CORS_ALLOWEDORIGINS) to adjust CORS-related behaviorStandardizer is integrated as an optionally licensed module
Molar mass and exact molar mass calculations are available for non-stored macromolecules. The new service calculates "average" or "exact" molar mass from HELM inputs.
Exact molar mass calculation for macromolecules is added to the Biomolecule Toolkit.
Average isotopic mass (molar mass) of a macromolecule can be calculated based on the atomic weights defined in the elements.txt
Option for expanding all monomers is added to the HELM to MOL conversion.
Option for expanding branching amino acids is added to the HELM to MOL conversion.
Option for expanding unnatural amino acids is added to the HELM to MOL conversion.
Registered monomer attributes are selectable in the monomer's additional data section when the remote library is selected in the Library Manager.
Monomers without attachment points can be submitted from the Library Manager interface to the monomer library.
Improved error message on supported monomer R attachment points in the Library Manager.
User warnings are displayed in the Library Manager's Marvin JS pop-up when a monomer structure does not have an R-group and/or a defined R-group is removed.
Leaving group average isotopic mass (molar mass) is calculated based on the atomic weights defined in the elements.txt
Molar mass calculation based on Mw monomer attribute can be applied on BLOB monomers only.
Option for contracting natural amino acids is removed from the HELM to MOL conversion.
{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.
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
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
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
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
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
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
Multi-letter monomer abbreviations with '.' separators in query sequences
Derivatives search filter is added to search filters
See the changes in the Biomolecule Toolkit 19.8.0 improvements and bugfixes.
Updating more than one BLOBs failed with duplication check error.
See the changes in the Biomolecule Toolkit 19.4.0 improvements and bugfixes.
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
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
First release of Biomolecule Toolkit Docker Image.
New Rest endpoint for health check: /health
See the detailed description in apichanges_18_24_0.html
{primary} Comprehensive API changes will happen in the next releases
“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.
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.
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.
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.
Macromolecule resolvation with bridge connections failed previously.
New default monomer library.
Oracle property template file has been changed.
Isoelectric point calculation API.
Fixes security issues for bioreg web client.
First release of Biomolecule Toolkit.