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r904
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DecoyScoring/ 904 (10 years ago) by duarte: Moved all decoy scoring stuff to its own package. Split CombinedScorer into two classes AtomCombinedScorer and ResCombinedScorer. Made combined scorer more efficient: now loading only once the graphs.
ContactType.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PirFileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbfileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
IntPairSet.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
GraphIdNotFoundError.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.
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.
PdbaseInconsistencyError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
Box.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
RIGNode.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
aapairsBounds.dat 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
FileFormatError.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.
GraphFileFormatError.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.
PdbLoadError.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.
FastaFileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
CiffileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
AIGNode.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
AlignmentConstructionError.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.
PdbCodeNotFoundError.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
Interval.java 515 (11 years ago) by stehr: Interval: allow spaces in residue selection strings RIGNbhood: added method getNeighbors
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
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
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
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
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
GraphIOGDLFile.java 635 (11 years ago) by duarte: Changed default gravity value and default IDENTITY_SCORE for similarity graph
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.
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.
PredEval.java 682 (11 years ago) by stehr: now handling special cases that used to give NaN values
Scop.java 685 (11 years ago) by filippis: getNumScopRes method added in Scop class
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
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
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.
PairwiseSequenceAlignment.java 709 (11 years ago) by stehr: added methods to return the residue mappings for this alignment
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.
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.
ProtStructGraph.java 725 (11 years ago) by duarte: Given a serialVersionUID to class to get rid of warning
HashGrid.java 737 (11 years ago) by stehr: Committing empty class HashGrid for later implementation
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.
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.
Template.java 753 (11 years ago) by duarte: Fixed bug: PDB/graph/scop data loading issues were not correctly implemented.
TemplateList.java 756 (11 years ago) by duarte: New static method in BlastHit to get subjectId from templateId New member source in TemplateList
Alignment.java 767 (11 years ago) by stehr: added getGaplessColumns(start, end)
PolyposeRunner.java 775 (11 years ago) by stehr: better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
AlignmentEvaluator.java 775 (11 years ago) by stehr: better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
PaulStructAligner.java 788 (11 years ago) by filippis: white TO talyn
DbRIGraph.java 788 (11 years ago) by filippis: white TO talyn
GraphIODb.java 788 (11 years ago) by filippis: white TO talyn
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)
BackboneCoords.java 827 (10 years ago) by stehr: New class GeometryTools for simple geometric operations (currently implemented: torsion angles)
GeometryTools.java 827 (10 years ago) by stehr: New class GeometryTools for simple geometric operations (currently implemented: torsion angles)
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
RIGCommonNbhood.java 840 (10 years ago) by duarte: New method getMotifNoGaps
RIGraph.java 842 (10 years ago) by duarte: New method to filter on minWeight
MaxClusterRunner.java 859 (10 years ago) by duarte: Fixed docs, now removing some temp files that weren't been removed
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
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
PrositeHit.java 870 (10 years ago) by stehr: New classes for scanning Prosite Database
PrositeScanner.java 870 (10 years ago) by stehr: New classes for scanning Prosite Database
IntervalSet.java 872 (10 years ago) by stehr: adding compareTo method to compare two IntervalSets
PdbSet.java 873 (10 years ago) by stehr: adding main method for testing
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
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
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.
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.
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.
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.
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.
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.
Residue.java 892 (10 years ago) by duarte: Added isAllAtom to Pdb and getNumHeavyAtoms to Pdb and Residue. Fixed some docs that were still not properly clarifying about hydrogens. Added complete main methods to AtomTypeScorer and ResTypeScorer with command line options and defaults.
Pdb.java 892 (10 years ago) by duarte: Added isAllAtom to Pdb and getNumHeavyAtoms to Pdb and Residue. Fixed some docs that were still not properly clarifying about hydrogens. Added complete main methods to AtomTypeScorer and ResTypeScorer with command line options and defaults.
PdbfilePdb.java 899 (10 years ago) by duarte: Fixed bug: parse() was not closing file when throwing an exception. The bug surfaced when parsing a dir with a lot of decoys that were somehow malformed PDB files, sometimes it would throw a FileNotFoundException with message "Too many open files".
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