-
Notifications
You must be signed in to change notification settings - Fork 0
/
mkdocs.yml
executable file
·289 lines (268 loc) · 9.01 KB
/
mkdocs.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
# Project information
site_name: xBFreE-Analyzer Documentation
site_url: https://xBFreEnergy.github.io/xBFreE-Analyzer/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-Analyzer
repo_url: https://github.com/xBFreEnergy/xBFreE-Analyzer
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: purple
accent: purple
toggle:
icon: material/weather-sunny
name: Switch to dark mode
- scheme: slate
primary: purple
accent: purple
toggle:
icon: material/weather-night
name: Switch to light mode
#
# - 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:
- tags:
tags_file: tags.md
- search
- git-revision-date-localized:
type: timeago
enable_creation_date: true
- 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="..." target="_blank" rel="noopener">feedback form</a>.
social:
- icon: fontawesome/brands/github
link: https://github.com/xBFreEnergy/xBFreE-Analyzer
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 Privacy Policy 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:
- xBFreE-Analyzer: analyzer.md
# - xBFreE in a nutshell: getting-started/summary.md
# - Installation: getting-started/installation.md
# - Command-line: getting-started/command-line.md
# - MMPBSA:
# - Introduction: mmpbsa/introduction.md
# - xBFreE vs other program: 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: mmpbsa/input_file.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:
# - 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:
# - Single Trajectory Protocol: examples/Protein_ligand/ST/README.md
# - Multiple Trajectory Protocol: examples/Protein_ligand/MT/README.md
# - BFE calculations:
# - 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:
# - 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
- 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
- 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
- https://polyfill.io/v3/polyfill.min.js?features=es6
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js