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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
Re-branching for JUNG2 development
extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph
Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type) New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds PRMInfo: now for amber "OXT" gets transformed into "O"
First commit of ConstraintsMaker (and PRMInfo needed for it) Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb) Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran Thus the PRMInfo class was needed, at the moment can read only amber prm files Some new methods and better javadoc in Pdb. Some new methods in AAinfo
Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file Changed all references accordingly
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