mkdocs.yml

# Project information
site_name: xBFreE Documentation
site_url: https://xbfreenergy.github.io/xBFreE/dev
site_author: Mario S. and Mario E. Valdés-Tresanco
site_description: >-
  xBFreE is a tool for Binding Free Energy calculations

# Repository
repo_name: xBFreE
repo_url: https://github.com/xBFreEnergy/xBFreE
edit_uri: ""

# Copyright
copyright: Copyright © 2020 - 2023 MS. and ME. Valdés-Tresanco

###########################



#############################
# Configuration
theme:
  name: material
  logo: assets/logo.svg
  custom_dir: docs/overrides


  # 404 page
  static_templates:
    - 404.html

  # Don't include MkDocs' JavaScript
  include_search_page: false
  search_index_only: true

  # Default values, taken from mkdocs_theme.yml
  language: en
  features:
    - announce.dismiss
    - content.action.edit
    - content.action.view
    - content.code.annotate
    - content.code.copy
    - content.tabs.link
    - content.tooltips
    # - header.autohide
    # - navigation.expand
    - navigation.footer
    - navigation.indexes
    # - navigation.instant
#    - navigation.expand
    - navigation.sections
    - navigation.tabs
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    # - header.autohide
#    - toc.integrate
    - toc.follow

  palette:
    - scheme: default
      primary: deep purple
      accent: deep purple
      toggle:
        icon: material/weather-sunny
        name: Switch to dark mode
    - scheme: slate
      primary: deep purple
      accent: deep purple
      toggle:
        icon: material/weather-night
        name: Switch to light mode

  font:
    text: Roboto
    code: Roboto Mono
  favicon: assets/logo.svg
  icon:
    logo: logo

# Plugins
plugins:
  - tags:
      tags_file: tags.md
  - search
  - git-revision-date-localized:
      type: timeago
      enable_creation_date: true
  - git-committers:
      repository: xBFreEnergy/xBFreE
      branch: master
  - minify:
      minify_html: true

# Customization
extra:
  analytics:
    provider: google
    property: !ENV GOOGLE_ANALYTICS_KEY
    feedback:
      title: Was this page helpful?
      ratings:
        - icon: material/emoticon-happy-outline
          name: This page was helpful
          data: 1
          note: >-
            Thanks for your feedback!
        - icon: material/emoticon-sad-outline
          name: This page could be improved
          data: 0
          note: >-
            Thanks for your feedback! Help us improve this page by
            using our <a href="https://github.com/xBFreEnergy/xBFreE/issues/new" target="_blank" rel="noopener">feedback form</a>.

  social:
    - icon: fontawesome/brands/github
      link: https://github.com/xBFreEnergy
  version:
    provider: mike
  consent:
    title: Cookie consent
    description: >-
      We use Google Analytics as a third party tracking service. We do not share, sell, rent, or trade this information 
      with third parties for their commercial purposes; and we only use it as this 
      <a href="/help/private_policy/">Privacy Policy</a> describes. This helps us improve documentation and have 
      usage statistics to apply for financing. Thank you.
    actions:
      - accept

# Extensions
markdown_extensions:
  - admonition
  - abbr
  - pymdownx.snippets:
      auto_append:
        - includes/abbreviations.md
  - attr_list
  - def_list
  - footnotes
  - meta
  - md_in_html
  - toc:
      permalink: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:materialx.emoji.twemoji
      emoji_generator: !!python/name:materialx.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.magiclink:
      repo_url_shorthand: true
      user: Valdes-Tresanco-MS
      repo: xBFreE
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

# Page tree
nav:
  - Home: index.md
  - Getting started:
    - Getting started: getting-started/getting-started.md
    - xBFreE in a nutshell: getting-started/summary.md
    - Installation: getting-started/installation.md
  - MMPBSA:
      - MMPBSA: mmpbsa/index.md
      - xBFreE vs other programs: mmpbsa/versus.md
      - How it works: mmpbsa/howworks.md
      - Command-line: mmpbsa/command-line.md
      - Running MMPBSA calculations: mmpbsa/running_mmpbsa.md
      - The input file:
          - Input file: mmpbsa/input_file/index.md
          - Name List:
              - General: mmpbsa/input_file/general.md
              - GB: mmpbsa/input_file/gb.md
              - GBNSR6: mmpbsa/input_file/gbnsr6.md
              - PB: mmpbsa/input_file/pb.md
#              - DelPhi: mmpbsa/input_file/delphi.md
              - 3D-RISM: mmpbsa/input_file/rism.md
              - Decomposition: mmpbsa/input_file/decomp.md
              - Alanine Scanning: mmpbsa/input_file/cas.md
              - Nmodes: mmpbsa/input_file/nmodes.md
      - PBRadii: mmpbsa/pbradii.md
      - The output file: mmpbsa/output.md
#  - LIE:
#      - Introduction: lie/introduction.md
#      - xBFreE vs other program: lie/versus.md
#      - Command-line: lie/command-line.md
#      - Running LIE calculations: lie/running_lie.md
#      - The input file: lie/input_file.md
#      - The output file: lie/output.md
#  - FEP:
#      - Introduction: fep/introduction.md
#      - xBFreE vs other program: fep/versus.md
#      - Command-line: fep/command-line.md
#      - Running LIE calculations: fep/running_fep.md
#      - The input file: fep/input_file.md
#      - The output file: fep/output.md
#  - TI:
#      - Introduction: ti/introduction.md
#      - xBFreE vs other program: ti/versus.md
#      - Command-line: ti/command-line.md
#      - Running LIE calculations: ti/running_ti.md
#      - The input file: ti/input_file.md
#      - The output file: ti/output.md

  - Examples:
    - Examples: examples/README.md
    - gmx_MMPBSA_test: examples/gmx_MMPBSA_test.md
    - Systems:
        - Systems: examples/Protein_protein/README.md
        - Protein-protein: examples/Protein_protein/README.md
        - Protein-ligand: examples/Protein_ligand/ST/README.md
#      - Protein-DNA: examples/Protein_DNA/README.md
#      - Protein-glycan: examples/Protein_glycan/README.md
#      - Membrane proteins: examples/Protein_membrane/README.md
#      - Metalloprotein-ligand: examples/Metalloprotein_ligand/README.md
#      - Multicomponent system: examples/Comp_receptor/README.md
#      - COVID-19 related proteins:
#          - Info: examples/COVID-19_related_proteins/README.md
#          - Main protease: examples/COVID-19_related_proteins/Main_protease_7l5d/README.md
#          - Papain-like protease: examples/COVID-19_related_proteins/Papain-like_protease_7koj/README.md
#          - S1-ACE2 complex: examples/COVID-19_related_proteins/S1-ACE2_complex_7dmu/README.md
#          - S1 RBD with antibody: examples/COVID-19_related_proteins/S1_RBD_with_antibody_6zlr/README.md
#    - CHARMMff Support:
#        - Protein-ligand: examples/Protein_ligand_CHARMMff/README.md
#        - Protein-ligand complex embedded in membrane: examples/Protein_membrane_CHARMMff/README.md
#        - Protein-ligand with LPH particles (ST): examples/Protein_ligand_LPH_atoms_CHARMMff/README.md
#    - OPLSff Support:
#        - Protein-protein: examples/OPLS/protein_protein/README.md
    - Analysis:
        - Analysis: examples/Protein_ligand/ST/README.md
        - Single Trajectory Protocol: examples/Protein_ligand/ST/README.md
        - Multiple Trajectory Protocol: examples/Protein_ligand/MT/README.md
        - BFE calculations:
            - BFE calculations: examples/Protein_ligand/ST/README.md
            - BFE calculation with GB: examples/Protein_ligand/ST/README.md
            - BFE calculation with GBNSR6: examples/GBNSR6/README.md
            - BFE calculation with Linear PB: examples/Linear_PB_solver/README.md
            - BFE calculation with NonLinear PB : examples/NonLinear_PB_solver/README.md
            - BFE calculation with 3D-RISM: examples/3D-RISM/README.md
        - Alanine scanning: examples/Alanine_scanning/README.md
        - Decomposition analysis: examples/Decomposition_analysis/README.md
        - Entropy calculations:
            - Entropy calculations: examples/Entropy_calculations/Interaction_Entropy/README.md
            - Interaction Entropy: examples/Entropy_calculations/Interaction_Entropy/README.md
            - nmode Entropy: examples/Entropy_calculations/nmode/README.md
            - C2 Entropy calculations: examples/Entropy_calculations/C2_Entropy/README.md
        - Stability calculations: examples/Stability/README.md
        - QM/MMGBSA: examples/QM_MMGBSA/README.md
        - Correlation: examples/Correlation/README.md

  - More Info:
    - Help:
      - Help: Q&A/README.md
      - Installation: Q&A/installation.md
      - OS issues: Q&A/OS_issues.md
      - Calculations: Q&A/calculations.md
    - Info:
      - Changelog: changelog.md
      - Compatibility: compatibility.md
      - Private Policy: private_policy.md
      - Tags: tags.md
    - Support: support.md

  - Cite xBFreE: cite_us.md

extra_css:
  - assets/stylesheets/termynal.css
  - assets/stylesheets/custom.css
extra_javascript:
  - assets/js/termynal.js
  - assets/js/custom.js
  - assets/js/mathjax.js
  - assets/js/news.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js