rmsd:使用xyz或pdb格式旋转计算两个分子的均方根偏差(RMSD)-源码

上传者: 42122838 | 上传时间: 2021-06-03 19:55:41 | 文件大小: 138KB | 文件类型: ZIP
使用旋转计算两个分子的均方根偏差(RMSD) 使用.xyz或.pdb格式的两个笛卡尔坐标之间的旋转,使用Kabsch算法(1976)或四元数算法(1991)计算均方根偏差(RMSD),从而得到最小的RMSD。 有关更多信息,请阅读和。 动机 您拥有分子A和B,并想要计算两者之间的结构差异。 如果仅直接计算 ,则可能会产生太大的值,如下所示。 您需要首先使这两个分子重新居中,然后将它们彼此旋转以获得真正的最小RMSD。 这就是该脚本的作用。 没有变化 重新居中 旋转的 RMSD 2.50 RMSD 1.07 RMSD 0.25 引文 实施方式: 使用旋转计算两个分子的均方根偏差(RMSD),GitHub, , Kabsch算法: Kabsch W.,1976年,“最佳旋转与两个向量相关联的解决方案”,《晶体学报》,A32:922-

文件下载

资源详情

[{"title":"( 55 个子文件 138KB ) rmsd:使用xyz或pdb格式旋转计算两个分子的均方根偏差(RMSD)-源码","children":[{"title":"rmsd-master","children":[{"title":"setup.py <span style='color:#111;'> 1.29KB </span>","children":null,"spread":false},{"title":".gitignore <span style='color:#111;'> 344B </span>","children":null,"spread":false},{"title":"requirements.txt <span style='color:#111;'> 12B </span>","children":null,"spread":false},{"title":"Makefile <span style='color:#111;'> 55B </span>","children":null,"spread":false},{"title":".pre-commit-config.yaml <span style='color:#111;'> 2.78KB </span>","children":null,"spread":false},{"title":"LICENSE <span style='color:#111;'> 1.31KB </span>","children":null,"spread":false},{"title":".github","children":[{"title":"workflows","children":[{"title":"test.yml <span style='color:#111;'> 938B </span>","children":null,"spread":false},{"title":"publish.yml <span style='color:#111;'> 718B </span>","children":null,"spread":false}],"spread":true}],"spread":true},{"title":"requirements.dev.txt <span style='color:#111;'> 18B </span>","children":null,"spread":false},{"title":"example.py <span style='color:#111;'> 1.29KB </span>","children":null,"spread":false},{"title":"README.rst <span style='color:#111;'> 4.41KB </span>","children":null,"spread":false},{"title":"tests","children":[{"title":"test_kabsch_weighted.py <span style='color:#111;'> 1.04KB </span>","children":null,"spread":false},{"title":"test_centroid.py <span style='color:#111;'> 421B </span>","children":null,"spread":false},{"title":"resources","children":[{"title":"ethane_bond.xyz <span style='color:#111;'> 395B </span>","children":null,"spread":false},{"title":"ci2_12.pdb <span style='color:#111;'> 69.77KB </span>","children":null,"spread":false},{"title":"c6h7-int1-c.xyz <span style='color:#111;'> 615B </span>","children":null,"spread":false},{"title":"c6h7-int1-a.xyz <span style='color:#111;'> 615B </span>","children":null,"spread":false},{"title":"ci2_1r+t.pdb <span style='color:#111;'> 82.45KB </span>","children":null,"spread":false},{"title":"water_swapped.xyz <span style='color:#111;'> 150B </span>","children":null,"spread":false},{"title":"water_16_idx.xyz <span style='color:#111;'> 2.30KB </span>","children":null,"spread":false},{"title":"CHEMBL3039407.xyz <span style='color:#111;'> 2.88KB </span>","children":null,"spread":false},{"title":"c6h7-int2-t-b.xyz <span style='color:#111;'> 615B </span>","children":null,"spread":false},{"title":"ci2_1.pdb <span style='color:#111;'> 69.72KB </span>","children":null,"spread":false},{"title":"ethane_translate.xyz <span style='color:#111;'> 395B </span>","children":null,"spread":false},{"title":"water_16.xyz <span style='color:#111;'> 2.30KB </span>","children":null,"spread":false},{"title":"SF2HClBrI-b-nxnz.xyz <span style='color:#111;'> 262B </span>","children":null,"spread":false},{"title":"SF2HClBrI-xy.xyz <span style='color:#111;'> 301B </span>","children":null,"spread":false},{"title":"c6h7-int1-b.xyz <span style='color:#111;'> 615B </span>","children":null,"spread":false},{"title":"c6h7-int1-xz.xyz <span style='color:#111;'> 615B </span>","children":null,"spread":false},{"title":"SF2HClBrI-yz.xyz <span style='color:#111;'> 273B </span>","children":null,"spread":false},{"title":"c6h7-int2-t.xyz <span style='color:#111;'> 615B </span>","children":null,"spread":false},{"title":"SF2HClBrI-xz.xyz <span style='color:#111;'> 294B </span>","children":null,"spread":false},{"title":"SF2HClBrI-a.xyz <span style='color:#111;'> 297B </span>","children":null,"spread":false},{"title":"ethane_mini.xyz <span style='color:#111;'> 395B </span>","children":null,"spread":false},{"title":"SF2HClBrI-xnz.xyz <span style='color:#111;'> 294B </span>","children":null,"spread":false},{"title":"ci2_2.pdb <span style='color:#111;'> 69.67KB </span>","children":null,"spread":false},{"title":"water.xyz <span style='color:#111;'> 150B </span>","children":null,"spread":false},{"title":"ethane.xyz <span style='color:#111;'> 395B </span>","children":null,"spread":false},{"title":"SF2HClBrI-nyz.xyz <span style='color:#111;'> 318B </span>","children":null,"spread":false},{"title":"SF2HClBrI-nxnz.xyz <span style='color:#111;'> 311B </span>","children":null,"spread":false}],"spread":false},{"title":"test_rmsd.py <span style='color:#111;'> 0B </span>","children":null,"spread":false},{"title":"test_reorder_qml.py <span style='color:#111;'> 2.84KB </span>","children":null,"spread":false},{"title":"test_reorder.py <span style='color:#111;'> 3.44KB </span>","children":null,"spread":false},{"title":"context.py <span style='color:#111;'> 64B </span>","children":null,"spread":false},{"title":"test_kabsch.py <span style='color:#111;'> 947B </span>","children":null,"spread":false},{"title":"test_file_reading.py <span style='color:#111;'> 2.02KB </span>","children":null,"spread":false},{"title":"test_reflections.py <span style='color:#111;'> 3.48KB </span>","children":null,"spread":false},{"title":"test_args.py <span style='color:#111;'> 1.39KB </span>","children":null,"spread":false},{"title":"test_quaternion.py <span style='color:#111;'> 1.71KB </span>","children":null,"spread":false},{"title":"test_reorder_inertia.py <span style='color:#111;'> 1.80KB </span>","children":null,"spread":false}],"spread":false},{"title":"rmsd","children":[{"title":"__init__.py <span style='color:#111;'> 601B </span>","children":null,"spread":false},{"title":"calculate_rmsd.py <span style='color:#111;'> 47.78KB </span>","children":null,"spread":false}],"spread":true},{"title":"img","children":[{"title":"plot_rotated.png <span style='color:#111;'> 12.10KB </span>","children":null,"spread":false},{"title":"plot_beginning.png <span style='color:#111;'> 13.36KB </span>","children":null,"spread":false},{"title":"plot_translated.png <span style='color:#111;'> 13.22KB </span>","children":null,"spread":false}],"spread":true}],"spread":false}],"spread":true}]

评论信息

免责申明

【只为小站】的资源来自网友分享,仅供学习研究,请务必在下载后24小时内给予删除,不得用于其他任何用途,否则后果自负。基于互联网的特殊性,【只为小站】 无法对用户传输的作品、信息、内容的权属或合法性、合规性、真实性、科学性、完整权、有效性等进行实质审查;无论 【只为小站】 经营者是否已进行审查,用户均应自行承担因其传输的作品、信息、内容而可能或已经产生的侵权或权属纠纷等法律责任。
本站所有资源不代表本站的观点或立场,基于网友分享,根据中国法律《信息网络传播权保护条例》第二十二条之规定,若资源存在侵权或相关问题请联系本站客服人员,zhiweidada#qq.com,请把#换成@,本站将给予最大的支持与配合,做到及时反馈和处理。关于更多版权及免责申明参见 版权及免责申明