Helmkit: fast and robust conversion of HELM notation to atomistic representations for large-scale macromolecular informatics
Ramon Adàlia, Gemma Sanjuan, Tomàs Margalef, Ismael Zamora · 2026
Read Helmkit: fast and robust conversion of HELM notation to atomistic representations for large-scale macromolecular informatics by Ramon Adàlia, Gemma Sanjuan, Tomàs Margalef, Ismael Zamora (2026) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-13449311.txt.
Description
Ramon Adàlia and coauthors offer a 2026 open-source Python library, helmkit, for fast change of HELM big-molecule code into atom-level models. Older changers lag on speed, scope, and toughness, so helmkit converts HELM strings straight to RDKit objects across protein bits, nucleic acids, linkers, and hybrids with side-by-side work.
Checks on nearly 879,000 PubChem entries and over 7,000 cyclic protein bit entries showed near-perfect exactness, including shapes other toolkits fail to parse, at up to 5,000 items per second. The lightweight tool suits drug finding, virtual screening, and bio building at large scale.
Catalog record
| CREATOR | Ramon Adàlia, Gemma Sanjuan, Tomàs Margalef, Ismael Zamora |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 40 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |