from oeommtools import packmol
from openeye import oechem
from openeye import oeomega

# Benzene smiles string
benzene = 'c1ccccc1'
# Empty OEMol
solute = oechem.OEMol()


# Conformer generation
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetMaxConfs(1)
omega = oeomega.OEOmega(omegaOpts)

# OEMol generation
if not oechem.OESmilesToMol(solute, benzene):
    oechem.OEThrow.Fatal("SMILES string parsing fails for the string: {}".format(benzene))
if not omega(solute):
    oechem.OEThrow.Fatal("Conformer generation fails for the molecule with smiles string: {}".format(benzene))

# Solvate the system in water
solvate_mol = packmol.oesolvate(solute, density=1.0, padding_distance=10.0, geometry='box',
                                solvents='[H]O[H]', molar_fractions='1.0', close_solvent=True,
                                salt='[Na+], [Cl-]', salt_concentration=0.0, neutralize_solute=True)

# Save the solvated system
ofs = oechem.oemolostream("solvated.pdb")
oechem.OEWriteConstMolecule(ofs, solvate_mol)
ofs.close()