Biomolecule Toolkit History of Changes

    Aug 10th, 2020: Biomolecule Toolkit Docker Image 20.16.0-0.13.1-4f26aeaf​


    • Updating Monomer grouping options failed when BMT was configured to use Oracle database with Japanese character set.


    • New settings to configure location of Oracle JDBC driver

    {info} Oracle JDBC drivers are no longer shipping with Biomolecule Toolkit. It is the responsibility of the customer to obtain the Oracle JDBC driver and add it to the BMT classpath.

    July 24th, 2020: Biomolecule Toolkit Docker Image 20.16.0-0.13.0-54f619e70


    • MOL to HELM conversion produces in-line smiles RNA sugars in the HELM string from unknown sugars between known linkers and nucleobases


    • HELM to MOL conversion removed the stereo-information of unknown monomers.

    July 6th, 2020: Biomolecule Toolkit Docker Image 20.15.0-0.12.0-a5de31878


    • New endpoints are introduced in the Biomolecule Toolkit's admin-controller:

      • List all monomer grouping options

      • Update monomer grouping options

    • Options can be set for monomer grouping performed in BioEddie based on monomer properties (text, number)

    • The recommended way to configure chemical structure format conversion is to leverage the newly added Biomolecule Toolkit API endpoint /api/molecules/convert instead of JChem Web Services /rest-v0/util/calculate/molExport endpoint.

    • Error messages related to chemical structure conversion are more general instead of pointing at JChem Web Services as a potential root cause

    • The Library Manager shows notifications upon monomer modifications if the monomer of interest has changed on server side

    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

    {primary} 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.