A set of shell scripts are provided to test the installation of fast_protein_cluster

The 1af7_ decoy set from Yang Zhang's Spicker test set is used. A file with the
Tmscores and RMSDs from the experimental structure is also provided to evaluate
the different methods

20 tests are provided. 

test_rmsd_density_avx.sh   
test_rmsd_density_gpu.sh
test_rmsd_density.sh
test_rmsd_density_sse2.sh
test_rmsd_density_sse3.sh
  
Use RMSD as the metric to calculate density without creating a similarity matrix
Best measure of RMSD calculation speed as write times to matrix are significant 
given the speed of the RMSD calculations

test_rmsd_avx.sh
test_rmsd_gpu.sh
test_rmsd.sh
test_rmsd_sse2.sh
test_rmsd_sse3.sh

Use RMSD as the metric to cluster 10,000 decoys using hierarchical clustering 
with complete linkage.

test_tmscore_avx.sh
test_tmscore_gpu.sh
test_tmscore.sh
test_tmscore_sse2.sh
test_tmscore_sse3.sh

Use TMscore as the metric to cluster 300 decoys using hierarchical clustering 
with complete linkage.

test_rmsd_tmscore_avx.sh
test_rmsd_tmscore_gpu.sh
test_rmsd_tmscore.sh
test_rmsd_tmscore_sse2.sh
test_rmsd_tmscore_sse3.sh

Use RMSD as the metric and iterative density to prune an intial set of 10000
structures to 300 and then using TMscore as a metric to cluster using kmeans.

Hong Hung 1-14

