Biomolecule Toolkit History of Changes

May 18th, 2020: Biomolecule Toolkit Docker Image 20.12.0-0.11.0-abdc3378e


  • Explicit hydrogens, that are belonging to unused attachment points where H is leaving group, can be removed during exporting to MOL format (default setting)

  • Multiple errors in Monomer controller are collected and returned when monomer validation fails

April 6th, 2020: Biomolecule Toolkit Docker Image 20.10.0-0.10.0- 1fff86c7


  • The Library Manager is integrated to the Biomolecule Toolkit

  • HELM to MOL conversion produces better quality head-to-tail cyclic peptide structures with contracted groups

  • Option for generating peptides with contracted, 1-letter coded natural amino acids during HELM to MOL conversion is added and it is set to default

March 17th, 2020: Biomolecule Toolkit Docker Image 20.8.0-0.9.0- a594ab3d


  • Now Biomolecule Toolkit can produce MOL files with Al, Br and Cx tags in the SAP blocks of amino acids


  • Registration of a monomer with unknown attribute produced undefined error message

  • Monomer registration and update failed if only the Biomolecule Toolkit is upgraded to a newer version

  • Improved error message upon attempting to convert wildcard 'X' in peptides, and wildcard 'N' in nucleotides to a molfile

February 7th, 2020: Biomolecule Toolkit Docker Image 20.4.0-0.8.2- 800c77d7


  • Speed of SVG generation is increased for sequential (10-fold) and parallel (15-fold) conversions

January 17th, 2020: Biomolecule Toolkit Docker Image 20.1.0-0.8.1-62d50e33


  • MOL to HELM conversion of oligonucleotides with a chemical modification on 3' prime broke the phosphate-sugar backbone

  • HELM to MOL conversion of phosphate linkers was not handled correctly

December 20th, 2019: Biomolecule Toolkit Docker Image 19.27.0-0.8.0-6e217040


  • Inline chemistry image generation for BioEddie did not include SVG content

December 2nd, 2019: Biomolecule Toolkit Docker Image 19.25.0-0.8.0-ee57fa39


  • Single residue placeholder 'X' in peptide query sequences and single residue placeholder 'N' in nucleotide query sequences. Placeholder '*' to define any number of unknown monomers (0, 1... n) in peptide and nucleotide query sequences

  • Import of sequences containing unnatural monomers with separators


  • HELM to MOL conversion failed for RNAs when 5'-linkers or sugars without nucleobases are present.

  • MOL to HELM conversion of cyclic structures created invalid HELM strings by swapping R1 and R2 attachment points

November 7th, 2019: Biomolecule Toolkit Docker Image 19.22.0-0.7.0-898dfcbd


  • Multi-letter monomer abbreviations with '.' separators in query sequences

  • Derivatives search filter is added to search filters

  • 4th attachment point support is now supported


  • Upper case and lowercase letters caused errors in searches

April 2nd, 2019: Biomolecule Toolkit Docker Image 19.8.0-0.6.3-999fab6e

See the changes in the Biomolecule Toolkit 19.8.0 improvements and bugfixes.

March 29th, 2019: Biomolecule Toolkit 19.8.0


  • Updating more than one BLOBs failed with duplication check error.

  • Sequence converter was not working with cyclic flag.

March 1st, 2019: Biomolecule Toolkit Docker Image 19.6.0-0.6.2-977fa56d


  • Oracle 11 support was not available.

March 1st, 2019: Biomolecule Toolkit Docker Image 19.6.0-0.6.1-7a656806

See the changes in the Biomolecule Toolkit 19.4.0 improvements and bugfixes.

March 1st, 2019: Biomolecule Toolkit 19.6.0


  • Security improvement, database endpoints are disabled by default.

February 26th, 2019: Biomolecule Toolkit 19.4.0


  • Error and result code improvements

  • Distance based similarity filter is added to search filters

  • MOL to HELM conversion reduces the number of generated CHEMs that are attached to a e.g. CHEM monomer if their heavy atom number is below four

  • New parameter for sequence conversion for cyclic sequences


  • Macromolecule by helm lookup (POST /rest/macromolecules/helm) failed when sending a HELM which did not match any registered macromolecules

  • New attachment point creation (POST /rest/admin/attachmentPointTypes) failed in Oracle

  • The entityType property of AttributeOption appeared in Swagger two times under different names: entityType and macromoleculeTypeName

  • Multiple sugars differing only in stereo information were not recognised correctly

  • Canonicalization of cyclic RNA sequences resulted in incorrect attachment point information

  • HELM to MOL conversion failed for RNAs which had a connection at the terminal P linker

  • New macromolecule type registration failed

February 19th, 2019: Biomolecule Toolkit Docker Image 19.4.0-0.6.0-dfee79db

First release of Biomolecule Toolkit Docker Image.

October 11st, 2018: Biomolecule Toolkit 18.24.0


  • New Rest endpoint for health check: /health

  • Data migration from older versions handled automatically

API changes

See the detailed description in apichanges_18_24_0.html

Comprehensive API changes will happen in the next releases

July 31st, 2018: Biomolecule Toolkit 18.16.0


  • “No structure” registration.

    • New options for entity types to control the rules of structureless macromolecules. The entity type has MUST_CONTAIN, CAN_CONTAIN and MUST_NOT_CONTAIN options.

    • Structureless rules validation on entity registration.

  • Lot registration.

    • Lot level registration without structure but with lot level attributes.

    • Attribute data validation on lot level.

    • LOT ID generation based on parent ID. (CID)

    • New page for Lot registration in the Biomolecule registration client.

  • Flexible ID generation for entity types.

    • Default settings for generating corporate ID for macromolecules

    • Admin service to create new ID generating rules by entity types.

  • Data type validation for attributes.

  • More flexible additional data definition on macromolecule and component level.

  • Registering biomolecules with domains.


  • Response code of get macromolecules by helm service (/rest/macromolecules/helm) was incorrect when the result set was empty.

  • Macromolecule annotations were not appeared in the output HELM string.

  • Retrieving macromolecules was slow for 100 monomers components.

July 17th, 2018: Biomolecule Toolkit 18.4.0


HELM2 format has become the primary format in Biomolecule Toolkit.


  • Cyclic HELM conversion to sequence format failed.

  • Search with entity type filter in biotoolkit demo page caused error.

  • Synchronization problem was present in aromatic MonomerCount service.

February 8th, 2018: Biomolecule Toolkit 18.3.0


  • Two new endpoints for macromolecule property calculation:

    • Pairwise SequenceAlignment calculation

    • Aromatic MonomerCount calculation

  • IsoelectricPoint web service input type has changed, it has fored to text/plain.

  • HELM2 formatted macromolecule registration is available.


Macromolecule resolvation with bridge connections failed previously.

January 5th, 2018: Biomolecule Toolkit 17.29.0


  • New default monomer library.

  • Oracle property template file has been changed.

  • Isoelectric point calculation API.

  • Prepare macromolecule domain handling on database level


  • There were Oracle specific issues.

November 16th, 2017: Biomolecule Toolkit 17.28.0

Fixes security issues for bioreg web client.

November 2nd, 2017: Biomolecule Toolkit 17.22.1

Fixes for build package.

October 18th, 2017: Biomolecule Toolkit 17.22.0

First release of Biomolecule Toolkit.