ChemAssist introduces a new sample field option called Chemical that can be added to a sample-type template.
Note: this functionality needs to be activated within the add-on Configuration: by activating Enable MarvinJS chemical structure as field type in Sample Types.
When selected, a new sample specification field option containing a MarvinJS sketchpad becomes available when adding a sample.
Adding structures to the chemical structure sample field
When creating a new sample or editing an existing sample in eLabInventory, users can add a molecule drawing to the chemical structure field via two methods:
- Draw a molecule: Users can draw their chemical structure on the sketchpad, which is supported by the MarvinJS add-on
- Upload a structure file: Users can upload a molfile of an entire molecule to the sketchpad.
Adding structure by drawing manually
ChemAssist provides a simple and clean sketchpad interface for visualizing the structural characteristics of drawn or imported molecules. Users can rotate, mirror, and edit molecules by section or entirely.
To draw a chemical structure, Edit the sample. ChemAssist’s sketchpad is powered by the Marvin JS add-on; for more information on how to use MarvinJS, please refer to the MarvinJS User Guide.
Uploading a molecular structure as a mol file
To upload a molfile, click the Import (open folder) icon in the top-left corner of the Sketchpad interface to open the Import pop-up window. Then click the Choose File button and select the molfile from the desktop to upload it to Sketchpad.
Once the sample has been saved, the entire chemical structure will be visible on the sample data sheet, along with its Absolute and Unique SMILES codes. Additionally, ChemAssist will generate an MDL molfile of the structure, which can be downloaded by clicking on the “Download MDL molfile” link.
Note: the most common molecule mol files can be downloaded from the internet, which can be imported as a base structure of a new molecule and then modified. In the case of more complex structures, the structure can be drawn once, exported as a mol file, and then reimported into eLab to create new variations.
Importing and Updating Chemical Structures in Bulk
ChemAssist enables users to create and update chemical structures for multiple samples simultaneously. The Sample Batch Import and Sample Batch Update add-ons, available in the Marketplace, support these bulk actions.
When initiating a Sample Batch Import or Update action, users can select the Chemical Structure field as a column option within the table view. The field is displayed as a text field that exclusively accepts a chemical structure in SMILES notation. Once the import or update action has been initiated, the SMILES notation will be translated into a structural diagram and displayed for the sample accordingly.
Note: If users do not have the generated SMILES code for all their compounds in advance, they can add a general structure SMILES and, after the import, adjust the structures manually for their sample by redrawing it.
Users with a Private Cloud or On-Premises installation can also use the System Admin Sample Import function to import samples with Chemical Field. As with the Sample Batch Import and Update add-ons, the Bulk Import template accepts the chemical structure in SMILES notation for the field’s value.
Tracking derivates by creating your Compound Library
Users can use the Sample Parent and Sample Lineage add-ons to symbolize derivatives of their molecules and compounds. Once activated, the Lineage add-on will display all the connected samples and experiments related to a given compound.