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r701
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contactTypes.dat 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.
TemplateList.java 695 (11 years ago) by duarte: Now averageGraph can use PDB/CASP TS files as templates. TemplateList/Template classes now can read PDB data either from pdbase database or from files.
Template.java 695 (11 years ago) by duarte: Now averageGraph can use PDB/CASP TS files as templates. TemplateList/Template classes now can read PDB data either from pdbase database or from files.
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 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.
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
RIGraph.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.
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 512 (11 years ago) by duarte: Added getCommanSeparatedResSerials to RIGCommonNbhood
ProtStructGraph.java 659 (11 years ago) by stehr: Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates
PredEval.java 682 (11 years ago) by stehr: now handling special cases that used to give NaN values
PirFileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbfilePdb.java 661 (11 years ago) by stehr: Now enforcing that atom serials have to be in ascending order
PdbfileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
PdbasePdb.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.
PdbaseInconsistencyError.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.
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 689 (11 years ago) by filippis: -OligomericState class added -Pdb a.checkOligomeric and getOligomericState methods added b.calcVolume, calcSurface and calcCompactnessCoefficient methods added
PairwiseSequenceAlignment.java 575 (11 years ago) by filippis: reconstruct: -rmsd to mirrored pdb has been added in the report file Pdb: -comment for outputing missing atoms added PairwiseSequenceAlignment: -constructor with parameters openScore and extendScore for the gaps has been added
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.
MsdsdPdb.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.
MsdsdInconsistentResidueNumbersError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
MaxClusterRunner.java 585 (11 years ago) by stehr: added method calculateSequenceIndependentMatrix()
IntervalSet.java 592 (11 years ago) by stehr: fixed one null pointer bug and some spelling mistakes
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.
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 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.
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 551 (11 years ago) by duarte: Fixed bug: now reading/writing #MODEL field in contact map files In Pdb writeAtomLines now prints a nicer header with source info depending on source: file or db
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
DbRIGraph.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.
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 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.
CiffileFormatError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
CatalyticSite.java 503 (11 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.
CatalSiteSet.java 514 (11 years ago) by filippis: Latest scop and csa versions updated.
CaspRRFileRIGraph.java 543 (11 years ago) by duarte: Now forcing i<j in CASP RR files (as specified by the CASP RR format)
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.
AlignmentConstructionError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
Alignment.java 694 (11 years ago) by duarte: Now considering also '.' (dots) part of the FASTA header tags.
AIGraph.java 659 (11 years ago) by stehr: Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates
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 524 (11 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()
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