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