更换pdb文件中的特定的字符使之转换为能够在AMBER中运行的pdb文件

最新推荐文章于 2023-07-06 13:31:22 发布

rogerzhanglijie

最新推荐文章于 2023-07-06 13:31:22 发布

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分类专栏： Python 文章标签： file list lambda

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""""
author:lijie zhang
data:2012-05-24
func:this script is used to remove the atom or line which is not needed in the file form
"""
import glob
L=["HB","O5T", "H2A*", "O3T","HN6A","HN6B","HE","HN2A","HN2B","H2B*","HN4A","HN4B"]
def file_list():
   files=[]
   for file in glob.glob("./*.pdb"):
       files.append(file)
   files=sorted(files,key=lambda x:int(x[-5:-4]))
   return files
def deal_atom(old_pdb,new_pdb,L_list):
   f=open(old_pdb,'r')
   store_pdb=open(new_pdb,"w")
   lines=f.readlines()
   for atom in L_list:
       for line in lines:
           data=line.split()
           if atom in data:
               lines.remove(line)
   for line in lines:
       store_pdb.write(line)
   store_pdb.close()
   f.close()
if __name__=="__main__":
   print file_list()
   s=1
   for file in file_list():
       deal_atom(file,"new%i.pdb"%s,L)
       s+=1