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Revision 503 - (view) (annotate) - [select for diffs]
Modified Tue Jan 8 19:51:39 2008 UTC (13 years, 1 month ago) by filippis
File length: 3310 byte(s)
Diff to previous 492
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned

-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added

-getResidueSerial method added

-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field

-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.

-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

- removeCatalSiteRes(int resser) method added

-remRes(int resser) method added

-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.

Revision 492 - (view) (annotate) - [select for diffs]
Modified Wed Jan 2 13:18:57 2008 UTC (13 years, 1 month ago) by duarte
File length: 2653 byte(s)
Copied from: branches/aglappe-jung/ revision 491
Diff to previous 419
Copied the aglappe-jung branch into trunk.

Revision 419 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 14:09:18 2007 UTC (13 years, 3 months ago) by duarte
Original Path: branches/aglappe-jung/
File length: 2653 byte(s)
Diff to previous 413
Re-branching for JUNG2 development
Revision 413 - (view) (annotate) - [select for diffs]
Modified Wed Nov 21 21:23:19 2007 UTC (13 years, 3 months ago) by filippis
File length: 2653 byte(s)
Diff to previous 409
-pchain_code is now modified to VARCHAR(2) from CHAR(1) due to pdbase_chain_code
-index for pdb_residue_info table added
Revision 409 - (view) (annotate) - [select for diffs]
Added Tue Nov 20 19:09:21 2007 UTC (13 years, 3 months ago) by filippis
File length: 2527 byte(s) added

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