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
1recfile受体pdb
2pitfile口袋的格点文件
3volume口袋体积（立方埃）
4num_residue口袋的氨基酸数目
5second_H二级结构中的helix
6second_B二级结构中的beta-sheet
7asadssp计算的Relative   ASAhttps://biopython.org/DIST/docs/api/Bio.PDB.DSSP%27-module.html
8residue_depthResidue 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
9hydrophilic
10hydrophobic
11hydrophobic_half
12HSE_UPHalf-Sphere Exposurehttps://biopython.org/DIST/docs/api/Bio.PDB.HSExposure._AbstractHSExposure-class.html
13HSE_DOWNHalf-Sphere Exposurehttps://biopython.org/DIST/docs/api/Bio.PDB.HSExposure._AbstractHSExposure-class.html
14stable
15coverage