initial commit
Added sample ssi, pdb, fasta files
Add Alpha Helix Output
Detecting left-handed alpha helices

New function added to chain.c: AreLeftHanded
Printing alpha annotations is added.
unknown
ignore stuff
fix conflict
AlphaHelices in consensus
Some changes made to avoid fatal errors on linux machine
Reindex from 1 instead of 0
Errors related to memory management fixed.
Some more miscellaneous changes
System modified to handle more than 100000 atoms
Makefile and Executable added
bugs in annotatin beta strands only are fixed.
set up new github home
clean up
Merge branch 'master' of https://github.com/ndaniels/SSAnnotate

Conflicts:
	.gitignore