OEMolToHelm

Attention

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

OEMolToHelm(mol: Union[OEGraphMol,OEMol,OEQMol],
            monomers: OEMonomerSet) -> str
OEMolToHelm(mol: Union[OEGraphMol,OEMol,OEQMol],
            monomers: OEMonomerSet, result: OEHelmGenerationResult) -> str
OEMolToHelm(mol: Union[OEGraphMol,OEMol,OEQMol],
            monomers: OEMonomerSet, options: OEHelmGenerationOptions) -> str
OEMolToHelm(mol: Union[OEGraphMol,OEMol,OEQMol],
            monomers: OEMonomerSet, options: OEHelmGenerationOptions,
            result: OEHelmGenerationResult) -> str

Converts a molecule into HELM string. The function will return HELM string if it can be generated successfully, otherwise the function will return an empty string.

mol

The molecule (OEMolBase) the HELM string is generated from.

monomers

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

If the given monomer set supports multiple code sets, OEHelmToMol automatically selects the primary code set.

options

The options for HELM generation (OEHelmGenerationOptions).

result

Is specified, the OEHelmGenerationResult object will store additional information about the success or failure of the HELM generation.

Example

from openeye import oechem

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

# generate HELM
mol = oechem.OEGraphMol()
smiles = (
    "CC[C@H](C)[C@H]1C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CSSC[C@@H](C(=O)N[C@H]"
    "(C(=O)N1)Cc2ccc(cc2)O)N)C(=O)N3CCC[C@H]3C(=O)N[C@@H](CC(C)C)C(=O)NCC(=O)N)CC(=O)N)CCC(=O)N"
)
oechem.OESmilesToMol(mol, smiles)

result = oechem.OEHelmGenerationResult()
helm = oechem.OEMolToHelm(mol, monomers, result)
if helm:
    # successful generation
    print("Peptide HELM: ", helm)
    codes = oechem.OEGetHelmMonomerCodes(helm)
    print(f"Monomer sequence length: {len(codes)}")
    print(f"Monomer sequence: {' '.join(codes)}")
else:
    # failed generation
    print(f"Warning: {result.GetWarning()}")