for dssp_secondary.py

picup_alpha_helix.sh

#!/bin/sh
#sed -e 's/[^3 ^4 ^5]/0/g' -e 's/[3 4 5]/1/g' $1 $1.helicity # for helicity
#sed -e 's/[^4 ]/0/g' -e 's/[4]/1/g' $1 # > $1.ahelix  # for alpha-helix
i=1
max=1
file_head="../data/out.condition."
file_ext=".out"

new_ext=".ahelix"
while [ $i -le $max ]
do
filename=$file_head$i$file_ext
fileout=$file_head$i$new_ext

sed -e 's/[^4 ]/0/g' -e 's/[4]/1/g' $filename | awk '{$1=""; print}' > $fileout # for alpha-helix

i=$((i+1))
done