From 56cf35ee8b8603f6078edbe02306ef1a7fdbb220 Mon Sep 17 00:00:00 2001 From: CyberCatQ <544158656@qq.com> Date: Mon, 4 Mar 2024 13:13:57 +0800 Subject: [PATCH] doc update --- .buildinfo | 2 +- README.html | 2 +- _modules/index.html | 2 +- _sources/dynamic.md.txt | 2 ++ dance.html | 2 +- demand.html | 2 +- density.html | 2 +- dock.html | 2 +- dynamic.html | 4 +++- genindex.html | 2 +- index.html | 2 +- modules.html | 2 +- py-modindex.html | 2 +- pyCADD.Dance.algorithm.html | 2 +- pyCADD.Dance.html | 2 +- pyCADD.Demand.html | 2 +- pyCADD.Density.html | 2 +- pyCADD.Dock.html | 2 +- pyCADD.Dynamic.html | 2 +- pyCADD.VSW.html | 2 +- pyCADD.html | 2 +- pyCADD.utils.html | 2 +- search.html | 2 +- searchindex.js | 2 +- 24 files changed, 27 insertions(+), 23 deletions(-) diff --git a/.buildinfo b/.buildinfo index af39255..7a38012 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: b7be94ff9a7cd59a7eb0e8897f0ad85f +config: 691426e65b111dd3fdee72aca3bc5871 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/README.html b/README.html index 1b72fd1..16f42cb 100644 --- a/README.html +++ b/README.html @@ -435,7 +435,7 @@

更新日志 -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/_modules/index.html b/_modules/index.html index 7d097f5..4662718 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -120,7 +120,7 @@

All modules for which code is available

-

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/_sources/dynamic.md.txt b/_sources/dynamic.md.txt index 6697fca..52c5e69 100644 --- a/_sources/dynamic.md.txt +++ b/_sources/dynamic.md.txt @@ -210,7 +210,9 @@ processor.add_process('input_file/heat.in', 'heat', 'heat') processor.add_process('input_file/eq_npt.in', 'eq_npt', 'npt') processor.add_process('input_file/eq_nvt.in', 'eq_nvt', 'nvt') processor.add_process('input_file/production.in', 'production', 'npt') + simulator = Simulator(processor) +simulator.run_simulation(with_gpu=0) ``` ## 模拟结果分析 diff --git a/dance.html b/dance.html index 003c5d9..c0367aa 100644 --- a/dance.html +++ b/dance.html @@ -236,7 +236,7 @@

建模与评估 Modeling and Evaluation -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/demand.html b/demand.html index 152b79b..d73b324 100644 --- a/demand.html +++ b/demand.html @@ -168,7 +168,7 @@

通过 python 包检索 PDB 数据
-

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/density.html b/density.html index 6e76f1f..6e97256 100644 --- a/density.html +++ b/density.html @@ -121,7 +121,7 @@

Function -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/dock.html b/dock.html index 2feb3fd..d9e99f5 100644 --- a/dock.html +++ b/dock.html @@ -237,7 +237,7 @@

为系综对接构建Dock输入文件的示例 -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/dynamic.html b/dynamic.html index f7c98c7..bf74793 100644 --- a/dynamic.html +++ b/dynamic.html @@ -318,7 +318,9 @@

构建MD工作流并执行模拟processor.add_process('input_file/eq_npt.in', 'eq_npt', 'npt') processor.add_process('input_file/eq_nvt.in', 'eq_nvt', 'nvt') processor.add_process('input_file/production.in', 'production', 'npt') + simulator = Simulator(processor) +simulator.run_simulation(with_gpu=0) @@ -471,7 +473,7 @@

MM-GBSA 结合自由能计算与能量分解 -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/genindex.html b/genindex.html index c78c199..cbcb4c6 100644 --- a/genindex.html +++ b/genindex.html @@ -1380,7 +1380,7 @@

V

-

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/index.html b/index.html index 2cbdf8f..5fc6528 100644 --- a/index.html +++ b/index.html @@ -163,7 +163,7 @@

Indices and tables -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/modules.html b/modules.html index db13ce3..d033ed1 100644 --- a/modules.html +++ b/modules.html @@ -181,7 +181,7 @@

pyCADD
-

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/py-modindex.html b/py-modindex.html index 432d107..4b329e6 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -316,7 +316,7 @@

Python Module Index

-

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/pyCADD.Dance.algorithm.html b/pyCADD.Dance.algorithm.html index 25e283d..eed9ca2 100644 --- a/pyCADD.Dance.algorithm.html +++ b/pyCADD.Dance.algorithm.html @@ -410,7 +410,7 @@

Return
-

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/pyCADD.Dance.html b/pyCADD.Dance.html index 0f97c4e..f273ac8 100644 --- a/pyCADD.Dance.html +++ b/pyCADD.Dance.html @@ -625,7 +625,7 @@

Parameters -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/pyCADD.Demand.html b/pyCADD.Demand.html index 096f5c1..c720610 100644 --- a/pyCADD.Demand.html +++ b/pyCADD.Demand.html @@ -248,7 +248,7 @@

Parameters -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/pyCADD.Density.html b/pyCADD.Density.html index 34cdedf..dd88bbe 100644 --- a/pyCADD.Density.html +++ b/pyCADD.Density.html @@ -494,7 +494,7 @@

Return
-

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/pyCADD.Dock.html b/pyCADD.Dock.html index 7ae3e3a..bb3859e 100644 --- a/pyCADD.Dock.html +++ b/pyCADD.Dock.html @@ -1156,7 +1156,7 @@

Returns -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/pyCADD.Dynamic.html b/pyCADD.Dynamic.html index 63aae38..09d4e26 100644 --- a/pyCADD.Dynamic.html +++ b/pyCADD.Dynamic.html @@ -1202,7 +1202,7 @@

Returns
-

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/pyCADD.VSW.html b/pyCADD.VSW.html index bf6849d..0a89a93 100644 --- a/pyCADD.VSW.html +++ b/pyCADD.VSW.html @@ -357,7 +357,7 @@

Parameters -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/pyCADD.html b/pyCADD.html index 5c87dca..750671c 100644 --- a/pyCADD.html +++ b/pyCADD.html @@ -642,7 +642,7 @@

Subpackages -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/pyCADD.utils.html b/pyCADD.utils.html index ea53006..fcaa261 100644 --- a/pyCADD.utils.html +++ b/pyCADD.utils.html @@ -414,7 +414,7 @@

Parameters -

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/search.html b/search.html index b555b79..064d6bb 100644 --- a/search.html +++ b/search.html @@ -104,7 +104,7 @@
-

© Copyright 2024, Yuhang Wu.

+

© Copyright 2023, Yuhang Wu.

Built with Sphinx using a diff --git a/searchindex.js b/searchindex.js index 4b5b4d5..fb9a9f0 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["README", "dance", "demand", "density", "dock", "dynamic", "index", "modules", "pyCADD", "pyCADD.Dance", "pyCADD.Dance.algorithm", "pyCADD.Demand", "pyCADD.Density", "pyCADD.Dock", "pyCADD.Dynamic", "pyCADD.VSW", "pyCADD.utils"], "filenames": ["README.md", "dance.md", "demand.md", "density.md", "dock.md", "dynamic.md", "index.rst", "modules.rst", "pyCADD.rst", "pyCADD.Dance.rst", "pyCADD.Dance.algorithm.rst", "pyCADD.Demand.rst", "pyCADD.Density.rst", "pyCADD.Dock.rst", "pyCADD.Dynamic.rst", "pyCADD.VSW.rst", "pyCADD.utils.rst"], "titles": ["pyCADD", "Dance User Guide", "Demand User Guide", "Density User Guide", "Dock User Guide", "Dynamic User Guide", "pyCADD Documentation", "pyCADD", "pyCADD package", "pyCADD.Dance package", "pyCADD.Dance.algorithm package", "pyCADD.Demand package", "pyCADD.Density 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