adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10082 7c6358e6-4a41-0410-a743-a5b2a554c398
adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10083 7c6358e6-4a41-0410-a743-a5b2a554c398
adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10084 7c6358e6-4a41-0410-a743-a5b2a554c398
adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10085 7c6358e6-4a41-0410-a743-a5b2a554c398
adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10086 7c6358e6-4a41-0410-a743-a5b2a554c398
adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10087 7c6358e6-4a41-0410-a743-a5b2a554c398
adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10088 7c6358e6-4a41-0410-a743-a5b2a554c398
adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10089 7c6358e6-4a41-0410-a743-a5b2a554c398
adding support for new parameter cacheFilePath to (optionally) allow to separate PDB files from other data

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10090 7c6358e6-4a41-0410-a743-a5b2a554c398
using new cache path for storing chemp comps

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10091 7c6358e6-4a41-0410-a743-a5b2a554c398
using new cache path for storing chemp comps

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10092 7c6358e6-4a41-0410-a743-a5b2a554c398
updating to latest jmol version

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10093 7c6358e6-4a41-0410-a743-a5b2a554c398
fixing a problem with 2F03

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10094 7c6358e6-4a41-0410-a743-a5b2a554c398
new flag to update remediated files

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10095 7c6358e6-4a41-0410-a743-a5b2a554c398
new flag to update remediated files

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10096 7c6358e6-4a41-0410-a743-a5b2a554c398
updated toString method

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10097 7c6358e6-4a41-0410-a743-a5b2a554c398
Reverting debugging statements introduced in r10020

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10098 7c6358e6-4a41-0410-a743-a5b2a554c398
fixing broken print functionality

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10099 7c6358e6-4a41-0410-a743-a5b2a554c398
Minor bug fixes in AlignmentTools (rmsd calculation) 

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10100 7c6358e6-4a41-0410-a743-a5b2a554c398
now threads sleep longer

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10101 7c6358e6-4a41-0410-a743-a5b2a554c398