HELM Parsers and Writers
Many organisations have macromolecule information in a variety of formats. Converting HELM to an atom/bond molecular representation is a relatively straightforward process since the monomers and attachment points between monomers are defined, so assembly is straightforward.
Converting an atom/bond representation to HELM is more complex, since you have to decide what the monomers are.
Identifying monomers is not always straightforward. There are decisions about where the backbone actually is which is not always straightforward. See this cyclic peptide as an example:
And there are decisions about capping groups; whether groups such as N-methyl lysine are single monomers or lysine is one monomer and the methyl group a second one.
Free to use toolsets
The HELM toolkit contains a basic fragmenter, and the EBI has completed some work in this area, details of which would be available from them on request.
RDKit
RDKit (open source cheminformatics software released under the BSD license) now includes HELM readers and writers for peptides courtesy of Roger Sayle of NextMove Software. This adds HELM as a supported format to the existing options of SMILES/SMARTS, SDF, TDT, SLN, Corina mol2 and PDB.
A brief overview can be found in some slides presented at the RDKit 2015 user group meeting – see slides 18-22.
https://github.com/rdkit/UGM_2015/tree/master/Presentations
RDKit Github project can be found at:
https://github.com/rdkit/rdkit
The specific code is at:
rdkit/Code/GraphMol/FileParsers/SequenceParsers.cpp
rdkit/Code/GraphMol/FileParsers/SequenceWriters.cpp
NB the free open-source code only covers peptides
Commercial converters
So far we are only aware of NextMove Software's commercial product Sugar & Splice. This supports peptides along with DNA/RNA, inline HELM and XHELM [and IUPAC name generation, and depiction, and peptide name generation, and variable attachment points, and oligosaccharides etc.]
If you know of or indeed sell a commercial HELM conversion tool, please let us know at info@openhelm.org and we will add it to this list.