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Latest scop and csa versions updated.
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.
Copied the aglappe-jung branch into trunk.
Fixed bug: -r option was not being set by default
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial) New methods getChains() and getModels() in all Pdb classes New Exception PdbLoadError New tester for getChains and getModels: testGetChains Changed all calls to Pdb construction accordingly (includes changing excpetions)
AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
Re-branching for JUNG2 development
Changes in Pdb -checkConsurfHssp: in the mistakes calculated I add now at the end the difference between the number of residues and the number of consurf scores -writeAtomLines has now a boolean argument called pdbCompatible: if pdbCompatible is true, then only the first character of chainCode and not the 'whole' chainCode is exported to the file. -another WriteAtomLines has also been added without this extra argument for backwards compatibility: default value for pdbCompatible is false -dump2pdbfile has also been changed in similar way -runDssp and runNaccess now call the above methods with true pdbCompatible Changes in genDbGraph -1 summary output line has been added to provide info about csa, naccess, scop, ec, dssp, ... -DSSP is run with 3state
minor changes
contactTypes.dat -SC_CAGLY contact type added SecStrucElement.java -getSheetSerial method is now public Pdb.java -writeToDbFast added Graph.java -write_graph_to_db_fast -expBB,CW,CT,CR,w,d are now taken into account in a correct way -node_id, sssid, sheetSerial and turn are now also filled in DbGraph.java -expBB,CW,CT,CR,w,d are now taken into account in a correct way -directionality is also taken into account now when reading edges genDbGraph.java -sequence separation added as option createGraphDb.java added
added class PairwiseSequenceAlignment
Minor changes
Added mode option in genDbGraph whether to find and store info for the residues (SCOP,NACCESS,EC,CSA,...)
Now can do multiple contact types/cutoffs per pdb structure
Now closing db connection. Better help string.
Fixed a few bugs in reading of list file Better output and error messages
New script genGraph (generates graph to files) Better error messages in both
Initial commit of genDbGraph script
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