# struct — structural biology / ESM / torch (Python 3.13)
#
# Derived from all_env_packages.csv. Lists the headline scientific packages
# only; conda resolves the full dependency tree. Versions match the CSV where
# they are meaningful top-level packages.
#
# NOTE: torch is installed via pip (the safest portable CPU build). To use a
# GPU/accelerated build instead, substitute a conda pytorch build here, e.g.
#   dependencies:
#     - pytorch=2.12.1   # (from the conda-forge / pytorch channel)
# and drop torch from the pip: section below.
#
# RFdiffusion is intentionally NOT installed in this shared environment. Its
# official environment/container is Python 3.9 plus a CUDA-specific older
# PyTorch/DGL stack, which is incompatible with this portable Python 3.13 CPU
# environment. Run RFdiffusion in a pinned dedicated env or container; keep
# interoperable structure-analysis dependencies here.
name: struct
channels:
  - conda-forge
  - bioconda
dependencies:
  - python=3.13
  # structural biology
  - biotite=1.7.1
  - biotraj=1.2.2
  - biopython=1.88
  - freesasa=2.2.1
  - dssp=4.6.1
  # numerics / plotting
  - numpy
  - scipy
  - matplotlib
  - networkx
  - sympy
  # pip-only packages (torch via pip = safest portable CPU build)
  - pip
  - pip:
      - torch==2.12.1
      - fair-esm==2.0.0