批量获得多肽smiles序列求助

qiuqiuren

求助各位老师，我现在有大量多肽的pdb文件和氨基酸序列，我想得到多肽的smiles序列，是直接从pdb转化成smiles，还是利用序列生成smiles（之前尝试过用pdb转，但rdkit显示warning）（多肽氨基酸序列含有非标准氨基酸，也有的多肽是环肽），还望各位老师多多指教

qiuqiuren

老师，您好，我用obabel生成smiles,有一部分序列显示

*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is 6rhe_D.pdb)

然后把生成的SMILES.txt用rdkit读取，部分报错
[13:04:14] Explicit valence for atom # 38 N, 4, is greater than permitted
[13:04:14] Explicit valence for atom # 38 N, 4, is greater than permitted
[13:04:14] Explicit valence for atom # 26 N, 4, is greater than permitted
[13:04:14] Explicit valence for atom # 125 O, 2, is greater than permitted
[13:04:14] Explicit valence for atom # 18 N, 4, is greater than permitted
[13:04:15] Explicit valence for atom # 26 N, 4, is greater than permitted
[13:04:15] Explicit valence for atom # 71 O, 2, is greater than permitted
[13:04:15] Explicit valence for atom # 38 N, 4, is greater than permitted
[13:04:15] Explicit valence for atom # 38 N, 4, is greater than permitted
[13:04:15] Explicit valence for atom # 18 N, 4, is greater than permitted
[13:04:15] Explicit valence for atom # 26 N, 4, is greater than permitted
[13:04:15] Explicit valence for atom # 30 N, 4, is greater than permitted，

这种情况是只能对报错的pdb单独处理吗

UW_0728.

用OpenBabel直接从pdb转SMILES即可。先装好OpenBabel、配置好环境变量，然后运行类似如下命令（假设所有pdb都在当前目录下）：

1. for n in $(basename -s .pdb ./*.pdb); do
   
2.   echo $n
   
3.   obabel -ipdb $n.pdb -osmi | head -n 1 | awk '{print $1}'
   
4.   echo
   
5. done > SMILES.txt

复制代码

执行完后当前目录下出现的SMILES.txt文件就包含了各个结构的SMILES了
不放心的话，可以选一部分环比较多/杂、构型略显奇怪的结构把相应的SMILES复制粘贴到https://pubchem.ncbi.nlm.nih.gov/edit3/index.html，生成二维结构图验证验证