mkdocs.yml

site_name: Rowan Python API
theme:
  name: material
  logo: images/RowanSquareLogo.png
  favicon: images/favicon.svg
  palette:
    - scheme: default # ← light mode
      primary: custom # tell Material we’re supplying a color
      accent: custom
    - scheme: slate # ← dark mode
      primary: custom
      accent: custom
  features:
    - navigation.sections
    - navigation.indexes
    - navigation.top
    - navigation.tracking
    - toc.follow
    - content.code.copy
    - content.code.annotate
    - content.tabs.link
    - search.suggest
    - search.highlight
extra_css:
  - stylesheets/colors.css
markdown_extensions:
  - admonition
  - attr_list
  - md_in_html
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.inlinehilite
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          paths: ["."]
          options:
            extensions:
              - griffe_pydantic:
                  schema: true
            heading_level: 3
            docstring_style: sphinx # ← "sphinx", "google" or "numpy"
            docstring_section_style: table # or "table" if you prefer grids
            show_signature_annotations: true
            merge_init_into_class: true # if you want __init__ docs on the class
            separate_signature: true # uses Black if it’s on your PATH
            line_length: 65
            unwrap_annotated: true
nav:
  - "← docs.rowansci.com": https://docs.rowansci.com
  - Get started: index.md
  - Account:
      - User: api/user.md
      - API keys: api/api-keys.md
      - Webhooks: api/webhooks.md
  - Objects:
      - Project: api/project.md
      - Folder: api/folder.md
      - Workflow: api/workflow.md
      - Calculation: api/calculation.md
      - Molecule: api/molecule.md
      - Protein: api/protein.md
  - Settings:
      - Settings: workflows/settings.md
      - Conformer search settings: workflows/conformer-search-settings.md
      - Types: workflows/types.md
  - Molecular modeling:
      - Basic calculation: workflows/basic-calculation.md
      - Conformer search: workflows/conformer-search.md
      - Solvent-dependent conformers: workflows/solvent-dependent-conformers.md
      - Scan: workflows/scan.md
      - Multistage optimization: workflows/multistage-optimization.md
      - Electronic properties: workflows/electronic-properties.md
      - IRC: workflows/irc.md
      - Double-ended TS search: workflows/double-ended-ts-search.md
      - Strain: workflows/strain.md
      - Interaction energy decomposition: workflows/interaction-energy-decomposition.md
      - Covalent inhibitor scan: workflows/covalent-inhibitor-scan.md
  - Property prediction:
      - Macroscopic pKa: workflows/macropka.md
      - pKa: workflows/pka.md
      - Redox potential: workflows/redox-potential.md
      - Fukui: workflows/fukui.md
      - Tautomer search: workflows/tautomer-search.md
      - Solubility: workflows/solubility.md
      - LogP: workflows/logp.md
      - Hydrogen bond donor/acceptor strength: workflows/hydrogen-bond-donor-acceptor-strength.md
      - Bond dissociation energy: workflows/bond-dissociation-energy.md
      - Spin states: workflows/spin-states.md
      - ADME-tox prediction: workflows/admet.md
      - Membrane permeability: workflows/membrane-permeability.md
  - Protein–ligand:
      - Protein preparation: workflows/protein-preparation.md
      - Docking: workflows/docking.md
      - Protein co-folding: workflows/protein-cofolding.md
      - Binding affinity: workflows/binding-affinity.md
      - Protein MD: workflows/protein-md.md
      - Pose-analysis MD: workflows/pose-analysis-md.md
      - Protein binder design: workflows/protein-binder-design.md
      - Pocket detection: workflows/pocket-detection.md
      - MSA: workflows/msa.md
      - Batch docking: workflows/batch-docking.md
      - Analogue docking: workflows/analogue-docking.md
      - RBFE graph: workflows/rbfe-graph.md
      - Relative binding free-energy perturbation: workflows/relative-binding-free-energy-perturbation.md
  - Spectrometry:
      - NMR prediction: workflows/nmr.md
      - Ion-mobility mass spectrometry prediction: workflows/ion-mobility.md
  - Cheminformatics:
      - Descriptors: workflows/descriptors.md

copyright: Copyright © 2023–2026 Rowan Scientific Corporation
extra:
  homepage: https://rowansci.com
  generator: true
  social:
    - icon: fontawesome/brands/x-twitter
      link: https://x.com/rowansci
    - icon: fontawesome/brands/linkedin
      link: https://www.linkedin.com/company/rowansci
    - icon: fontawesome/brands/github
      link: https://github.com/rowansci