OEAddCustomFASTAResidueΒΆ

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

Add a custom residue to the OEChem FASTA parser. The code is the string surrounded in square brackets. The smiles is the structure of the un-natural nucliec 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.

#!/usr/bin/env python
from openeye.oechem import *

ifs = oemolistream()

flavor = (OEIFlavor_Generic_Default |
          OEIFlavor_FASTA_CustomResidues |
          OEIFlavor_FASTA_EmbeddedSMILES)

ifs.SetFlavor(OEFormat_FASTA, flavor)
ifs.SetFormat(OEFormat_FASTA)

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

custom_fasta = """>Custom FASTA
FVVVSTDPWVNGLY[dI]D[NC(=O)CNC(=O)[C@@H](N[R16])CSCC(=O)[R1]]"""

ifs.openstring(custom_fasta)

mol = OEGraphMol()
OEReadMolecule(ifs, mol)

Warning

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