ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/proteinstructure
r518
File (rev) Last Change
 ../
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.
SecondaryStructure.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
SecStrucElement.java 505 (11 years ago) by duarte: Now converting also secondary structure in pairwise alignment graph conversion
ScopRegion.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
Scop.java 514 (11 years ago) by filippis: Latest scop and csa versions updated.
RIGraph.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.
RIGNode.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
RIGNbhood.java 515 (11 years ago) by stehr: Interval: allow spaces in residue selection strings RIGNbhood: added method getNeighbors
RIGEnsemble.java 495 (11 years ago) by stehr: added main function and loading from Multi-model PDB files
RIGEdge.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
RIGCommonNbhood.java 512 (11 years ago) by duarte: Added getCommanSeparatedResSerials to RIGCommonNbhood
ProtStructGraph.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.
PredEval.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.
PdbfilePdb.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.
PdbasePdb.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.
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 518 (11 years ago) by filippis: checkConsurf: if the file is not found and the chain code given is "A", we check now also for results for NULL chain code
PairwiseSequenceAlignment.java 499 (11 years ago) by duarte: Got rid of check for equality of tags
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
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 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
MsdsdInconsistentResidueNumbersError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
MaxClusterRunner.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
IntervalSet.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
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 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
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 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
FileRIGraph.java 497 (11 years ago) by duarte: Extracted some constants: NO_PDB_CODE, NO_PDB_CHAIN_CODE, NO_CONTACT_TYPE, NO_CUTOFF
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 513 (11 years ago) by filippis: Fixing the fixed bug! -if graph read is chain graph, then fullLength is set to the maximum observed residue serial -else if graph is scop graph, then fullLength is set to the number of observed residues NOTE:In the case of a wholechain scop graph, there might be inconsistensy between a graph I created with Pdb/RIGraph classes and stored in db and the corresponding graph i read from db. Specifically, the fullLength of graph I equals the length of the chain while the fullLength of graph i equals the number of observed residues.
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 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.
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 497 (11 years ago) by duarte: Extracted some constants: NO_PDB_CODE, NO_PDB_CHAIN_CODE, NO_CONTACT_TYPE, NO_CUTOFF
CaspRRFileData.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.
AlignmentConstructionError.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
Alignment.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
AIGraph.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.
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 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
(Current path doesn't exist after revision 950)
         60 files shown