PDB renumbering

#usage python renumber.py -i xxx.pdb -a -r > new.pdb

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 = ''
        cur_chain = ''
        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'
                    next_chain = row[21]
                    
                    if next_chain != cur_chain:
                        count = start - 1
                        cur_chain = next_chain
                    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)