Python：PDB文件中原子和残基重新编号

Python脚本：PDB文件中原子和残基重新编号

Command:

python renumber_pdb.py -i protein.pdb -a -r > output.pdb

renumber_pdb.py

  

   

    

     

    
    

     

      # Python 3 script to atoms and residues in a PDB file.
     
    
   

    

     

    
    

     

      #
     
    
   

    

     

    
    

     

      # run
     
    
   

    

     

    
    

     

      # ./renumber.py -h
     
    
   

    

     

    
    

     

      # for help
     
    
   

    

     

    
    

     

      #
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

      class Pdb(object):
     
    
   

    

     

    
    

     
 """ Object that allows operations with protein files in PDB format. """
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 def __init__(self, file_cont = [], pdb_code = ""):
     
    
   

    

     

    
    

     

       self.cont = []
     
    
   

    

     

    
    

     

       self.atom = []
     
    
   

    

     

    
    

     

       self.hetatm = []
     
    
   

    

     

    
    

     

       self.fileloc = ""
     
    
   

    

     

    
    

     
 if isinstance(file_cont, list):
     
    
   

    

     

    
    

     

       self.cont = file_cont[:]
     
    
   

    

     

    
    

     
 elif isinstance(file_cont, str):
     
    
   

    

     

    
    

     
 try:
     
    
   

    

     

    
    

     
 with open(file_cont, 'r') as pdb_file:
     
    
   

    

     

    
    

     

       self.cont = [row.strip() for row in pdb_file.read().split('\n') if row.strip()]
     
    
   

    

     

    
    

     
 except FileNotFoundError as err:
     
    
   

    

     

    
    

     

       print(err)
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 if self.cont:
     
    
   

    

     

    
    

     

       self.atom = [row for row in self.cont if row.startswith('ATOM')]
     
    
   

    

     

    
    

     

       self.hetatm = [row for row in self.cont if row.startswith('HETATM')]
     
    
   

    

     

    
    

     

       self.conect = [row for row in self.cont if row.startswith('CONECT')]
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 def renumber_atoms(self, start=1):
     
    
   

    

     

    
    

     
 """ Renumbers atoms in a PDB file. """
     
    
   

    

     

    
    

     

       out = list()
     
    
   

    

     

    
    

     

       count = start
     
    
   

    

     

    
    

     
 for row in self.cont:
     
    
   

    

     

    
    

     
 if len(row) > 5:
     
    
   

    

     

    
    

     
 if row.startswith(('ATOM', 'HETATM', 'TER', 'ANISOU')):
     
    
   

    

     

    
    

     

       num = str(count)
     
    
   

    

     

    
    

     
 while len(num) < 5:
     
    
   

    

     

    
    

     

       num = ' ' + num
     
    
   

    

     

    
    

     

       row = '%s%s%s' %(row[:6], num, row[11:])
     
    
   

    

     

    
    

     

       count += 1
     
    
   

    

     

    
    

     

       out.append(row)
     
    
   

    

     

    
    

     
 return out
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 def renumber_residues(self, start=1, reset=False):
     
    
   

    

     

    
    

     
 """ Renumbers residues in a PDB file. """
     
    
   

    

     

    
    

     

       out = list()
     
    
   

    

     

    
    

     

       count = start - 1
     
    
   

    

     

    
    

     

       cur_res = ''
     
    
   

    

     

    
    

     
 for row in self.cont:
     
    
   

    

     

    
    

     
 if len(row) > 25:
     
    
   

    

     

    
    

     
 if row.startswith(('ATOM', 'HETATM', 'TER', 'ANISOU')):
     
    
   

    

     

    
    

     

       next_res = row[22:27].strip() # account for letters in res., e.g., '1A'
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 if next_res != cur_res:
     
    
   

    

     

    
    

     

       count += 1
     
    
   

    

     

    
    

     

       cur_res = next_res
     
    
   

    

     

    
    

     

       num = str(count)
     
    
   

    

     

    
    

     
 while len(num) < 3:
     
    
   

    

     

    
    

     

       num = ' ' + num
     
    
   

    

     

    
    

     

       new_row = '%s%s' %(row[:23], num)
     
    
   

    

     

    
    

     
 while len(new_row) < 29:
     
    
   

    

     

    
    

     

       new_row += ' '
     
    
   

    

     

    
    

     

       xcoord = row[30:38].strip()
     
    
   

    

     

    
    

     
 while len(xcoord) < 9:
     
    
   

    

     

    
    

     

       xcoord = ' ' + xcoord
     
    
   

    

     

    
    

     

       row = '%s%s%s' %(new_row, xcoord, row[38:])
     
    
   

    

     

    
    

     
 if row.startswith('TER') and reset:
     
    
   

    

     

    
    

     

       count = start - 1
     
    
   

    

     

    
    

     

       out.append(row)
     
    
   

    

     

    
    

     
 return out
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

      if __name__ == '__main__':
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 import argparse
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

       parser = argparse.ArgumentParser(
     
    
   

    

     

    
    

     

       description='Renumber residues in a pdb file',
     
    
   

    

     

    
    

     

       formatter_class=argparse.RawTextHelpFormatter
     
    
   

    

     

    
    

     

       )
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

       parser.add_argument('-i', '--input', help='Input PDB file')
     
    
   

    

     

    
    

     

       parser.add_argument('-s', '--start', help='Number of the first residue in the renumbered file (default = 1)')
     
    
   

    

     

    
    

     

       parser.add_argument('-a', '--atoms' ,action='store_true', help='Renumbers atoms')
     
    
   

    

     

    
    

     

       parser.add_argument('-r', '--residues', action='store_true', help='Renumbers residues')
     
    
   

    

     

    
    

     

       parser.add_argument('-c', '--chainreset', action='store_true', help='Resets the residue renumbering after encountering a new chain.')
     
    
   

    

     

    
    

     

       parser.add_argument('-v', '--version', action='version', version='v. 1.0')
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

       args = parser.parse_args()
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 if not args.input:
     
    
   

    

     

    
    

     

       print('{0}\nPlease provide an input file.\n{0}'.format(50* '-'))
     
    
   

    

     

    
    

     

       parser.print_help()
     
    
   

    

     

    
    

     

       quit()
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 if not args.start:
     
    
   

    

     

    
    

     

       start = 1
     
    
   

    

     

    
    

     
 else:
     
    
   

    

     

    
    

     

       start = int(args.start)
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 if not args.atoms and not args.residues:
     
    
   

    

     

    
    

     

       print('{0}\nPlease provide at least the --atoms or --residues flag.\n{0}'.format(50* '-'))
     
    
   

    

     

    
    

     

       parser.print_help()
     
    
   

    

     

    
    

     

       quit()
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

       pdb1 = Pdb(args.input)
     
    
   

    

     

    
    

     
 if args.atoms:
     
    
   

    

     

    
    

     

       pdb1.cont = pdb1.renumber_atoms(start=start)
     
    
   

    

     

    
    

     
 if args.residues:
     
    
   

    

     

    
    

     

       pdb1.cont = pdb1.renumber_residues(start=start, reset=args.chainreset)
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 for line in pdb1.cont:
     
    
   

    

     

    
    

     

       print(line)
     
    
  
 

效果：

参考：

https://github.com/AspirinCode/protein-science/tree/master/scripts-and-tools/renumber_pdb

文章来源: drugai.blog.csdn.net，作者：DrugAI，版权归原作者所有，如需转载，请联系作者。

原文链接：drugai.blog.csdn.net/article/details/81008736