Page Comparison

...

rdkit/Code/GraphMol/FileParsers/SequenceWriters.cpp

NB the free open-source code only covers peptides

Commercial converters

Below is a list of the commercial conversion tools we are 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 Sugar and Splice 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.]. Further details can be found at https://www.nextmovesoftware.com/sugarnsplice.html 

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.

Biovia Pipeline Pilot

Biovia's Pipeline Pilot contains HELM reader and writer components in its chemistry collection. It does not fragment atom/bond representations but can convert sequence-based notations. There is HELM support in some other Biovia tools - see the PDF below for details.

 Perkin-Elmer's ChemDraw

Version 17 of ChemDraw allows you to draw HELM molecules directly using the monomer.org monomer set. A video is available to show you how.