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r503
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branches/ 488 (12 years ago) by duarte: T
tags/ 494 (12 years ago) by stehr: Tagging version 0.9 to use with CMView 0.9 (same as aglappe-jung 0.1.2 but moved to trunk)
trunk/ 503 (12 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.
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