# chinese-pyrosetta **Repository Path**: zerodesigner/chinese-pyrosetta ## Basic Information - **Project Name**: chinese-pyrosetta - **Description**: No description available - **Primary Language**: Unknown - **License**: Not specified - **Default Branch**: master - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2021-04-22 - **Last Updated**: 2021-05-18 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README # PyRosetta Basic 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 ## 大纲内容: ### 零、安装与入门介绍 0.0 [Installation](https://github.com/guyujun/chinese-pyrosetta/blob/master/0_0_Installation.ipynb) 0.1 [Python_Basic](https://github.com/guyujun/chinese-pyrosetta/blob/master/0_1_Python_Basic.ipynb) 0.2 Utils ### 一、Pose与Structure IO: 负责介绍PyRosetta对结构文件的处理，以及Pose对象的重要作用 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](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/1_PoseIO/1_0_Pose_Abstract.ipynb) - 1.1 [Pose IO](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/1_PoseIO/1_1_Pose_IO.ipynb) - 1.2 [PymolMover](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/1_PoseIO/1_2_PyMover_PyRosetta.ipynb) - 1.3 [Pose & PDBinfo](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/1_PoseIO/1_3_Pose_PDBinfo.ipynb) - 1.4 [Atom & Residue](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/1_PoseIO/1_4_Atom_Residue.ipynb) - 1.5 [Conformation & Protein Geometry](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/1_PoseIO/1_5_Conformation_Geometry.ipynb) - 1.6 [Pose Operation](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/1_PoseIO/1_6_Pose_Operating.ipynb) ### 二、Energy Function与Constraint: 介绍Rosetta的能量函数与物理约束 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](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/2_Energy/2_1_Atom_Model.ipynb) - 2.1 [Energy Terms and Score Function](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/2_Energy/2_2_Energy_Function.ipynb) - 2.2 [Constraints](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/2_Energy/2_3_Constraint.ipynb) ### 三、Kinematics与Trees: 介绍Rosetta的骨架自由度控制 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](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/3_Kinematics/3_0_FoldTree.ipynb) - 3.1 Docking Tree & Jumps - 3.2 MoveMap ### 四、Monte Carlo: 介绍Rosetta中的蒙特卡洛算法【核心】 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](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/4_MCMC/4_0_Metropolis_Monte_Carlo.ipynb) - 4.1 [Movers & MC object ](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/4_MCMC/4_1_Movers_MC_object.ipynb) - 4.2 [Fragment_Folding](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/4_MCMC/4_2_Fragment_Folding.ipynb) ### 五、Residue Selector: 介绍残基选择器 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](https://nbviewer.jupyter.org/github/guyujun/chinese-pyrosetta/blob/master/ResidueSelectors.ipynb) - 5.0 [Residue Selector的逻辑](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/5_Residue_Selector/5_0_ResidueSelectors_Logic.ipynb) - 5.1 [Residue Selector的API查询](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/5_Residue_Selector/5_1_ResidueSelector_ApiSearch.ipynb) ### 六、Packer与TaskOperation: 介绍Packer与氨基酸侧链自由度控制 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](https://nbviewer.jupyter.org/github/guyujun/pyrosetta-basic/blob/master/6_Packer_TaskOperation/6_0_Rotamer_Packer.ipynb) - 6.2 TaskOperation、TaskFactory与PackTask（Rotamer自由度控制） - 6.3 NCAA(调色板) ### 七、SimpleMetric: 新一代特征计算和记录工具 负责人:@槐喆 @黄健 进度: 30% > SimpleMetric的API总结 https://zhuanlan.zhihu.com/p/58383955 - 7.0 SimpleMetric - ???? ### 八、Filters: 过滤器，大过滤器！ 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 ### 九、xmlObject & RosettaScript: xmlObject如何解决Rosetta历史遗留问题 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 ### ## 参考资料: 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