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Revision 580 - (view) (annotate) - [select for diffs]
Modified Tue Apr 8 10:01:57 2008 UTC (14 years, 5 months ago) by filippis
File length: 3694 byte(s)
Diff to previous 576
-the node_id in the single_model_node table changed to AUTO_INCREMENT

-the interSS for CR added

-write_graph_to_db methods treat the node_id field in the single_model_node table as AUTO_INCREMENT
-write_graph_to_motiffile method added
Revision 576 - (view) (annotate) - [select for diffs]
Modified Tue Apr 1 15:56:06 2008 UTC (14 years, 6 months ago) by filippis
File length: 3636 byte(s)
Diff to previous 503
RIGraph:Now you can store unweighted graphs in db and also select the db that contains the ids for the single models.
-paramater weighted added to write_graph_to_db and write_graph_to_db_fast methods. If true, it works as before (atomWeight is written to db field weight) else the db field weight gets always value 1. Methods without this parameter still exist and work as before.
-protected field singleModelsDb and corresponding methods getSingleModelsDb and setSingleModelsDb have been added. All constructors set the singleModelsDb field to DEFAULT_SINGLEMODELS_DB which equals to "ioannis". Changes have been also made to write_graph_to_db and write_graph_to_db_fast methods to deal with the singleModelsDb field.

DbRIGraph, testDbRIGraph:Changes have been also made to address the reading of (un)weighted graphs from db. has been added. You can create your own table with ids for the single models wherever you want. mode to drop tables has been added.

Revision 503 - (view) (annotate) - [select for diffs]
Modified Tue Jan 8 19:51:39 2008 UTC (14 years, 8 months 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 (14 years, 9 months 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 (14 years, 10 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 (14 years, 10 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 (14 years, 10 months ago) by filippis
File length: 2527 byte(s) added

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