bool OEAddCustomFASTAResidue(const char *code, const char *smiles)

Add a custom residue to the OEChem TK FASTA parser. The code is the string surrounded in square brackets. The smiles is the structure of the un-natural nucleic acid to add to the internal dictionary. Note, the hydroxyl from the background will be automatically stripped and removed by this function.

In order for these residues to be used, the OEIFlavor.FASTA.CustomResidues flavor must be specified. The following code snippet demonstrates how to register a custom D-isoleucine with the FASTA reader named with [dI]. It also demonstrates using the OEIFlavor.FASTA.EmbeddedSMILES flavor to define a tether that can cyclize the peptide.

package openeye.docexamples.oechem;

import openeye.oechem.*;

public class CustomFASTA { 
    public static void main(String[] args)
        oemolistream ifs = new oemolistream();

        int flavor = OEIFlavor.Generic.Default |
                     OEIFlavor.FASTA.CustomResidues |

      ifs.SetFlavor(OEFormat.FASTA, flavor);

      oechem.OEAddCustomFASTAResidue("dI", "CC[C@@H](C)[C@@H](C(=O)O)N");

      final String customFasta = ">Custom FASTA\nFVVVSTDPWVNGLY[dI]D[NC(=O)CNC(=O)[C@@H](N[R16])CSCC(=O)[R1]]";


      OEGraphMol mol = new OEGraphMol();
      oechem.OEReadMolecule(ifs, mol); 


This is an experimental API that may change in the future.