PyRosetta Basic中文教程，讲解Rosetta的基本原理以及在PyRosetta中的应用实例。

@文档贡献者：

1. 吴炜坤 @晶泰人工智能研发中心
2. 黄健 @晶泰人工智能研发中心
3. 张博文 @晶泰人工智能研发中心
4. 槐喆 @晶泰人工智能研发中心 实习生

@校对：

1. 王天元 @晶泰人工智能研发中心
2. 郭宁 @晶泰人工智能研发中心
3. 张晨虹 @晶泰人工智能研发中心

@外援支持:

1. 刘源 博士后 北京大学王初课题组

0.0 Installation

0.1 Python_Basic

0.2 Utils

负责人:@吴炜坤 进度: 100%

相关的官方章节: http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.00-Introduction-to-PyRosetta.ipynb

• 1.0 Pose Object Abstract

• 1.1 Pose IO

• 1.2 PymolMover

• 1.3 Pose & PDBinfo

• 1.4 Atom & Residue

• 1.5 Conformation & Protein Geometry

• 1.6 Pose Operation

负责人: @黄健 进度: 60%

相关的官方章节: http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.00-Rosetta-Energy-Score-Functions.ipynb

Constraint的API总结: https://zhuanlan.zhihu.com/p/58897635

• 2.0 Atom Model

• 2.1 Energy Terms and Score Function

• 2.2 Constraints

负责人:@张博文 进度: 33%

相关的官方章节: http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.00-Introduction-to-Folding.ipynb

Foldtree的概念: https://zhuanlan.zhihu.com/p/59863638

• 3.0 FoldTree与顺序性

• 3.1 Docking Tree & Jumps

• 3.2 MoveMap

负责人:@吴炜坤 进度: 100%

相关的官方章节:https://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/4.02-Low-Res-Scoring-and-Fragments.ipynb

相关的官方章节: http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.00-Structure-Refinement.ipynb

• 4.0 Metropolis & Simulated annealing

• 4.1 Movers & MC object

• 4.2 Fragment_Folding

负责人:@槐喆 进度: 50% 。校对:@吴炜坤

中文总结：https://zhuanlan.zhihu.com/p/58348980

官网资料: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/ResidueSelectors/ResidueSelectors

residue selector preview

• 5.0 Residue Selector的逻辑

• 5.1 Residue Selector的API查询

负责人:@吴炜坤 进度: 50%

相关的官方章节: http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.00-Introduction-to-Packing-and-Design.ipynb

• 6.1 Rotamers & Packer

• 6.2 TaskOperation、TaskFactory与PackTask（Rotamer自由度控制）

• 6.3 NCAA(调色板)

负责人:@槐喆 @黄健 进度: 30%

SimpleMetric的API总结 https://zhuanlan.zhihu.com/p/58383955

• 7.0 SimpleMetric

• ????

负责人: @黄健 @张博文 进度: 0%

官网资料: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Filters/Filters-RosettaScripts

• 8.0 Filters的逻辑

• 8.1 Filters的API

负责人:@黄健 进度: 0%

xmlObject的API总结: https://zhuanlan.zhihu.com/p/58381573

官网资料:

1. https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/RosettaScripts
2. https://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.07-RosettaScripts-in-PyRosetta.ipynb

• 9.0 RosettaScript

• 9.1 XmlObject

• 9.2 自定义Mover

• 9.3 PyRosetta的多进程化

中文开源计划的地址: https://github.com/guyujun/chinese-pyrosetta

PyRosetta Notebook开源地址: https://github.com/RosettaCommons/PyRosetta.notebooks

PyRosetta API查询: https://graylab.jhpytu.edu/PyRosetta.documentation/search.html?q=cdr

Rosetta中文知乎: https://www.zhihu.com/column/rosettastudy