A clustering routines of evolutionary conserved regions (helical regions) for RNA fold prediction.
# evoClustRNA clustering procedure
evoClustRNA.py -a rp13finalX_noSSperSeq_ref.sto -o out/ -i ~/EvoClustRNA/test_data/rp13/evox/structures -m mapping_ref.txt -f
# *.matrix was created which took almost 10 mins
# cluster the matrix
evoClust_autoclustix.py rp13finalX_noSSperSeq_ref_mapping_refX.matrix
# rp13finalX_noSSperSeq_ref_mapping_refX_n1c166_cf9.00.out was created
# copy the best cluster medoids from structures to reps_ns
evoClust_get_models.py -i evox/structures/ *.out -n tar -u
# rep_ns/ and reps_motifs_ns(empty) were created.
# compare to the reference structure
evoClust_calc_rmsd.py -a rp13finalX_noSSperSeq_ref.sto -t target_13_solution_0_renumber_puzzle_ref.pdb -m mapping_ref.txt -o rmsd_motif. csv -n rp13 reps_ns/*.pdb
# rmsd_motif.csv and rmsd_motif.png were created.