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Author: filippis
Date: Wed Nov 28 15:44:57 2007 UTC (11 years, 10 months ago)
Log Message:
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


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