# Path: paratemp/exceptions.py
# class UnknownEnergyError(Exception):
#     """
#     Exception raised when an object does not know it's energy, but it's queried
# 
#     """
# 
#     def __init__(self, msg=None):
#         self.msg = msg
# 
#     def __str__(self):
#         standard_response = (
#             "The energy is unknown either because it wasn't "
#             "in the original file or the coordinates have "
#             "changed.\nCould try XYZ.original_energy"
#         )
#         if self.msg is None:
#             return repr(standard_response)
#         else:
#             return repr(self.msg)
# 
# class InputError(Exception):
#     """Exception raised for errors in the input.
# 
#     Attributes:
#         expr -- input expression in which the error occurred
#         msg  -- explanation of the error
#     """
# 
#     def __init__(self, expr, msg):
#         self.expr = expr
#         self.msg = msg
# 
#     def __str__(self):
#         output = 'Incorrect input "{}". {}'.format(self.expr, self.msg)
#         return repr(output)


import re
import numpy as np
from numpy.linalg import norm
from .exceptions import UnknownEnergyError, InputError
class XYZ(object):
    def __init__(self, f_name):
        self.file = f_name
        with open(f_name, "r") as f_file:
            f_lines = f_file.readlines()
        if len(f_lines) < 2:
            raise TypeError("The given file {} appears " "to be empty".format(f_name))
        self._header = f_lines[0:2]
        if "Energy" in self._header[1]:
            energy_match = re.search(r"(?:Energy:\s+)(-\d+\.\d+)", self._header[1])
            self._energy = float(energy_match.group(1))
        else:
            self._energy = None
        self._original_energy = self._energy
        data = [line.split() for line in f_lines[2:]]
        if not data[-1]:
            data = data[:-1]  # Ignore blank last line
        atom = None
        try:
            self.atoms = []
            for atom in data:
                self.atoms.append(atom[0])
        except IndexError:
            raise ValueError("invalid line in xyz file: {}".format(atom))
        if re.search(r"([a-z]|[A-Z])+\d+", self.atoms[0]):
            self._fix_atom_names()
        try:
            self.coords = list()
            for atom in data:
                self.coords.append(Vector([float(coord) for coord in atom[1:4]]))

# Path: paratemp/exceptions.py
# class UnknownEnergyError(Exception):
#     """
#     Exception raised when an object does not know it's energy, but it's queried
# 
#     """
# 
#     def __init__(self, msg=None):
#         self.msg = msg
# 
#     def __str__(self):
#         standard_response = (
#             "The energy is unknown either because it wasn't "
#             "in the original file or the coordinates have "
#             "changed.\nCould try XYZ.original_energy"
#         )
#         if self.msg is None:
#             return repr(standard_response)
#         else:
#             return repr(self.msg)
# 
# class InputError(Exception):
#     """Exception raised for errors in the input.
# 
#     Attributes:
#         expr -- input expression in which the error occurred
#         msg  -- explanation of the error
#     """
# 
#     def __init__(self, expr, msg):
#         self.expr = expr
#         self.msg = msg
# 
#     def __str__(self):
#         output = 'Incorrect input "{}". {}'.format(self.expr, self.msg)
#         return repr(output)


# Path: paratemp/geometries.py
import re
import numpy as np
from numpy.linalg import norm
from .exceptions import UnknownEnergyError, InputError

class XYZ(object):
    def __init__(self, f_name):
        self.file = f_name
        with open(f_name, "r") as f_file:
            f_lines = f_file.readlines()
        if len(f_lines) < 2:
            raise TypeError("The given file {} appears " "to be empty".format(f_name))
        self._header = f_lines[0:2]
        if "Energy" in self._header[1]:
            energy_match = re.search(r"(?:Energy:\s+)(-\d+\.\d+)", self._header[1])
            self._energy = float(energy_match.group(1))
        else:
            self._energy = None
        self._original_energy = self._energy
        data = [line.split() for line in f_lines[2:]]
        if not data[-1]:
            data = data[:-1]  # Ignore blank last line
        atom = None
        try:
            self.atoms = []
            for atom in data:
                self.atoms.append(atom[0])
        except IndexError:
            raise ValueError("invalid line in xyz file: {}".format(atom))
        if re.search(r"([a-z]|[A-Z])+\d+", self.atoms[0]):
            self._fix_atom_names()
        try:
            self.coords = list()
            for atom in data:
                self.coords.append(Vector([float(coord) for coord in atom[1:4]]))

        except (IndexError, InputError):