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

""""
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