How can HELM Monomer Libraries be shared across BIOVIA Applications?
Several BIOVIA applications such as Draw, Direct, Pipette or Registration depend on libraries of HELM monomer definitions for the creation of HELM strings or inter-conversion of those with the BIOVIA SCSR format for biological sequences.
Central libraries are created and maintained in Pipeline Pilot using a set of protocols that is part of the Chemistry Collection. Before version 2022 an active connection to Foundation Hub was required where the central libraries were stored. Starting with 2022 central libraries can now also be saved in Pipeline Pilot without Foundation Hub.
A similar set of protocols is available:
- For Hub libraries
- For Pipeline Pilot libraries
You can create new libraries and add to existing libraries in Foundation Hub from source SCSR template or HELM monomer files. New custom templates or monomers are normally created using BIOVIA Draw, for SCSR templates, or Pipette Sketcher or the Pistoia Alliance HELM Editor, for HELM monomers.
There are also protocols for deleting library entries or entire libraries.
HELM Libraries can be converted into SCSR and vice versa.
To use centralized libraries in Pipeline Pilot, Direct and Registration, libraries must be exported as configuration files:
- SCSRTemplates.mol (library in SCSR format)
- HELMMonomers.sd (library in HELM format)
- HELM SCSR Mapping File
The applications must be configured to use the exported files.
Synchronizing Centralized Libraries with BIOVIA Draw
In Draw go to Chemistry > Manage Centralized Libraries
BIOVIA Draw includes a default set of SCSR templates. Users can create personal templates and administrators can extend the default templates with a customized installation package. However, these
local templates are used only with Draw.
When Draw is connected to a centralized library, the templates in the library are synchronized once per session. Therefore, new templates are available to all Draw users as soon as they are loaded into the central library. The centralized libraries are downloaded and displayed in the Centralized Library toolbars. The libraries in Draw remain synchronized with centralized libraries of the selected storage location, unless you turn off Check for updated libraries.
All configuration aspects of central libraries are detailed in the document SYNCHRONIZING CHEMISTRY CONFIGURATION FILES that can be found in the Pipeline Pilot Help Center or in the BIOVIA Draw documentation download.
