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
