# Path: acpype/utils.py
# def _getoutput(cmd):
#     """
#     To simulate commands.getoutput
#     shell=True is necessary despite security issues
#     """
#     out = sub.Popen(cmd, shell=True, stderr=sub.STDOUT, stdout=sub.PIPE).communicate()[0][:-1]
#     return out.decode()


import fnmatch
import os
import sys
from acpype.utils import _getoutput
            "0 E, 3 W, ET , WT _0_1_5",
            "0 E, 3 W, ET , WT _0_2_5",
            "0 E, 4 W, ET , WT _0_1_2_5",
        ],
    ],
    [
        "irregular bonds and atoms in close contact",
        "Mols have irregular bonds and atoms in close contact",
        [
            "0 E, 3 W, ET , WT _0_5_7",
            "0 E, 4 W, ET , WT _0_1_5_7",
            "0 E, 4 W, ET , WT _0_2_5_7",
            "0 E, 5 W, ET , WT _0_1_2_5_7",
            "0 E, 6 W, ET , WT _0_1_2_3_5_7",
            "0 E, 4 W, ET , WT _0_3_5_7",
        ],
    ],
    [
        "couldn't determine all parameters",
        "Mols have missing parameters",
        ["0 E, 3 W, ET , WT _0_2_4", "0 E, 3 W, ET , WT _0_1_4", "0 E, 2 W, ET , WT _0_4"],
    ],
    [
        "missing parameters and atoms in close contact",
        "Mols have missing parameters and atoms in close contact",
        ["0 E, 4 W, ET , WT _0_1_4_7"],
    ],
    [
        "missing parameters, irregular bonds and atoms in close contact",
        "Mols have missing parameters, irregular bonds and atoms in close contact",

# Path: acpype/utils.py
# def _getoutput(cmd):
#     """
#     To simulate commands.getoutput
#     shell=True is necessary despite security issues
#     """
#     out = sub.Popen(cmd, shell=True, stderr=sub.STDOUT, stdout=sub.PIPE).communicate()[0][:-1]
#     return out.decode()


# Path: scripts/analyse_test_acpype_db_ligands.py
import fnmatch
import os
import sys
from acpype.utils import _getoutput

            "0 E, 3 W, ET , WT _0_1_5",
            "0 E, 3 W, ET , WT _0_2_5",
            "0 E, 4 W, ET , WT _0_1_2_5",
        ],
    ],
    [
        "irregular bonds and atoms in close contact",
        "Mols have irregular bonds and atoms in close contact",
        [
            "0 E, 3 W, ET , WT _0_5_7",
            "0 E, 4 W, ET , WT _0_1_5_7",
            "0 E, 4 W, ET , WT _0_2_5_7",
            "0 E, 5 W, ET , WT _0_1_2_5_7",
            "0 E, 6 W, ET , WT _0_1_2_3_5_7",
            "0 E, 4 W, ET , WT _0_3_5_7",
        ],
    ],
    [
        "couldn't determine all parameters",
        "Mols have missing parameters",
        ["0 E, 3 W, ET , WT _0_2_4", "0 E, 3 W, ET , WT _0_1_4", "0 E, 2 W, ET , WT _0_4"],
    ],
    [
        "missing parameters and atoms in close contact",
        "Mols have missing parameters and atoms in close contact",
        ["0 E, 4 W, ET , WT _0_1_4_7"],
    ],
    [
        "missing parameters, irregular bonds and atoms in close contact",
        "Mols have missing parameters, irregular bonds and atoms in close contact",

        ["0 E, 5 W, ET , WT _0_2_4_5_7"],