years ago) by duarte: Fixed bug: PDB/graph/scop data loading issues were not correctly implemented.
StructAlignmentError.java 747 (11 years ago) by duarte: Initial commit of StructAligner interface and implementation PaulStructAligner. New reader in Alignment: now we can read CLUSTAL alignment files, not extensively tested. Also Alignment now only throws generic FileFormatErrors instead of specific file format errors.
StructAligner.java 747 (11 years ago) by duarte: Initial commit of StructAligner interface and implementation PaulStructAligner. New reader in Alignment: now we can read CLUSTAL alignment files, not extensively tested. Also Alignment now only throws generic FileFormatErrors instead of specific file format errors.
SecondaryStructure.java 639 (11 years ago) by duarte: Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class. New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references. New method in Alignment to print a "graphical" matching of secondary structures.
SecStrucElement.java 818 (10 years ago) by stehr: added method getTypeDescription to output a string representation of the secondary structure type (currently not distinguishing between different numbers of states)
ScopRegion.java 589 (11 years ago) by duarte: New classes Template, TemplateList to be used in homology modelling pipeline. Modified BlastUtils to use TemplateList class
Scop.java 685 (11 years ago) by filippis: getNumScopRes method added in Scop class
Residue.java 885 (10 years ago) by duarte: Major change: now hydrogens are read in Pdb and subclasses New getChirality method in Residue. Added some more unit tests.
ResTypeScorer.java 891 (10 years ago) by duarte: New classes for scoring protein structures based on residue/atom type empirical potentials.
RIGraphMinSpanningTree.java 705 (11 years ago) by duarte: New class RIGraphMinSpanningTree for getting the Minimum Spanning Tree of a RIGraph. This is simply a wrapper around JUNG's PrimMinimumSpanningTree. New method setSerials2NodesMap in RIGraph.
RIGraph.java 842 (10 years ago) by duarte: New method to filter on minWeight
RIGNode.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
RIGNbhood.java 529 (11 years ago) by spriya: Drop sequence comparison in compare. Now we compare only length New method getSize in RIGNbhood to be used instead of size that returns neighborhood size + 1
RIGEnsemble.java 688 (11 years ago) by duarte: Fixed bugs in averageGraph: - output of benchmark statistics and pairwise comparison was overlapping - benchmark mode was broken after introduction of align mode (when no sequence file given we were always creating dummy sequence in both align or benchmark modes) Improved: - better handling of modes through mode variable that takes 1 of 3 states - better input check - in align mode now calling another GraphAverager constructor instead of creating dummy seq/tag within averageGraph - changed constructor in GraphAverager: now sequence not a parameter, instead taken from alignment. Check for input moved down to averageGraph - now allowing alignments that contain other sequences than the target and the templates - new exception GraphAveragerError thrown in GraphAverager constructor when sequences of alignment and templates don't match
RIGEdge.java 546 (11 years ago) by duarte: New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble Fixed bug in RIGEnsemble: was not working for cif files. Added a graph averaging output to main() in RIGEnsemble
RIGCommonNbhood.java 840 (10 years ago) by duarte: New method getMotifNoGaps
ProtStructGraph.java 725 (11 years ago) by duarte: Given a serialVersionUID to class to get rid of warning
PrositeScanner.java 870 (10 years ago) by stehr: New classes for scanning Prosite Database
PrositeHit.java 870 (10 years ago) by stehr: New classes for scanning Prosite Database
PredEval.java 682 (11 years ago) by stehr: now handling special cases that used to give NaN values
PolyposeRunner.java 775 (11 years ago) by stehr: better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
Polymer.java 866 (10 years ago) by duarte: Refactored Residue->PolResidue. Now Residue will be the proper implementation of a residue as part of a Pdb
PolResidue.java 866 (10 years ago) by duarte: Refactored Residue->PolResidue. Now Residue will be the proper implementation of a residue as part of a Pdb
PirFileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbfilePdb.java 890 (10 years ago) by duarte: Bug fixes in pdb file parser. Was throwing string out of bounds exception with some pdb files.
PdbfileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbasePdb.java 885 (10 years ago) by duarte: Major change: now hydrogens are read in Pdb and subclasses New getChirality method in Residue. Added some more unit tests.
PdbaseInconsistencyError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbSet.java 873 (10 years ago) by stehr: adding main method for testing
PdbLoadError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbCodeNotFoundError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbChainCodeNotFoundError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
Pdb.java 887 (10 years ago) by stehr: rewrote method getPerAtomDistances such that atom serials do not need to match between the two structures (matching corresponding atoms based in resser)
PaulStructAligner.java 788 (10 years ago) by filippis: white TO talyn
PairwiseSequenceAlignment.java 709 (11 years ago) by stehr: added methods to return the residue mappings for this alignment
PairwiseAlignmentConverter.java 517 (11 years ago) by duarte: Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps. Changed all other classes using Alignment to accommodate this. NOTE: graph averaging hasn't been tested after the change
OligomericState.java 689 (11 years ago) by filippis: -OligomericState class added -Pdb a.checkOligomeric and getOligomericState methods added b.calcVolume, calcSurface and calcCompactnessCoefficient methods added
NbhoodBackgrnd.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
NbhProbDistribution.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
MaxClusterRunner.java 859 (10 years ago) by duarte: Fixed docs, now removing some temp files that weren't been removed
IntervalSet.java 872 (10 years ago) by stehr: adding compareTo method to compare two IntervalSets
Interval.java 515 (11 years ago) by stehr: Interval: allow spaces in residue selection strings RIGNbhood: added method getNeighbors
IntPairSet.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
IntPairComparator.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
HashGrid.java 737 (11 years ago) by stehr: Committing empty class HashGrid for later implementation
GraphIdNotFoundError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
GraphIOGDLFile.java 635 (11 years ago) by duarte: Changed default gravity value and default IDENTITY_SCORE for similarity graph
GraphIODb.java 788 (10 years ago) by filippis: white TO talyn
GraphFileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
GeometryTools.java 827 (10 years ago) by stehr: New class GeometryTools for simple geometric operations (currently implemented: torsion angles)
FileTypeGuesser.java 550 (11 years ago) by stehr: changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility
FileRIGraph.java 884 (10 years ago) by duarte: Major commit: - change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors - added many tests and test files for Pdb (and merged some already existing tests from the default package) - removed obsolete classes related to msd - bug fix: PdbfilePdb now properly reads files with alt codes - all tests passed
FileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
FastaFileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
ECRegion.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
EC.java 502 (11 years ago) by stehr: EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning Interval: added typing to Comparator to avoid eclipse warning
DecoyScoreSet.java 891 (10 years ago) by duarte: New classes for scoring protein structures based on residue/atom type empirical potentials.
DecoyScore.java 891 (10 years ago) by duarte: New classes for scoring protein structures based on residue/atom type empirical potentials.
DbRIGraph.java 788 (10 years ago) by filippis: white TO talyn
ContactType.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
ConformationsNotSameSizeError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
CiffilePdb.java 885 (10 years ago) by duarte: Major change: now hydrogens are read in Pdb and subclasses New getChirality method in Residue. Added some more unit tests.
CiffileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
CatalyticSite.java 829 (10 years ago) by stehr: updated to latest CSA version, added toString() methods
CatalSiteSet.java 829 (10 years ago) by stehr: updated to latest CSA version, added toString() methods
CaspRRFileRIGraph.java 712 (11 years ago) by duarte: Switching to JUNG2-beta1: - got rid of our custom fix to removeEdge - now both addVertex and removeVertex are correctly implemented: they update properly the nodes2serials map.
CaspRRFileData.java 644 (11 years ago) by duarte: New feature: averageGraph now also writes out the CASP RR file (if -c specified) for the average graph at Cb 8. Made a bit prettier the CASP RR output: now contacts sorted and weights with only 2 decimal figures.
Box.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
BackboneCoords.java 827 (10 years ago) by stehr: New class GeometryTools for simple geometric operations (currently implemented: torsion angles)
AtomTypeScorer.java 891 (10 years ago) by duarte: New classes for scoring protein structures based on residue/atom type empirical potentials.
AtomType.java 884 (10 years ago) by duarte: Major commit: - change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors - added many tests and test files for Pdb (and merged some already existing tests from the default package) - removed obsolete classes related to msd - bug fix: PdbfilePdb now properly reads files with alt codes - all tests passed
Atom.java 886 (10 years ago) by stehr: New executable writePerAtomDistancesToBFactor (see doc for details), new method Pdb.getPerAtomDistances(Pdb referencePdb), made Atom.DEFAULT_B_FACTOR public.
AminoAcid.java 885 (10 years ago) by duarte: Major change: now hydrogens are read in Pdb and subclasses New getChirality method in Residue. Added some more unit tests.
AlignmentEvaluator.java 775 (11 years ago) by stehr: better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
AlignmentConstructionError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
Alignment.java 767 (11 years ago) by stehr: added getGaplessColumns(start, end)
AIGraph.java 712 (11 years ago) by duarte: Switching to JUNG2-beta1: - got rid of our custom fix to removeEdge - now both addVertex and removeVertex are correctly implemented: they update properly the nodes2serials map.
AIGNode.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
AIGEdge.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
AAinfo.java 885 (10 years ago) by duarte: Major change: now hydrogens are read in Pdb and subclasses New getChirality method in Residue. Added some more unit tests.
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