# Path: molml/io.py
# def read_file_data(path):
#     """
#     Determine the file type and call the correct parser.
# 
#     The accepted file types are .out and .xyz files.
# 
#     Parameters
#     ----------
#     path : str
#         A path to a file to read
# 
#     Returns
#     -------
#     elements : list
#         All the elements in the molecule.
# 
#     numbers : list
#         All the atomic numbers in the molecule.
# 
#     coords : numpy.array, shape=(n_atoms, 3)
#         The atomic coordinates of the molecule.
#     """
#     end = path.split('.')[-1]
#     mapping = {
#         'out': read_out_data,
#         'xyz': read_xyz_data,
#         'mol2': read_mol2_data,
#         'cry': read_cry_data,
#     }
#     if end in mapping:
#         return mapping[end](path)
#     else:
#         raise ValueError("Unknown file type")
# 
# Path: molml/io.py
# def read_out_data(path):
#     """
#     Read an out and extract the molecule's geometry.
# 
#     The file should be in the format::
# 
#         ele0 x0 y0 z0
#         ele1 x1 y1 z1
#         ...
# 
#     Parameters
#     ----------
#     path : str
#         A path to a file to read
# 
#     Returns
#     -------
#     val : LazyValues
#         An object storing all the data
#     """
#     elements = []
#     coords = []
#     with open(path, 'r') as f:
#         for line in f:
#             ele, x, y, z = line.strip().split()
#             point = (float(x), float(y), float(z))
#             elements.append(ele)
#             coords.append(point)
#     return LazyValues(elements=elements, coords=coords)
# 
# def read_xyz_data(path):
#     """
#     Read an xyz file and extract the molecule's geometry.
# 
#     The file should be in the format::
# 
#         num_atoms
#         comment
#         ele0 x0 y0 z0
#         ele1 x1 y1 z1
#         ...
# 
#     Parameters
#     ----------
#     path : str
#         A path to a file to read
# 
#     Returns
#     -------
#     val : LazyValues
#         An object storing all the data
#     """
#     elements = []
#     coords = []
#     with open(path, 'r') as f:
#         for i, line in enumerate(f):
#             if i < 2:
#                 continue
#             ele, x, y, z = line.strip().split()
#             point = (float(x), float(y), float(z))
#             elements.append(ele)
#             coords.append(point)
#     return LazyValues(elements=elements, coords=coords)
# 
# def read_mol2_data(path):
#     """
#     Read a mol2 file and extract the molecule's geometry.
# 
#     Roughly, the file format is something like::
# 
#         @<TRIPOS>MOLECULE
#         ...
#         @<TRIPOS>ATOM
#          1 ele0id x0 y0 z0 ele0.type 1 MOL charge0
#          2 ele1id x1 y1 z1 ele1.type 1 MOL charge1
#         ...
#         @<TRIPOS>BOND
#         ...
# 
#     Parameters
#     ----------
#     path : str
#         A path to a file to read
# 
#     Returns
#     -------
#     val : LazyValues
#         An object storing all the data
#     """
#     elements = []
#     coords = []
#     with open(path, 'r') as f:
#         start = False
#         for line in f:
#             if "@<TRIPOS>ATOM" in line:
#                 start = True
#                 continue
#             if "@<TRIPOS>BOND" in line:
#                 break  # can't use connection info yet
#             if not start:
#                 continue
#             vals = line.split()
#             ele = vals[5].split('.')[0]
#             elements.append(ele)
#             coords.append([float(x) for x in vals[2:5]])
#     return LazyValues(elements=elements, coords=coords)
# 
# Path: molml/io.py
# def read_cry_data(path):
#     """
#     Read a cry file and extract the molecule's geometry.
# 
#     The format should be as follows::
# 
#         U_xx U_xy U_xz
#         U_yx U_yy U_yz
#         U_zx U_zy U_zz
#         energy (or comment, this is ignored for now)
#         ele0 x0 y0 z0
#         ele1 x1 y1 z1
#         ...
#         elen xn yn zn
# 
#     Where the U matrix is made of the unit cell basis vectors as column
#     vectors.
# 
#     Parameters
#     ----------
#     path : str
#         A path to a file to read
# 
#     Returns
#     -------
#     val : LazyValues
#         An object storing all the data
#     """
#     unit = []
#     coords = []
#     elements = []
#     with open(path, 'r') as f:
#         for line in f:
#             parts = line.strip().split()
#             if len(parts) == 3:
#                 unit.append([float(x) for x in parts])
#             if len(parts) == 4:
#                 elements.append(parts[0])
#                 coords.append([float(x) for x in parts[1:]])
#     return LazyValues(elements=elements, coords=coords, unit_cell=unit)


import unittest
import os
import numpy
from molml.io import read_file_data
from molml.io import read_out_data, read_xyz_data, read_mol2_data
from molml.io import read_cry_data




DATA_PATH = os.path.join(os.path.dirname(__file__), "data")
ELEMENTS = ['C', 'H', 'H', 'H', 'H']
NUMBERS = [6, 1, 1, 1, 1]

# Path: molml/io.py
# def read_file_data(path):
#     """
#     Determine the file type and call the correct parser.
# 
#     The accepted file types are .out and .xyz files.
# 
#     Parameters
#     ----------
#     path : str
#         A path to a file to read
# 
#     Returns
#     -------
#     elements : list
#         All the elements in the molecule.
# 
#     numbers : list
#         All the atomic numbers in the molecule.
# 
#     coords : numpy.array, shape=(n_atoms, 3)
#         The atomic coordinates of the molecule.
#     """
#     end = path.split('.')[-1]
#     mapping = {
#         'out': read_out_data,
#         'xyz': read_xyz_data,
#         'mol2': read_mol2_data,
#         'cry': read_cry_data,
#     }
#     if end in mapping:
#         return mapping[end](path)
#     else:
#         raise ValueError("Unknown file type")
# 
# Path: molml/io.py
# def read_out_data(path):
#     """
#     Read an out and extract the molecule's geometry.
# 
#     The file should be in the format::
# 
#         ele0 x0 y0 z0
#         ele1 x1 y1 z1
#         ...
# 
#     Parameters
#     ----------
#     path : str
#         A path to a file to read
# 
#     Returns
#     -------
#     val : LazyValues
#         An object storing all the data
#     """
#     elements = []
#     coords = []
#     with open(path, 'r') as f:
#         for line in f:
#             ele, x, y, z = line.strip().split()
#             point = (float(x), float(y), float(z))
#             elements.append(ele)
#             coords.append(point)
#     return LazyValues(elements=elements, coords=coords)
# 
# def read_xyz_data(path):
#     """
#     Read an xyz file and extract the molecule's geometry.
# 
#     The file should be in the format::
# 
#         num_atoms
#         comment
#         ele0 x0 y0 z0
#         ele1 x1 y1 z1
#         ...
# 
#     Parameters
#     ----------
#     path : str
#         A path to a file to read
# 
#     Returns
#     -------
#     val : LazyValues
#         An object storing all the data
#     """
#     elements = []
#     coords = []
#     with open(path, 'r') as f:
#         for i, line in enumerate(f):
#             if i < 2:
#                 continue
#             ele, x, y, z = line.strip().split()
#             point = (float(x), float(y), float(z))
#             elements.append(ele)
#             coords.append(point)
#     return LazyValues(elements=elements, coords=coords)
# 
# def read_mol2_data(path):
#     """
#     Read a mol2 file and extract the molecule's geometry.
# 
#     Roughly, the file format is something like::
# 
#         @<TRIPOS>MOLECULE
#         ...
#         @<TRIPOS>ATOM
#          1 ele0id x0 y0 z0 ele0.type 1 MOL charge0
#          2 ele1id x1 y1 z1 ele1.type 1 MOL charge1
#         ...
#         @<TRIPOS>BOND
#         ...
# 
#     Parameters
#     ----------
#     path : str
#         A path to a file to read
# 
#     Returns
#     -------
#     val : LazyValues
#         An object storing all the data
#     """
#     elements = []
#     coords = []
#     with open(path, 'r') as f:
#         start = False
#         for line in f:
#             if "@<TRIPOS>ATOM" in line:
#                 start = True
#                 continue
#             if "@<TRIPOS>BOND" in line:
#                 break  # can't use connection info yet
#             if not start:
#                 continue
#             vals = line.split()
#             ele = vals[5].split('.')[0]
#             elements.append(ele)
#             coords.append([float(x) for x in vals[2:5]])
#     return LazyValues(elements=elements, coords=coords)
# 
# Path: molml/io.py
# def read_cry_data(path):
#     """
#     Read a cry file and extract the molecule's geometry.
# 
#     The format should be as follows::
# 
#         U_xx U_xy U_xz
#         U_yx U_yy U_yz
#         U_zx U_zy U_zz
#         energy (or comment, this is ignored for now)
#         ele0 x0 y0 z0
#         ele1 x1 y1 z1
#         ...
#         elen xn yn zn
# 
#     Where the U matrix is made of the unit cell basis vectors as column
#     vectors.
# 
#     Parameters
#     ----------
#     path : str
#         A path to a file to read
# 
#     Returns
#     -------
#     val : LazyValues
#         An object storing all the data
#     """
#     unit = []
#     coords = []
#     elements = []
#     with open(path, 'r') as f:
#         for line in f:
#             parts = line.strip().split()
#             if len(parts) == 3:
#                 unit.append([float(x) for x in parts])
#             if len(parts) == 4:
#                 elements.append(parts[0])
#                 coords.append([float(x) for x in parts[1:]])
#     return LazyValues(elements=elements, coords=coords, unit_cell=unit)


# Path: tests/test_io.py
import unittest
import os
import numpy
from molml.io import read_file_data
from molml.io import read_out_data, read_xyz_data, read_mol2_data
from molml.io import read_cry_data





DATA_PATH = os.path.join(os.path.dirname(__file__), "data")
ELEMENTS = ['C', 'H', 'H', 'H', 'H']
NUMBERS = [6, 1, 1, 1, 1]

COORDS = [