conda_env_colab.yml

name: symdesign-dev
channels:
  - conda-forge
#  - defaults
  - pytorch
  - nvidia
  - bioconda
## PyMol
#  - schrodinger
dependencies:
  - python=3.9  # =3.10
  - numpy
  - pandas
  - scikit-learn
  - scipy
  - numba
  - sqlalchemy=1.4 # Remove to 2.0 once finished with warnings
  - mysqlclient
  - alembic
  - psutil
  - pytorch
  - torchvision
  - torchaudio
  - cudatoolkit=11.3
  - hhsuite
  - requests
  - biopython<=1.81
  - matplotlib
  - tqdm
  - proglog
  - flametree
# Alphafold
  - cudnn # ==8.0.4
  - jax==0.4.2 # jax/jaxlib 0.4.4 broke jnp.asarray() for me ...
  - jaxlib==0.4.2
  - cuda-nvcc=11.3 # Used to ensure same version as cudatoolkit
  - hmmer
  - kalign2
#  - openmm=7.5.1 # version causes conflicts, alphafold needs to update to 8.0.0 to be compatible without versions
  - openmm=7.7.0
  - pdbfixer
  - pip
# Dev below here
  - memory_profiler
# Notebook packages
  - jupyter
  - ipykernel < 6
  - ipywidgets < 8
  - py3dmol
  - seaborn
  - google-colab
## PyMol
#  - pymol-bundle
  - pip:
    - absl-py==1.0.0
    - chex==0.0.7
    - dm-haiku==0.0.9
    - dm-tree==0.1.6
    - immutabledict==2.0.0
    - ml-collections==0.1.0
    - tensorflow-cpu==2.11.0
    - pdbecif
    - dnachisel