<commit_before>"""Atom class - contains all atom information found in the PDB file"""
import string
import propka.lib
import propka.group
from . import hybrid36


# Format strings that get used in multiple places (or are very complex)
PKA_FMT = "{:6.2f}"
INPUT_LINE_FMT = (
    "{type:6s}{r.numb:>5d} {atom_label} {r.res_name}{r.chain_id:>2s}"
    "{r.res_num:>4d}{r.x:>12.3f}{r.y:>8.3f}{r.z:>8.3f}{group:>6s}{pka:>6s} \n")
PDB_LINE_FMT1 = (
    "{type:6s}{r.numb:>5d} {atom_label} {r.res_name}{r.chain_id:>2s}"
    "{r.res_num:>4d}{r.x:>12.3f}{r.y:>8.3f}{r.z:>8.3f}{r.occ:>6s}"
    "{r.beta:>6s}\n")
MOL2_LINE_FMT = (
    "{id:<4d} {atom_label:4s} "
    "{r.x:>10.4f} {r.y:>10.4f} {r.z:>10.4f} "
    "{r.sybyl_type:>6s} {r.res_num:>6d} {r.res_name:>10s}     0.0000\n")
PDB_LINE_FMT2 = (
    "ATOM {numb:>6d} {atom_label} {res_name}{chain_id:>2s}{res_num:>4d}"
    "{x:>12.3f}{y:>8.3f}{z:>8.3f}{occ:>6.2f}{beta:>6.2f}\n")
STR_FMT = (
    "{r.numb:>5d}-{r.name:>4s} {r.res_num:>5d}-{r.res_name:>3s} "
    "({r.chain_id:1s}) [{r.x:>8.3f} {r.y:>8.3f} {r.z:>8.3f}] {r.element:s}")


class Atom(object):
    """Atom class - contains all atom information found in the PDB file"""

    def __init__(self, line=None, _=False):
        """Initialize Atom object.

        Args:
            line:  Line from a PDB file to set properties of atom.
            _:  TODO - this does not appear to be used. Can we remove it?
        """
        self.occ = None
        self.numb = None
        self.res_name = None
        self.type = None
        self.chain_id = None
        self.beta = None
        self.icode = None
        self.res_num = None
        self.name = None
        self.element = None
        self.x = None
        self.y = None
        self.z = None<commit_msg>Remove unused argument from Atom() constructor.<commit_after>"""Atom class - contains all atom information found in the PDB file"""
import string
import propka.lib
import propka.group
from . import hybrid36


# Format strings that get used in multiple places (or are very complex)
PKA_FMT = "{:6.2f}"
INPUT_LINE_FMT = (
    "{type:6s}{r.numb:>5d} {atom_label} {r.res_name}{r.chain_id:>2s}"
    "{r.res_num:>4d}{r.x:>12.3f}{r.y:>8.3f}{r.z:>8.3f}{group:>6s}{pka:>6s} \n")
PDB_LINE_FMT1 = (
    "{type:6s}{r.numb:>5d} {atom_label} {r.res_name}{r.chain_id:>2s}"
    "{r.res_num:>4d}{r.x:>12.3f}{r.y:>8.3f}{r.z:>8.3f}{r.occ:>6s}"
    "{r.beta:>6s}\n")
MOL2_LINE_FMT = (
    "{id:<4d} {atom_label:4s} "
    "{r.x:>10.4f} {r.y:>10.4f} {r.z:>10.4f} "
    "{r.sybyl_type:>6s} {r.res_num:>6d} {r.res_name:>10s}     0.0000\n")
PDB_LINE_FMT2 = (
    "ATOM {numb:>6d} {atom_label} {res_name}{chain_id:>2s}{res_num:>4d}"
    "{x:>12.3f}{y:>8.3f}{z:>8.3f}{occ:>6.2f}{beta:>6.2f}\n")
STR_FMT = (
    "{r.numb:>5d}-{r.name:>4s} {r.res_num:>5d}-{r.res_name:>3s} "
    "({r.chain_id:1s}) [{r.x:>8.3f} {r.y:>8.3f} {r.z:>8.3f}] {r.element:s}")


class Atom(object):
    """Atom class - contains all atom information found in the PDB file"""

    def __init__(self, line=None):
        """Initialize Atom object.

        Args:
            line:  Line from a PDB file to set properties of atom.
        """
        self.occ = None
        self.numb = None
        self.res_name = None
        self.type = None
        self.chain_id = None
        self.beta = None
        self.icode = None
        self.res_num = None
        self.name = None
        self.element = None
        self.x = None
        self.y = None
        self.z = None
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