old_contents: #!/usr/bin/env python3
  
  import sys
  import subprocess
  
  gnina = sys.argv[1]  # path to gnina executable
  
  subprocess.check_call('%s  -r data/rec.pdb -l data/lig.mol2 \
      --cnn_scoring --minimize \
      -o lig-min.pdb --out_flex flex.pdb \
      --gpu'
      %(gnina), shell=True)
new_contents: #!/usr/bin/env python3
  
  import sys
  import subprocess
  
  gnina = sys.argv[1]  # path to gnina executable
  
  subprocess.check_call('%s  -r data/rec.pdb -l data/lig.mol2 \
      --cnn_scoring --minimize \
      --flexdist 3 --flexdist_ligand data/lig.mol2 \
      -o lig-min.pdb --out_flex flex.pdb \
      --gpu'
      %(gnina), shell=True)
subject: enable flexible minimisation for test