...
NB the free open-source code only covers peptides
Commercial converters
So far Below is a list of the commercial conversion tools we are only aware of. 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.
NextMove Software's
...
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.
ChemAxon Biomolecule Toolkit
ChemAxon provides various conversion utilities from and to HELM within their Biomolecule Toolkit for peptide- and nucleic acid-derived molecules . (https://www.chemaxon.com/products/biomolecule-toolkit/)
Supported file formats for exporting include XHELM, FASTA, plain sequences and MDL/Mol files*. Sequences from HELM are generated using the Natural Analogue information of HELM monomers. Mol files will be exported in v3000 format containing S-group abbreviations for each monomer.
Supported file formats for importing include FASTA, plain sequences and MDL/Mol files*. FASTA headers are maintained in the HELM annotation section. Import of Mol files is currently limited to molecules, which are fully represented by a given monomer dictionary. This dictionary may be a fully custom/proprietary one.
Until mid 2016 import of PDB files is expected to become available.
*Other chemical file formats can be converted to MDL Mol-file representation using ChemAxon's Molconvert.