some formatting and main loop

updated protein class
added target id to input
Pulling in BLAST results

BLAST alignments working
Pulling in PDBs and sorting by alignment next
Still have to throw out templates too close to target so we don't use
the target to model itself
PDB Downloads Working

PDBs are now downloaded on run
BLAST runs on PDB for alignment
IDs are taken from the alignments and pull down PDBs
updating gitignore preemptively