Parse PDB Files to get Atom information.

PDBAtom.py

import sys

class PDBAtom:
    """
    It defines a PDB Atom object.
    """
    def __init__(self, line):
        self.type = self._get_type(line)  # from columns 1-7
        self.ser_num = self._get_serial_number(line)  # from columns 7-11
        self.at_name = self._get_atom_name(line)  # from columns 13-16
        self.alt_loc = self._get_alternate_location_indicator(line)
        self.res = self._get_residue(line)  # from columns 18-20
        self.chain = self._get_chain(line)  # column 22
        self.res_seqnum = self._get_residue_sequence_number(line)
        self.insertion_rescode = self._get_code_for_insertion_residues(line)
        self.x = self._get_coords_x(line)  # from columns 31-38
        self.y = self._get_coords_y(line)  # from columns 39-46
        self.z = self._get_coords_z(line)  # from columns 47-54
        self.occupancy = self._get_occupancy(line)  # from columns 55-60
        self.t_factor = self._get_temperature_factor(line)  # from columns 61-66
        self.elem_sym = self._get_element_symbol(line)  # from columns 77-78
        self.charge = self._get_charge(line)

    @staticmethod
    def _get_type(line):
        return line[0:6].strip()

    @staticmethod
    def _get_serial_number(line):
        return int(line[6:11].strip())

    @staticmethod
    def _get_atom_name(line):
        return line[12:16].strip()

    @staticmethod
    def _get_alternate_location_indicator(line):
        return line[16:17].strip()

    @staticmethod
    def _get_residue(line):
        return line[17:20].strip()

    @staticmethod
    def _get_chain(line):
        return line[21:22].strip()

    @staticmethod
    def _get_residue_sequence_number(line):
        return int(line[22:26].strip())

    @staticmethod
    def _get_code_for_insertion_residues(line):
        return line[26:27].strip()

    @staticmethod
    def _get_coords_x(line):
        return float(line[30:38].strip())

    @staticmethod
    def _get_coords_y(line):
        return float(line[38:46].strip())

    @staticmethod
    def _get_coords_z(line):
        return float(line[46:54].strip())

    @staticmethod
    def _get_occupancy(line):
        return float(line[55:60].strip())

    @staticmethod
    def _get_temperature_factor(line):
        return float(line[61:66].strip())

    @staticmethod
    def _get_element_symbol(line):
        return line[77:78].strip()

    @staticmethod
    def _get_charge(line):
        return line[78:80]

if __name__ == '__main__':
    pdb_file = open(sys.argv[1]).readlines()
    atoms_pdb = []
    
    for line in pdb_file:
        if 'ATOM' in line:
            atom = PDBAtom(line)
            atoms_pdb.append(atom)
    
    for atom in atoms_pdb:
      # Write PDB File from atom information
      pattern = "{:6s}{:5d} {:^4s}{:1s}{:3s} {:1s}{:4d}{:1s}" \
                "   {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}          {:>2s}{:2s}".format(
          atom.type, atom.ser_num, atom.at_name, atom.alt_loc, atom.res,atom.chain,
          atom.res_seqnum, atom.insertion_rescode, atom.x, atom.y, atom.z, atom.occupancy,
          atom.t_factor, atom.elem_sym, atom.charge
      )

      print(pattern)