Release Notes

What changed in each release of Biotoolkit Monomers, newest first. Every entry describes something you can see or do; internal changes are mentioned only where they change behaviour.

Each entry carries a tag for the part of the application it concerns:

Tag	Area
`[Catalogue]`	The Home page: report, filters, drawings, counters
`[Form]`	The monomer form: create, edit, preview, cap groups
`[Import]`	Bulk import and the import file
`[Version Log]`	History, deletion and revive
`[Chemistry]`	Structure handling, canonical forms, attachment points
`[Integration]`	Behaviour seen through other Discngine applications and the service interface

Planned for the end of November 2026

Subject to change

Biotoolkit Monomers is developed in an agile way, release by release. The list below is the backlog as planned today; items can be reordered, reshaped or moved to a later release as feedback comes in. Nothing here is a commitment until it appears in a released version above.

Catalogue and form

[Catalogue] Attachment point columns. The Home report shows one column per attachment point (R1, R2, …) with its cap group, so a monomer's connectivity can be read and filtered without opening it.
[Catalogue] Drawings with R-groups or with caps applied. A monomer can be shown either with its R1, R2 placeholders or as the molecule it becomes once its cap groups are applied.
[Catalogue] SD file export. Selected monomers can be exported as an SD file, with either the R-group placeholders or the cap groups applied.
[Chemistry] Aliases. One monomer can carry several symbols, so a library that names a residue MeNle and another that names it NMeNle resolve to the same structure instead of two duplicates.
[Chemistry] Enhanced stereo kept in SMILES. Stereo groups declared as and or or in CXSMILES are preserved in the SMILES shown and exported, instead of being flattened.
[Chemistry] Cap group vocabulary managed per organisation. Administrators can add, retire and describe cap groups from the application, and the service exposes the same vocabulary to integrations.

Administration and security

[Version Log] Every change carries the user's identity. Edits and imports are attributed to the person who made them, instead of System, in the Version Log and the audit columns.
[Integration] Roles are enforced end to end. The Viewer, Manager and Administrator roles apply to every entry point, including calls made through other Discngine applications.
[Integration] An organisation can start without the public library. A deployment can be configured with or without the shipped public monomers, for organisations that maintain their own reference set.

Integrations

[Integration] Automatic refresh across the toolkit. Registering or changing a monomer, or its attachment points, propagates without manual action: the web service reloads its monomer library, then every tool that depends on the monomers, such as PepSea and PepFuNN, refreshes in turn. The structure editor can also be asked to reload the library on demand from the application that embeds it.
[Integration] Structure editor manifest. The structure editor loads its monomer library from a manifest at initialisation, so it always starts on the current library and reloads from the same source.
[Integration] Monomer sets. Curated sets of monomers can be defined and fetched as a unit by other Discngine applications.
[Integration] Fixes on the service interface. Registering a monomer with an unknown monomer type is refused instead of storing an empty type; structure conversion no longer fails with Monomer library is empty right after a restart.

Data corrections

[Chemistry] Public library clean-up. Three seed entries with a wrong or duplicated structure, m3U among them, are corrected, and the remaining structures rejected at the last re-keying are triaged.

2026.09.10

New Features

[Catalogue] Structure viewer. Click a drawing in the Home report or the Version Log to open it full size, cropped to the molecule, with zoom, pan and full screen. The same viewer shows the structure in the monomer form.
[Catalogue] Catalogue totals in the report toolbar and footer: the overall count and the count per polymer type, next to the pager, which reads 1 - 50 of N so the filtered count sits beside the overall one.
[Catalogue] Compact rows toggle in the report toolbar, remembered by your browser.
[Catalogue] Structure column can be hidden, through Actions › Columns, for a denser table. Thumbnails load lazily, so a hidden column costs nothing.
[Catalogue] Dates are shown as YYYY-MM-DD (created and updated dates; archived dates in the Version Log carry the time), and the CSV export follows, so the columns stay sortable in a spreadsheet.
[Form] Structure and monomer type can be edited on a private monomer. They were locked once a monomer existed, a precaution from before versioning; every edit is now archived, so the lock is gone. Symbol and polymer type stay fixed, because they identify the monomer in HELM notations. See How to Create or Edit a Monomer.
[Version Log] Deleted monomers are remembered. Registering a symbol or a structure that matches a deleted monomer is held until an Administrator revives it, instead of silently creating a second one. See Versioning and Deletion.
[Import] SDF files accept a single rgroups field, in the R1:H;R2:OH syntax of the tabular formats, in place of the per-label R1, R2 fields, and every field name is matched ignoring case, spaces, underscores and hyphens.
[Integration] Conflict details on a duplicate. When a registration is refused because the symbol or the structure already exists, the response names the existing monomer in dedicated fields in addition to the message, so a calling application can point at it.
[Integration] Version endpoint. The service reports its build and the version of the notation toolkit it runs, so a support request can state both in one call.
[Version Log] Version Log for Administrators: every material edit and every deletion is archived with its before and after structure, and a deleted monomer can be revived with its metadata and set memberships. See How to Review a Monomer's Version History.
[Form] Structure preview: the SMILES is drawn with its R-group labels before saving, and the cap group of each attachment point is chosen from the vocabulary.
[Import] Bulk import from CSV, Excel and SDF, with a file history, progress, and a downloadable error file. See How to Import Monomers in Bulk.
[Catalogue] Public and Private saved views on the Home page.
[Chemistry] Canonical structure key: duplicate detection compares canonical isomeric SMILES within a polymer type, and checks private monomers against the public library by symbol and by structure. See Canonical SMILES and Duplicate Detection.
[Chemistry] Cap group vocabulary H, OH, NH2, Azide, Ethynyl, resolved from SMILES templates. An unknown cap is rejected instead of being replaced by a hydroxyl.

Improved

[Version Log] Version Log is listed in the navigation menu only for Administrators.
[Catalogue] Delete confirmation says that an Administrator can restore the monomer from the Version Log, instead of claiming the deletion cannot be undone.
[Form] Name is required, and validation messages are shown as plain sentences instead of a technical envelope.
[Import] Import help and import checks agree. Symbol, name, SMILES, polymer type and monomer type are mandatory, and natural analog for PEPTIDE and RNA. A missing name or monomer type is reported up front with a plain message. See Import File Format.

Fixed

[Catalogue] Filtering works with large drawings. Applying a filter, for example Polymer Type = CHEM, failed with a character string buffer too small error as soon as a monomer with a large drawing was on the page. Drawings are now served as images, and the reports filter on any column.
[Import] CSV and Excel imports work again. Every row of a tabular import was rejected with Monomer has no Molfile; a SMILES is enough, as documented.
[Chemistry] Multi-atom cap groups are accepted. Azide and Ethynyl were always rejected because the cap name was pasted into the SMILES as if it were an atom. Caps are now built from their structure, in the import, the form and the structure editor, where Alkynyl used to become an aluminium atom. See Attachment Points and CAP Groups.
[Import] Chemical monomers no longer need a natural analog. A CHEM row was rejected unless NATURAL_ANALOG was exactly -, while real libraries carry category values such as Linker. Whatever is submitted is stored as -. See Monomer Types, Polymer Types and Natural Analogs.
[Chemistry] Symbols with a + no longer break structure conversion.
[Integration] The structure editor loads the monomer library again when it contains characters outside ASCII.

Not included: case-insensitive filtering in the reports.

Known limitations

[Chemistry] Enhanced stereo groups in CXSMILES are not part of the canonical key: an enantiomer pair declared in an and group collides. Declare the centre as absolute.