../
|
AAinfo.java
|
524
(12 years ago)
by duarte:
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
|
AIGEdge.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
AIGNode.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
AIGraph.java
|
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.
|
Alignment.java
|
767
(12 years ago)
by stehr:
added getGaplessColumns(start, end)
|
AlignmentConstructionError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
AlignmentEvaluator.java
|
775
(12 years ago)
by stehr:
better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
|
Box.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
CaspRRFileData.java
|
644
(12 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.
|
CaspRRFileRIGraph.java
|
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.
|
CatalSiteSet.java
|
514
(13 years ago)
by filippis:
Latest scop and csa versions updated.
|
CatalyticSite.java
|
503
(13 years ago)
by filippis:
createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned
!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added
!!!!AIGraph:
-getResidueSerial method added
RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field
DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.
testDbRIGraph added:
It reads one graph from a source db based either
-on pdbcode, chaincode and graph properties or
-on scop id and graph properties or
-on a graph id
and it writes the graph to a destination db.
Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence
CatalSiteSet:
- removeCatalSiteRes(int resser) method added
CatalyticSite:
-remRes(int resser) method added
Scop:
-remove(ScopRegion e) method added
genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
|
CiffileFormatError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
CiffilePdb.java
|
639
(12 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.
|
ConformationsNotSameSizeError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
ContactType.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
DbRIGraph.java
|
788
(12 years ago)
by filippis:
white TO talyn
|
EC.java
|
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
|
ECRegion.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
FastaFileFormatError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
FileFormatError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
FileRIGraph.java
|
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.
|
FileTypeGuesser.java
|
550
(12 years ago)
by stehr:
changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility
|
GraphFileFormatError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
GraphIODb.java
|
788
(12 years ago)
by filippis:
white TO talyn
|
GraphIOGDLFile.java
|
635
(12 years ago)
by duarte:
Changed default gravity value and default IDENTITY_SCORE for similarity graph
|
GraphIdNotFoundError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
HashGrid.java
|
737
(12 years ago)
by stehr:
Committing empty class HashGrid for later implementation
|
IntPairComparator.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
IntPairSet.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
Interval.java
|
515
(13 years ago)
by stehr:
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
|
IntervalSet.java
|
592
(12 years ago)
by stehr:
fixed one null pointer bug and some spelling mistakes
|
MaxClusterRunner.java
|
714
(12 years ago)
by stehr:
added comment
|
MsdsdInconsistentResidueNumbersError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
MsdsdPdb.java
|
788
(12 years ago)
by filippis:
white TO talyn
|
NbhProbDistribution.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
NbhoodBackgrnd.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
OligomericState.java
|
689
(12 years ago)
by filippis:
-OligomericState class added
-Pdb
a.checkOligomeric and getOligomericState methods added
b.calcVolume, calcSurface and calcCompactnessCoefficient methods added
|
PairwiseAlignmentConverter.java
|
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
|
PairwiseSequenceAlignment.java
|
709
(12 years ago)
by stehr:
added methods to return the residue mappings for this alignment
|
PaulStructAligner.java
|
788
(12 years ago)
by filippis:
white TO talyn
|
Pdb.java
|
787
(12 years ago)
by duarte:
First implementation of the embedding part of the EMBED algorithm by Havel: from an exact complete distance matrix gives 3d coordinates for the embedding.
|
PdbChainCodeNotFoundError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
PdbCodeNotFoundError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
PdbLoadError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
PdbaseInconsistencyError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
PdbasePdb.java
|
783
(12 years ago)
by duarte:
Got rid of the hardcoded mysql server, user, password. Now read from .my.cnf file
|
PdbfileFormatError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
PdbfilePdb.java
|
661
(12 years ago)
by stehr:
Now enforcing that atom serials have to be in ascending order
|
PirFileFormatError.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
PolyposeRunner.java
|
775
(12 years ago)
by stehr:
better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
|
PredEval.java
|
682
(12 years ago)
by stehr:
now handling special cases that used to give NaN values
|
ProtStructGraph.java
|
725
(12 years ago)
by duarte:
Given a serialVersionUID to class to get rid of warning
|
RIGCommonNbhood.java
|
512
(13 years ago)
by duarte:
Added getCommanSeparatedResSerials to RIGCommonNbhood
|
RIGEdge.java
|
546
(12 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
|
RIGEnsemble.java
|
688
(12 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
|
RIGNbhood.java
|
529
(12 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
|
RIGNode.java
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
RIGraph.java
|
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.
|
RIGraphMinSpanningTree.java
|
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.
|
Scop.java
|
685
(12 years ago)
by filippis:
getNumScopRes method added in Scop class
|
ScopRegion.java
|
589
(12 years ago)
by duarte:
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
|
SecStrucElement.java
|
743
(12 years ago)
by duarte:
New tests package (should be a folder and under it packages, but for now we can't do that until we move all source code to a src folder).
Moved all existing tests to appropiate tests packages.
New test PdbParsersTest: does cif against pdbase at the moment.
Adde equals method to SecStrucElement
Added some getters to Pdb
|
SecondaryStructure.java
|
639
(12 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.
|
StructAligner.java
|
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.
|
StructAlignmentError.java
|
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.
|
Template.java
|
753
(12 years ago)
by duarte:
Fixed bug: PDB/graph/scop data loading issues were not correctly implemented.
|
TemplateList.java
|
756
(12 years ago)
by duarte:
New static method in BlastHit to get subjectId from templateId
New member source in TemplateList
|
aapairsBounds.dat
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
contactTypes.dat
|
492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|