 ../
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DecoyScoring/
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906
(11 years ago)
by duarte:
New classes for triplet scoring.
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AAinfo.java
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885
(11 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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AIGEdge.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AIGNode.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AIGraph.java
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712
(12 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.
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Alignment.java
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767
(12 years ago)
by stehr:
added getGaplessColumns(start, end)
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AlignmentConstructionError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AlignmentEvaluator.java
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775
(12 years ago)
by stehr:
better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
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AminoAcid.java
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885
(11 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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Atom.java
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886
(11 years ago)
by stehr:
New executable writePerAtomDistancesToBFactor (see doc for details), new method Pdb.getPerAtomDistances(Pdb referencePdb), made Atom.DEFAULT_B_FACTOR public.
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AtomType.java
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884
(11 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
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BackboneCoords.java
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827
(12 years ago)
by stehr:
New class GeometryTools for simple geometric operations (currently implemented: torsion angles)
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Box.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CaspRRFileData.java
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644
(13 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.
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CaspRRFileRIGraph.java
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712
(12 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.
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CatalSiteSet.java
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829
(12 years ago)
by stehr:
updated to latest CSA version, added toString() methods
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CatalyticSite.java
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829
(12 years ago)
by stehr:
updated to latest CSA version, added toString() methods
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CiffileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CiffilePdb.java
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885
(11 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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ConformationsNotSameSizeError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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ContactType.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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DbRIGraph.java
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788
(12 years ago)
by filippis:
white TO talyn
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EC.java
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502
(13 years ago)
by stehr:
EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning
Interval: added typing to Comparator to avoid eclipse warning
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ECRegion.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FastaFileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FileRIGraph.java
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884
(11 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
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FileTypeGuesser.java
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550
(13 years ago)
by stehr:
changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility
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GeometryTools.java
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827
(12 years ago)
by stehr:
New class GeometryTools for simple geometric operations (currently implemented: torsion angles)
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GraphFileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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GraphIODb.java
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788
(12 years ago)
by filippis:
white TO talyn
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GraphIOGDLFile.java
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635
(13 years ago)
by duarte:
Changed default gravity value and default IDENTITY_SCORE for similarity graph
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GraphIdNotFoundError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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HashGrid.java
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737
(12 years ago)
by stehr:
Committing empty class HashGrid for later implementation
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IntPairComparator.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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IntPairSet.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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Interval.java
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515
(13 years ago)
by stehr:
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
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IntervalSet.java
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872
(11 years ago)
by stehr:
adding compareTo method to compare two IntervalSets
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MaxClusterRunner.java
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859
(12 years ago)
by duarte:
Fixed docs, now removing some temp files that weren't been removed
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NbhProbDistribution.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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NbhoodBackgrnd.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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OligomericState.java
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689
(13 years ago)
by filippis:
-OligomericState class added
-Pdb
a.checkOligomeric and getOligomericState methods added
b.calcVolume, calcSurface and calcCompactnessCoefficient methods added
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PairwiseAlignmentConverter.java
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517
(13 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
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PairwiseSequenceAlignment.java
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709
(12 years ago)
by stehr:
added methods to return the residue mappings for this alignment
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PaulStructAligner.java
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788
(12 years ago)
by filippis:
white TO talyn
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Pdb.java
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892
(11 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.
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PdbChainCodeNotFoundError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbCodeNotFoundError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbLoadError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbSet.java
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873
(11 years ago)
by stehr:
adding main method for testing
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PdbaseInconsistencyError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbasePdb.java
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885
(11 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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PdbfileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbfilePdb.java
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899
(11 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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PirFileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PolResidue.java
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866
(11 years ago)
by duarte:
Refactored Residue->PolResidue. Now Residue will be the proper implementation of a residue as part of a Pdb
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Polymer.java
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866
(11 years ago)
by duarte:
Refactored Residue->PolResidue. Now Residue will be the proper implementation of a residue as part of a Pdb
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PolyposeRunner.java
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775
(12 years ago)
by stehr:
better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
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PredEval.java
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682
(13 years ago)
by stehr:
now handling special cases that used to give NaN values
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PrositeHit.java
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870
(11 years ago)
by stehr:
New classes for scanning Prosite Database
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PrositeScanner.java
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870
(11 years ago)
by stehr:
New classes for scanning Prosite Database
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ProtStructGraph.java
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906
(11 years ago)
by duarte:
New classes for triplet scoring.
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RIGCommonNbhood.java
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840
(12 years ago)
by duarte:
New method getMotifNoGaps
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RIGEdge.java
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546
(13 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
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RIGEnsemble.java
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688
(13 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
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RIGNbhood.java
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529
(13 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
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RIGNode.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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RIGraph.java
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842
(12 years ago)
by duarte:
New method to filter on minWeight
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RIGraphMinSpanningTree.java
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705
(12 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.
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Residue.java
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892
(11 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.
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Scop.java
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685
(13 years ago)
by filippis:
getNumScopRes method added in Scop class
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ScopRegion.java
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589
(13 years ago)
by duarte:
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
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SecStrucElement.java
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818
(12 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)
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SecondaryStructure.java
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639
(13 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.
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StructAligner.java
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747
(12 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.
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StructAlignmentError.java
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747
(12 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.
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Template.java
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753
(12 years ago)
by duarte:
Fixed bug: PDB/graph/scop data loading issues were not correctly implemented.
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TemplateList.java
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756
(12 years ago)
by duarte:
New static method in BlastHit to get subjectId from templateId
New member source in TemplateList
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aapairsBounds.dat
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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contactTypes.dat
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885
(11 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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