OEMolToHelm

Attention

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

std::string OEMolToHelm(const OEMolBase& mol,
                        const OEMonomerSet& monomers)
std::string OEMolToHelm(const OEMolBase& mol,
                        const OEMonomerSet& monomers,
                        OEHelmGenerationResult& result)
std::string OEMolToHelm(const OEMolBase& mol,
                        const OEMonomerSet& monomers,
                        const OEHelmGenerationOptions& options)
std::string OEMolToHelm(const OEMolBase& mol,
                        const OEMonomerSet& monomers,
                        const OEHelmGenerationOptions& options,
                        OEHelmGenerationResult& result)

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

#include <iterator>
#include <string>

#include <openeye.h>
#include <oechem.h>

using namespace OEChem;

int main()
{
  // read monomer set
  OEMonomerSet monomers;
  OELoadOpenEyeMonomerSet(monomers);

  // generate HELM
  OEGraphMol mol;
  const std::string 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";
  OESmilesToMol(mol, smiles);

  OEHelmGenerationResult result;
  const std::string helm = OEMolToHelm(mol, monomers, result);
  if (helm != "")
  { //  successful generation
    std::cout << "Peptide HELM: " << helm << std::endl;
    const std::vector<std::string> codes = OEGetHelmMonomerCodes(helm);
    std::cout << "Monomer sequence length: " << codes.size() << std::endl;
    std::cout << "Monomer sequence: ";
    std::copy(codes.begin(), codes.end(), std::ostream_iterator<std::string>(std::cout, " "));
    std::cout << std::endl;
  }
  else
  { // failed generation
    std::cout << "Warning:" << result.GetWarning() << std::endl;
  }
  return 0;
}