How to use the pdb2pqr.pdb2pqr.pdb function in pdb2pqr

title_err = []

    struct_obj = block.getObj("struct")

    title_string = struct_obj.getValue("title")
    title_chunk = int(ceil(len(title_string)/70.0))

    for i in range(title_chunk):
        line = "TITLE  "
        if i+1 > 1:
            line += " "*(2-len(str(i+1))) + str(i+1)
        else:
            line += "  "
        line += title_string[(i*70) : minimum(len(title_string), (i+1)*70)]
        try:
            title_arr.append(pdb.TITLE(line))
        # TODO - what are we catching here?
        except:
            _LOGGER.error("TITLE:    Error parsing line:\n%s", line)
            title_err.append("title")

    return title_arr, title_err

def get_old_header(pdblist):
    """Get old header from list of PDBs.

    Args:
        pdblist:  list of PDBs
    Returns:
        Old header as string.
    """
    old_header = io.StringIO()
    header_types = (pdb.HEADER, pdb.TITLE, pdb.COMPND, pdb.SOURCE, pdb.KEYWDS,
                    pdb.EXPDTA, pdb.AUTHOR, pdb.REVDAT, pdb.JRNL, pdb.REMARK,
                    pdb.SPRSDE, pdb.NUMMDL)
    for pdb_obj in pdblist:
        if not isinstance(pdb_obj, header_types):
            break
        old_header.write(str(pdb_obj))
        old_header.write('\n')
    return old_header.getvalue()

str(sc_obj.getValue("fract_transf_vector[2]", 0))

    scale3 = ""
    scale3 += "SCALE3    "
    scale3 += " "*(10 - len(str(sc_obj.getValue("fract_transf_matrix[3][1]", 0)))) + \
        str(sc_obj.getValue("fract_transf_matrix[3][1]", 0))
    scale3 += " "*(10 - len(str(sc_obj.getValue("fract_transf_matrix[3][2]", 0)))) + \
        str(sc_obj.getValue("fract_transf_matrix[3][2]", 0))
    scale3 += " "*(10 - len(str(sc_obj.getValue("fract_transf_matrix[3][3]", 0)))) + \
        str(sc_obj.getValue("fract_transf_matrix[3][3]", 0))
    scale3 += "     "
    scale3 += " "*(10 - len(str(sc_obj.getValue("fract_transf_vector[3]", 0)))) + \
        str(sc_obj.getValue("fract_transf_vector[3]", 0))

    try:
        sc_arr.append(pdb.SCALE1(scale1))
    # TODO - what are we catching here?
    except:
        _LOGGER.error("cif.scalen:    Error parsing line:\n%s", scale1)
        sc_err.append("SCALE1")

    try:
        sc_arr.append(pdb.SCALE2(scale2))
    # TODO - what are we catching here?
    except:
        _LOGGER.error("cif.scalen:    Error parsing line:\n%s", scale2)
        sc_err.append("SCALE2")

    try:
        sc_arr.append(pdb.SCALE3(scale3))
    # TODO - what are we catching here?
    except:

str(sc_obj.getValue("fract_transf_matrix[3][2]", 0))
    scale3 += " "*(10 - len(str(sc_obj.getValue("fract_transf_matrix[3][3]", 0)))) + \
        str(sc_obj.getValue("fract_transf_matrix[3][3]", 0))
    scale3 += "     "
    scale3 += " "*(10 - len(str(sc_obj.getValue("fract_transf_vector[3]", 0)))) + \
        str(sc_obj.getValue("fract_transf_vector[3]", 0))

    try:
        sc_arr.append(pdb.SCALE1(scale1))
    # TODO - what are we catching here?
    except:
        _LOGGER.error("cif.scalen:    Error parsing line:\n%s", scale1)
        sc_err.append("SCALE1")

    try:
        sc_arr.append(pdb.SCALE2(scale2))
    # TODO - what are we catching here?
    except:
        _LOGGER.error("cif.scalen:    Error parsing line:\n%s", scale2)
        sc_err.append("SCALE2")

    try:
        sc_arr.append(pdb.SCALE3(scale3))
    # TODO - what are we catching here?
    except:
        _LOGGER.error("cif.scalen:    Error parsing line:\n%s", scale3)
        sc_err.append("SCALE3")

    return sc_arr, sc_err

"""
        sample_atom = atoms[-1]
        self.atoms = []
        self.name = sample_atom.res_name
        self.chain_id = sample_atom.chain_id
        self.res_seq = sample_atom.res_seq
        self.ins_code = sample_atom.ins_code
        self.map = {}
        self.naname = None
        self.reference = None
        self.is_n_term = None
        self.is_c_term = None

        atomclass = ""
        for atom in atoms:
            if isinstance(atom, pdb.ATOM):
                atomclass = "ATOM"
            elif isinstance(atom, pdb.HETATM):
                atomclass = "HETATM"
            atom = structures.Atom(atom, atomclass, self)
            atomname = atom.name
            if atomname not in self.map:
                self.add_atom(atom)
            else: # Don't add duplicate atom
                oldatom = self.get_atom(atomname)
                oldatom.alt_loc = ""

        if self.name == "HOH":
            self.name = "WAT"
            for atom in self.atoms:
                atom.res_name = "WAT"

line += " "*(6 - len(str(atoms.getValue("occupancy", i)))) + \
                        str(atoms.getValue("occupancy", i))
                    # 61 - 66 TEMP FACTOR
                    line += " "*(6 - len(str(atoms.getValue("B_iso_or_equiv", i)))) + \
                        str(atoms.getValue("B_iso_or_equiv", i))
                    # 67 - 76
                    line += " "*(10)
                    # 77 - 78 ELEMENT SYMBOL
                    line += " "*(2 - len(atoms.getValue("type_symbol", i))) + \
                        atoms.getValue("type_symbol", i)
                    # 79 - 80 CHARGE OF ATOM
                    if atoms.getValue("pdbx_formal_charge", i) == "?":
                        line += " "*2
                    else:
                        atoms.getValue("pdbx_formal_charge", i)
                    pdb_arr.append(pdb.ATOM(line))
                # TODO - what are we catching here?
                except:
                    _LOGGER.error("atom_site: Error reading line: #%s#\n", line)

            elif atoms.getValue("group_PDB", i) == "HETATM":
                try:
                    line = ""
                    # 1  - 6 RECORD NAME (HETATM)
                    line += atoms.getValue("group_PDB", i) + \
                        ""*(6 - len(atoms.getValue("group_PDB", i)))
                    # 7  - 11 ATOM SERIAL
                    line += " "*(5 - len(str(atoms.getValue("id", i)))) + \
                        str(atoms.getValue("id", i))
                    # 12 - 13
                    line += "  "
                    # 14 - 16 ATOM NAME

ParseRadiiDict = {"C": 1.70,
                   "N": 1.50,
                   "O": 1.40,
                   "S": 1.85,
                   "H": 1.00,
                   "Br":2.50,
                   "F": 1.20,
                   "P": 1.90,
                   "Cl": 1.75}

#Add lower case keys to more lenient matching.
ParseRadiiDictLower = dict((key.lower(), value) for key, value in ParseRadiiDict.items())
ParseRadiiDict.update(ParseRadiiDictLower)

class ligand_charge_handler(pdb.Mol2Molecule):
    """Make sure that we are up to date with respect to the charge calculation"""

    def make_up2date(self,residue):
        #
        # Check if the structure of the ligand is
        # identical to the one we have
        #
        if not getattr(self,'ligand_props',None):
            self.recalc_charges(residue)
#            qqqgesges = 0.0
#            for aa in residue.atoms:
#                #print "newly_calced  %s  %1.4f " %(aa.name, aa.charge)
#                qqqgesges = qqqgesges +  aa.charge
            #print "-------------------------------"
            #print "newly_calced - net charge %1.4f" %(qqqgesges)
            #print

self.atoms = []
        self.name = sample_atom.res_name
        self.chain_id = sample_atom.chain_id
        self.res_seq = sample_atom.res_seq
        self.ins_code = sample_atom.ins_code
        self.map = {}
        self.naname = None
        self.reference = None
        self.is_n_term = None
        self.is_c_term = None

        atomclass = ""
        for atom in atoms:
            if isinstance(atom, pdb.ATOM):
                atomclass = "ATOM"
            elif isinstance(atom, pdb.HETATM):
                atomclass = "HETATM"
            atom = structures.Atom(atom, atomclass, self)
            atomname = atom.name
            if atomname not in self.map:
                self.add_atom(atom)
            else: # Don't add duplicate atom
                oldatom = self.get_atom(atomname)
                oldatom.alt_loc = ""

        if self.name == "HOH":
            self.name = "WAT"
            for atom in self.atoms:
                atom.res_name = "WAT"

if chain_id not in chain_dict:
                    my_chain = struct.Chain(chain_id)
                    chain_dict[chain_id] = my_chain

                if res_seq != previous_atom.res_seq or \
                      ins_code != previous_atom.ins_code or \
                      chain_id != previous_atom.chain_id:
                    my_residue = self.create_residue(residue, previous_atom.res_name)
                    chain_dict[previous_atom.chain_id].add_residue(my_residue)
                    residue = []

                residue.append(record)
                previous_atom = record

            elif isinstance(record, pdb.END):
                my_residue = self.create_residue(residue, previous_atom.res_name)
                chain_dict[previous_atom.chain_id].add_residue(my_residue)
                residue = []

            elif isinstance(record, pdb.MODEL):
                num_models += 1
                if residue == []:
                    continue
                if num_models > 1:
                    my_residue = self.create_residue(residue,
                                                     previous_atom.res_name)
                    chain_dict[previous_atom.chain_id].add_residue(my_residue)
                    break

            elif isinstance(record, pdb.TER):
                count += 1