OEHelmToMol

Attention

This is a preliminary API and may be improved based on user feedback. It is currently available in C++ and Python.

OEHelmToMol(mol: Union[OEGraphMol,OEMol,OEQMol], helm: str,
            monomers: OEMonomerSet) -> bool
OEHelmToMol(mol: Union[OEGraphMol,OEMol,OEQMol], helm: str,
            monomers: OEMonomerSet, result: OEHelmParsingResult) -> bool

Converts a HELM string into a molecule. The function will return true if the HELM string can be parsed and interpreted successfully, otherwise the function will return false and a given molecule will be cleared.

mol

The constructed molecule (OEMolBase).

helm

The HELM string that is parsed into the molecule.

monomers

The monomer set (OEMonomerSet) that stores the monomers that are used to interpret the HELM string.

If the given monomer set supports multiple code sets, OEHelmToMol automatically selects the code set that contains all monomer codes needed to parse the HELM string.

result

Is specified, the OEHelmParsingResult object will store additional parsing information.

After constructing the molecule the following properties are perceived:

Rings are perceived by calling the OEFindRingAtomsAndBonds function.
The aromaticity is assigned by calling the OEAssignAromaticFlags function using the OEAroModel_OpenEye aromaticity model.
The chirality is perceived by calling the OEPerceiveChiral function.

Warning

The current implementation of HELM parsing algorithm does not support RNA polymers.

Example

from openeye import oechem

# read monomer set
monomers = oechem.OEMonomerSet()
oechem.OELoadOpenEyeMonomerSet(monomers)

# parse HELM
mol = oechem.OEGraphMol()
helm = "PEPTIDE1{C.Y.I.Q.N.C.P.L.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$"

result = oechem.OEHelmParsingResult()
if oechem.OEHelmToMol(mol, helm, monomers, result):
    #  successful parsing
    print(f"Peptide SMILES: {oechem.OEMolToSmiles(mol)}")

    for group in mol.GetGroups(oechem.OEHasGroupType(oechem.OEGroupType_Monomer)):
        if group.HasData(oechem.OEProperty_Monomer):
            monomer_data: oechem.OEMonomerData = group.GetData(
                oechem.OEProperty_Monomer
            )
            code = monomer_data.GetCode("OpenEye")
            atoms_str = " ".join(
                f"{a.GetIdx():2d}{oechem.OEGetAtomicSymbol(a.GetAtomicNum())}"
                for a in group.GetAtoms()
            )
            print(f"{code=:6s} atoms={atoms_str}")

else:
    # failed parsing
    print(f"Warning: {result.GetWarning()}")
    print(helm)
    print("-" * result.GetErrorPosition(), "^")

OEHelmToMol can parse HELM strings with embedded SMILES in various styles. The examples below illustrate valid representations of eledoisin:

PEPTIDE1{[N1[C@@H](CCC1=O)C([R2])=O].P.S.K.D.A.F.I.G.L.M.[am]}$$$$
PEPTIDE1{[N1[C@@H](CCC1=O)C([*:2])=O].P.S.K.D.A.F.I.G.L.M.[am]}$$$$
PEPTIDE1{[N1[C@@H](CCC1=O)C(*)=O |$;;;;;;;_R2;$|].P.S.K.D.A.F.I.G.L.M.[am]}$$$$

In case when the OEHelmToMol function successfully parses a HELM string the atoms that are generated for a specific monomer are added to a molecule as a group (OEGroupBase)