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mkdocs.yml
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# Project information
site_name: gmx_MMPBSA Documentation
site_url: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
site_author: Mario S. and Mario E. Valdés Tresanco
site_description: >-
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS
files
# Repository
repo_name: gmx_MMPBSA
repo_url: https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA
edit_uri: ""
# Copyright
copyright: Copyright © 2020 - 2021 MS. and ME. Valdes Tresanco
# Configuration
theme:
name: material
logo: assets/logo_white_border.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:
# - navigation.instant
- navigation.expand
- navigation.sections
- navigation.tabs
- navigation.top
- header.autohide
- toc.integrate
palette:
- scheme: default
primary: black
accent: black
toggle:
icon: material/weather-sunny
name: Switch to dark mode
- scheme: slate
primary: black
accent: black
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:
- search
- git-revision-date-localized:
type: datetime
enable_creation_date: true
# - redirects:
# redirect_maps:
## extensions/admonition.md: reference/admonitions.md
## extensions/codehilite.md: reference/code-blocks.md
## extensions/footnotes.md: reference/footnotes.md
## extensions/metadata.md: reference/meta-tags.md
## extensions/permalinks.md: setup/setting-up-navigation.md #permalink
## extensions/pymdown.md: reference/admonitions.md
## plugins/revision-date.md: setup/adding-a-git-repository.md #revision-date
## plugins/search.md: setup/setting-up-site-search.md
## releases/4.md: upgrading.md #upgrading-from-4x-to-5x
## releases/5.md: upgrading.md #upgrading-from-3x-to-4x
## releases/changelog.md: changelog.md
## setup/adding-social-links.md: setup/setting-up-the-footer.md
## sponsorship.md: insiders.md
- minify:
minify_html: true
# Customization
extra:
social:
- icon: fontawesome/brands/github
link: https://github.com/Valdes-Tresanco-MS
# Extensions
markdown_extensions:
- admonition
- abbr
- 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
- pymdownx.inlinehilite
- pymdownx.keys
- pymdownx.magiclink:
repo_url_shorthand: true
user: Valdes-Tresanco-MS
repo: gmx_MMPBSA
- pymdownx.mark
- pymdownx.smartsymbols
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- pymdownx.tabbed
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
# Page tree
nav:
- Home: index.md
- Getting started:
- Getting started: getting-started.md
- Introduction: introduction.md
- gmx_MMPBSA in a nutshell: summary.md
- gmx_MMPBSA vs other programs: versus.md
- Installation: installation.md
- Command-line: command-line.md
- Hands to work:
- How gmx_MMPBSA works: howworks.md
- The input file: input_file.md
- Output Files: output.md
- Advanced Options: advanced.md
- Python API: api.md
- gmx_MMPBSA_ana: analyzer.md
- Examples:
- Examples: examples/README.md
- Analysis:
- Protein-Ligand (MT): examples/Protein_ligand/MT/README.md
- Stability calculations: examples/Stability/README.md
- Alanine scanning: examples/Alanine_scanning/README.md
- Decomposition analysis: examples/Decomposition_analysis/README.md
- Entropy calculation:
- Interaction Entropy: examples/Entropy_calculations/Interaction_Entropy/README.md
- nmode Entropy: examples/Entropy_calculations/nmode/README.md
- MM/3D-RISM: examples/3D-RISM/README.md
- QM/MMGBSA: examples/QM_MMGBSA/README.md
- Systems:
- Protein-protein: examples/Protein_protein/README.md
- Protein-Ligand (ST): examples/Protein_ligand/ST/README.md
- Protein-DNA: examples/Protein_DNA/README.md
- Metalloprotein-peptide: examples/Metalloprotein_peptide/README.md
- Protein-DNA-RNA-Ions-Ligand: examples/Protein_DNA_RNA_Ion_ligand/README.md
- Binding free energy calculations in multicomponent systems: examples/Comp_receptor/README.md
- Protein-glycan: examples/Protein_glycan/README.md
- Membrane proteins: examples/Protein_membrane/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
- Charmm Support:
- Protein-Ligand (ST): examples/Protein_ligand_CHARMMff/README.md
- Protein-ligand complex embedded in membrane: examples/Protein_membrane_CHARMMff/README.md
- Mycalamide A Bound to the Large Ribosomal Subunit: examples/Ribosomal50S_Mycalamide_A/README.md
- Protein-Ligand with LPH particles (ST): examples/Protein_ligand_LPH_atoms_CHARMMff/README.md
- Q&A:
- Support: Q&A/README.md
- Installation: Q&A/installation.md
- OS issues: Q&A/OS_issues.md
- Calculations: Q&A/calculations.md
- Changelog:
- Changelog: changelog.md
- Compatibility: compatibility.md
- Private Policy: private_policy.md
- Cite us: cite_us.md
google_analytics:
- !!python/object/apply:os.getenv ["GOOGLE_ANALYTICS_KEY"]
- auto