Protein Family Alignment Annotation Tool svncode

Brought to you by: carlsonjf, dcaffrey, eshuang, simonxi

svncode Commit Log

Commit	Date
[r1386] by adamwespiser updated to allow for GetCavity to properly work, allowing the following object relationship to hold: GetCavity.main -> PatchBuilder.buildPatchesCavity() -> PatchBuilderForPathConnectedResiduesCavity	2012-02-15 19:03:13	Tree
[r1385] by adamwespiser PatchBuilderForPathConnectedResiduesCavity contains the altered algorithm: patches that are not within -D specified distance from the -O coordinate are not	2012-02-15 18:43:56	Tree
[r1384] by adamwespiser For building patches within a cavity, instead of GetPatches being used as the main Java class, getCavity is used instead. note: getCavity has two additional options: [-D \| maximum seed distance from 3d point] (GetCavity.seedDistance) [-O \| x:y:z coordinates for 3d point] (GetCavity.cavityPoint) Object Dependencies: GetCavity -> PatchBuilder -> PatchBuilderForPathConnectedResiduesCavity(new) -> PatchGraph where PatchBuilderForPathConnectedResiduesCavity is a version of PatchBuilderForPathConnectedResidues with an altered algorithm that excludes patches from being seeds that are further than -D away from the -O specified point	2012-02-15 18:43:06	Tree
[r1383] by adamwespiser Added a method to determine the distance between PdbResidue and Point3d objects	2012-02-15 18:38:12	Tree
[r1382] by dcaffrey * empty log message *	2012-01-29 12:50:34	Tree
[r1381] by dcaffrey * empty log message *	2012-01-27 21:11:51	Tree
[r1380] by dcaffrey * empty log message *	2012-01-26 22:00:01	Tree
[r1379] by dcaffrey * empty log message *	2012-01-25 14:29:14	Tree
[r1378] by dcaffrey * empty log message *	2012-01-25 04:13:25	Tree
[r1377] by dcaffrey * empty log message *	2012-01-24 19:12:27	Tree

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