Bash shell answers for "Molecular modelling and computational biology 1"

first-test.sh

# 1. Create a directory with your name on your desktop
  mkdir ~/Desktop/Michal
# 2. Download a directory XYZ located in /home/login/somedir from login@host to your created directory
  cd ~/Desktop/Michal
  scp -r login@host:~/somedir/XYZ . # often you can skip '~/' after the colon - remote directories defaults to user's home
# 3. Merge files a.pdb with b.pdb, in this order, and save the result to c.pdb
  cd XYZ
  cat a.pdb b.pdb > c.pdb
# 4. Replace 'X' occurrences in lines 100-200 with 'Y' in the c.pdb file
  sed -ie '100,200s/X/Y/g' c.pdb  # the simplest way
  # echo "$(sed -e '100,200s/X/Y/g' c.pdb)" > c.pdb  # do this in a subshell
  # sed -e '100,200s/X/Y/g' c.pdb > c_new.pdb; mv c_new.pdb > c.pdb  # no way to forget this
# 5. Remove lines 100-101 from the c.pdb file
  sed -ie '100,101d' c.pdb