Protein Family Alignment Annotation Tool svncode

added comments renamed some vars

For Dan

comment out part preventing compile

updated dependencies

updated to allow for GetCavity to properly work, allowing the following object relationship to hold:
GetCavity.main
-> PatchBuilder.buildPatchesCavity()
-> PatchBuilderForPathConnectedResiduesCavity

PatchBuilderForPathConnectedResiduesCavity contains the altered algorithm:
patches that are not within -D specified distance from the -O coordinate are not

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

Added a method to determine the distance between PdbResidue and Point3d objects

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