# Path: perses/utils/openeye.py
# def smiles_to_oemol(smiles, title='MOL', max_confs=1):
#     """
#     Generate an oemol from a SMILES string
# 
#     Parameters
#     ----------
#     smiles : str
#         SMILES string of molecule
#     title : str, default 'MOL'
#         title of OEMol molecule
#     max_confs : int, default 1
#         maximum number of conformers to generate
#     Returns
#     -------
#     molecule : openeye.oechem.OEMol
#         OEMol object of the molecule
#     """
#     from openeye import oeomega, oechem
# 
#     # Create molecule
#     molecule = oechem.OEMol()
#     oechem.OESmilesToMol(molecule, smiles)
# 
#     # create unique atom names
#     if len([atom.GetName() for atom in molecule.GetAtoms()]) > len(set([atom.GetName() for atom in molecule.GetAtoms()])):
#         # the atom names are not unique
#         molecule = generate_unique_atom_names(molecule)
#     else:
#         pass
# 
#     # Set title.
#     molecule.SetTitle(title)
# 
#     # Assign aromaticity and hydrogens.
#     oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
#     oechem.OEAssignHybridization(molecule)
#     oechem.OEAddExplicitHydrogens(molecule)
#     oechem.OEPerceiveChiral(molecule)
# 
#     # Create atom names.
#     oechem.OETriposAtomNames(molecule)
#     oechem.OETriposBondTypeNames(molecule)
# 
#     # perceive chirality before attempting omega geometry proposal
#     assert oechem.OEPerceiveChiral(molecule), f"chirality perception failed"
# 
#     # Assign geometry
#     omega = oeomega.OEOmega()
#     omega.SetMaxConfs(max_confs)
#     omega.SetIncludeInput(False)
#     omega.SetStrictStereo(True)
# 
#     omega(molecule)
#     return molecule


import os
    import os
    import simtk.unit as unit
    import simtk.unit as unit
    import copy
    import simtk.openmm.app as app
    import simtk.unit as unit
   import copy
   import numpy as np
   import simtk.unit as unit
from perses.utils.openeye import smiles_to_oemol
from unittest import skipIf
    from perses.utils.data import get_data_filename
    from perses.utils.openeye import extractPositionsFromOEMol
    from perses.utils.openeye import giveOpenmmPositionsToOEMol
    from perses.utils.openeye import OEMol_to_omm_ff
    from simtk import openmm
    from openmmforcefields.generators import SystemGenerator
    from openff.toolkit.topology import Molecule
   from openmoltools.openeye import iupac_to_oemol
   from openeye import oechem
    from perses.utils.openeye import generate_expression
    ----------
    positions : openmm positions, default None
        openmm positions that will be used to update the OEMol
    molecule : openeye.oechem.OEMol
        OEMol object to update

    Returns
    -------
    updated_molecule : openeye.oechem.OEMol
        OEMol object with updated positions

    """

    if positions is None:
        positions = test_extractPositionsFromOEMol(molecule)
        update_positions = copy.deepcopy(positions)
        update_positions[0] += 1.*unit.angstrom
    else:
        update_positions = positions

    updated_molecule = copy.deepcopy(molecule)
    updated_molecule = giveOpenmmPositionsToOEMol(update_positions,updated_molecule)

    assert (molecule.GetCoords()[0] != updated_molecule.GetCoords()[0]), "Positions have not been updated successfully"
    new_positions = test_extractPositionsFromOEMol(updated_molecule)
    assert (new_positions.unit == unit.angstrom), "Positions returned are not in expected units of angstrom"

    return updated_molecule

@skipIf(running_on_github_actions, "Skip full test on GH Actions.")

# Path: perses/utils/openeye.py
# def smiles_to_oemol(smiles, title='MOL', max_confs=1):
#     """
#     Generate an oemol from a SMILES string
# 
#     Parameters
#     ----------
#     smiles : str
#         SMILES string of molecule
#     title : str, default 'MOL'
#         title of OEMol molecule
#     max_confs : int, default 1
#         maximum number of conformers to generate
#     Returns
#     -------
#     molecule : openeye.oechem.OEMol
#         OEMol object of the molecule
#     """
#     from openeye import oeomega, oechem
# 
#     # Create molecule
#     molecule = oechem.OEMol()
#     oechem.OESmilesToMol(molecule, smiles)
# 
#     # create unique atom names
#     if len([atom.GetName() for atom in molecule.GetAtoms()]) > len(set([atom.GetName() for atom in molecule.GetAtoms()])):
#         # the atom names are not unique
#         molecule = generate_unique_atom_names(molecule)
#     else:
#         pass
# 
#     # Set title.
#     molecule.SetTitle(title)
# 
#     # Assign aromaticity and hydrogens.
#     oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
#     oechem.OEAssignHybridization(molecule)
#     oechem.OEAddExplicitHydrogens(molecule)
#     oechem.OEPerceiveChiral(molecule)
# 
#     # Create atom names.
#     oechem.OETriposAtomNames(molecule)
#     oechem.OETriposBondTypeNames(molecule)
# 
#     # perceive chirality before attempting omega geometry proposal
#     assert oechem.OEPerceiveChiral(molecule), f"chirality perception failed"
# 
#     # Assign geometry
#     omega = oeomega.OEOmega()
#     omega.SetMaxConfs(max_confs)
#     omega.SetIncludeInput(False)
#     omega.SetStrictStereo(True)
# 
#     omega(molecule)
#     return molecule


# Path: perses/tests/test_utils.py
import os
    import os
    import simtk.unit as unit
    import simtk.unit as unit
    import copy
    import simtk.openmm.app as app
    import simtk.unit as unit
   import copy
   import numpy as np
   import simtk.unit as unit
from perses.utils.openeye import smiles_to_oemol
from unittest import skipIf
    from perses.utils.data import get_data_filename
    from perses.utils.openeye import extractPositionsFromOEMol
    from perses.utils.openeye import giveOpenmmPositionsToOEMol
    from perses.utils.openeye import OEMol_to_omm_ff
    from simtk import openmm
    from openmmforcefields.generators import SystemGenerator
    from openff.toolkit.topology import Molecule
   from openmoltools.openeye import iupac_to_oemol
   from openeye import oechem
    from perses.utils.openeye import generate_expression

    ----------
    positions : openmm positions, default None
        openmm positions that will be used to update the OEMol
    molecule : openeye.oechem.OEMol
        OEMol object to update

    Returns
    -------
    updated_molecule : openeye.oechem.OEMol
        OEMol object with updated positions

    """

    if positions is None:
        positions = test_extractPositionsFromOEMol(molecule)
        update_positions = copy.deepcopy(positions)
        update_positions[0] += 1.*unit.angstrom
    else:
        update_positions = positions

    updated_molecule = copy.deepcopy(molecule)
    updated_molecule = giveOpenmmPositionsToOEMol(update_positions,updated_molecule)

    assert (molecule.GetCoords()[0] != updated_molecule.GetCoords()[0]), "Positions have not been updated successfully"
    new_positions = test_extractPositionsFromOEMol(updated_molecule)
    assert (new_positions.unit == unit.angstrom), "Positions returned are not in expected units of angstrom"

    return updated_molecule

@skipIf(running_on_github_actions, "Skip full test on GH Actions.")

def test_OEMol_to_omm_ff(molecule=smiles_to_oemol('CC')):