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Now converting also secondary structure in pairwise alignment graph conversion
Copied the aglappe-jung branch into trunk.
Minor change : fixed comments
Re-branching for JUNG2 development
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
inSameSheet, isOther and getSheetSerial methods added in SecStrucElement
Methods added for: -parsing CSA -parsing EC -parsing CONSURF-HSSP -running & parsing Naccess -parsing SCOP -writing residues' info in a db table Modifications have been also made in DSSP parsing: -sheet serial is taken into account -flexibility in reduced state preferred
Added new SecondaryStructure object to Pdb and Graph
completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
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