q2mm/properdocs.yml at master · ericchansen/q2mm · GitHub

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site_name: Q2MM
site_url: https://ericchansen.github.io/q2mm/
site_description: Quantum-guided molecular mechanics force field optimization
repo_url: https://github.com/ericchansen/q2mm
repo_name: ericchansen/q2mm

theme:
  name: material
  palette:
    - scheme: default
      primary: deep purple
      accent: amber
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: deep purple
      accent: amber
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - content.code.copy
    - navigation.sections
    - navigation.top
    - toc.follow

nav:
  - Home: index.md
  - Getting Started: getting-started.md
  - Tutorial: tutorial.md
  - Platform Support: platform-support.md
  - How It Works:
    - Theory & Methods: how-it-works/theory.md
    - Architecture: how-it-works/architecture.md
    - Data Types: how-it-works/data-types.md
    - Optimization Guide: how-it-works/optimization-guide.md
    - Differences from v4: how-it-works/comparison.md
  - Backend Engines:
    - Overview: backends/index.md
    - OpenMM: backends/openmm.md
    - Tinker: backends/tinker.md
    - JAX: backends/jax-engine.md
    - JAX-MD: backends/jax-md.md
    - Psi4 (QM): backends/psi4.md
  - Benchmarks:
    - Overview: benchmarks/index.md
    - Optimizer Comparison: benchmarks/optimizer-comparison.md
    - GPU Acceleration: benchmarks/gpu.md
    - When Analytical Wins: benchmarks/crossover.md
    - Published FF Validation: benchmarks/published-ff-validation.md
    - QFUERZA Validation: benchmarks/qfuerza-validation.md
    - QFUERZA Recovery: benchmarks/qfuerza-recovery.md
  - Systems:
    - Small Molecules: systems/small-molecules.md
    - Rh-Enamide: systems/rh-enamide.md
    - Heck Relay: systems/heck-relay.md
    - Pd-Allyl: systems/pd-allyl.md
    - Pd 1,4-Conjugate: systems/pd-conjugate.md
    - Rh 1,4-Conjugate: systems/rh-conjugate.md
  - API Reference: reference/
  - References: references.md

markdown_extensions:
  - admonition
  - footnotes
  - pymdownx.details
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.inlinehilite
  - pymdownx.tabbed:
      alternate_style: true
  - tables
  - toc:
      permalink: true

extra_css:
  - stylesheets/extra.css

extra_javascript:
  - javascripts/mathjax.js
  - https://unpkg.com/mathjax@3.2.2/es5/tex-mml-chtml.js
  - javascripts/benchmarks.js

plugins:
  - search
  - gen-files:
      scripts:
        - scripts/gen_ref_pages.py
  - literate-nav:
      nav_file: SUMMARY.md
  - section-index
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          paths: [.]
          options:
            docstring_style: google
            show_source: true
            show_root_heading: true
            show_root_full_path: false
            show_symbol_type_heading: true
            show_symbol_type_toc: true
            members_order: source
            merge_init_into_class: true
            show_signature_annotations: true
            separate_signature: true
            signature_crossrefs: true