dependency_install.bsh

E_AMBER=False
USE_MSA=True
USE_TEMPLATES=False

 

if [ ! -f AF2_READY ]; then
  # install dependencies
  pip -q install biopython
  pip -q install dm-haiku
  pip -q install ml-collections
  pip -q install py3Dmol

 

  # download model
  if [ ! -d "alphafold/" ]; then
    git clone https://github.com/deepmind/alphafold.git --quiet
    mv alphafold alphafold_
    mv alphafold_/alphafold .
    # remove "END" from PDBs, otherwise biopython complains
    sed -i "s/pdb_lines.append('END')//" /content/alphafold/common/protein.py
    sed -i "s/pdb_lines.append('ENDMDL')//" /content/alphafold/common/protein.py
  fi

 

  # download model params (~1 min)
  if [ ! -d "params/" ]; then
    wget -qnc https://storage.googleapis.com/alphafold/alphafold_params_2021-07-14.tar
    mkdir params
    tar -xf alphafold_params_2021-07-14.tar -C params/
    rm alphafold_params_2021-07-14.tar
  fi
  touch AF2_READY
fi
# download libraries for interfacing with MMseqs2 API
if [ ${USE_MSA} == "True" ] || [ ${USE_TEMPLATES} == "True" ]; then
  if [ ! -f MMSEQ2_READY ]; then
    apt-get -qq -y update 2>&1 1>/dev/null
    apt-get -qq -y install jq curl zlib1g gawk 2>&1 1>/dev/null
    touch MMSEQ2_READY
  fi
fi