AutoDock-Pipeline/environment.yml at main · RahulRoktim/AutoDock-Pipeline · GitHub

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name: autodock_pipeline

channels:
  - conda-forge
  - defaults

dependencies:

  # ==================================================
  # Python
  # ==================================================

  - python=3.11

  # ==================================================
  # Scientific Computing
  # ==================================================

  - numpy
  - scipy
  - pandas
  - matplotlib

  # ==================================================
  # Chemistry
  # ==================================================

  - rdkit
  - openbabel
  - biopython

  # ==================================================
  # Utilities
  # ==================================================

  - pyyaml
  - requests
  - tqdm
  - joblib
  - networkx
  - psutil

  # ==================================================
  # Excel
  # ==================================================

  - openpyxl
  - xlsxwriter

  # ==================================================
  # Development
  # ==================================================

  - pytest
  - pip

  - pip:

      # Chemistry
      - meeko
      - gemmi
      - pubchempy
      - dimorphite-dl        # pH-based ligand protonation (audit finding 3.1)
      - pdb2pqr              # pKa-aware receptor protonation (audit finding 3.1)
      - propka               # pKa prediction backend used by pdb2pqr
      - prolif               # protein-ligand interaction fingerprints
      - MDAnalysis           # structure backend used by ProLIF

      # Reporting
      - jinja2
      - reportlab

      # Machine Learning
      - scikit-learn

      # Visualization
      - plotly

      # Development
      - black
      - ruff