D3pockets静态性质生成
服务器205
生成口袋
- python27ana /home/zqchen/D3Pockets_WEB_UCB/PyPocket_Detect.py -r test.pdb
生成口袋的atm和pit文件在同一个文件夹
生成静态性质
atm,pit以及原始的pdb需要在同一个文件夹下
- python27ana /home/zqchen/D3Pockets_Descriptors/d3pockets_desciptors_rec.py -r test.pdb
输出结果
result_descriptors.txt
参数具体意义
| 列数 | 参数名称 | 参数意义 | 参考资料 | ||||||||||||||
| 1 | recfile | 受体pdb | |||||||||||||||
| 2 | pitfile | 口袋的格点文件 | |||||||||||||||
| 3 | volume | 口袋体积（立方埃） | |||||||||||||||
| 4 | num_residue | 口袋的氨基酸数目 | |||||||||||||||
| 5 | second_H | 二级结构中的helix | |||||||||||||||
| 6 | second_B | 二级结构中的beta-sheet | |||||||||||||||
| 7 | asa | dssp计算的Relative ASA | https://biopython.org/DIST/docs/api/Bio.PDB.DSSP%27-module.html | ||||||||||||||
| 8 | residue_depth | Residue depth is the average distance of the atoms of a residue from the solvent accessible surface. | https://biopython.org/DIST/docs/api/Bio.PDB.ResidueDepth%27-module.html | ||||||||||||||
| 9 | hydrophilic | ||||||||||||||||
| 10 | hydrophobic | ||||||||||||||||
| 11 | hydrophobic_half | ||||||||||||||||
| 12 | HSE_UP | Half-Sphere Exposure | https://biopython.org/DIST/docs/api/Bio.PDB.HSExposure._AbstractHSExposure-class.html | ||||||||||||||
| 13 | HSE_DOWN | Half-Sphere Exposure | https://biopython.org/DIST/docs/api/Bio.PDB.HSExposure._AbstractHSExposure-class.html | ||||||||||||||
| 14 | stable | ||||||||||||||||
| 15 | coverage | ||||||||||||||||