OECreatePeptideMonomerConnectionSmiles

Attention

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

OECreatePeptideMonomerConnectionSmiles(monomerSmiles: str) -> str

The function identifies the backbone of the amino acid represented in the input string and marks the backbone connections in the output smiles:

the hydrogen of the amino group of the backbone will be have atom mapping 1
the oxygen of the amino acid of the backbone with be have atom mapping 2

For example, in case of the input smiles C[C@@H](C(=O)O)N, the function will return [H:1]N[C@@H](C)C(=O)[OH:2].

If the input smiles does not represent an amino-acid or its backbone can not be identified, and empty string will be returned.

The current implementation supports the identification of backbone connection for alpha-, beta-, gamma-, and delta- amino acids. However, it does not identify connection point(s) on the side chain of the amino acid.

For example, in case of the input smiles C([C@@H](C(=O)[OH:2])N)S representing cystine, the function will return [H:1]N[C@@H](CS)C(=O)[OH:2]", rather than [H:1]N[C@@H](CS[H:3])C(=O)[OH:2] where R3 could be used to form disulfide cross-links.

When identifying the backbone of an amino acid, backbone is always selected as the shortest path between identified amino and carboxylic acid groups.

For example, in case of the input smiles C(CC(=O)O)[C@@H](C(=O)O)N representing glutamic acid, the function will return [H:1]N[C@@H](CCC(=O)O)C(=O)[OH:2], rather than [H:1]N[C@@H](CCC(=O)[OH:3])C(=O)[OH:2] where R3 could be used to form isopeptide bond.

When creating a custom monomer set, side-chain interactions of amino acids, along with the identification of connection points for C- and N-terminal monomers and generic non-peptidic monomers, must be specified manually.