You can create molecules by importing them or by drawing individual molecules. Molecule drawing is enabled by RDKit with ChemAxon’s Marvin JS sketcher.
This article explains:
Create individual molecules
You can create individual molecules in the global, project, or Registry create menus. The instructions below are for the global create menu.
Tip: To input schema fields during molecule creation, we recommend using the Registry create menu.
To create a molecule:
Click + in the left-side menu.
Hover over Molecule, then click New Molecule.
In the Create Molecule modal, enter the molecule name and select the folder. You can also select a schema.
If you’re using the global or project create menus and select a schema, you’ll complete the schema fields later.
Complete the chemical structure of the molecule.
Complete a chemical structure
You can complete the chemical structure of your molecules by drawing the structure in the Marvin canvas or uploading a chemical structure.
To upload a chemical structure:
Click the Import icon from the top-left corner of the Marvin window.
Click Choose file, select the file, then click Open.
You can select the file format from the drop-down menu or choose to let Marvin auto recognize the file format.
Tip: To enhance your workflow, use Marvin JS keyboard shortcuts.
You can create new molecules and register existing molecules through registration tables by specifying a SMILES string to represent the chemical structure.
Import molecules via spreadsheet
You can import molecules in bulk from a spreadsheet, raw text, or .sdf file.
To bulk import molecules:
Click + in the left-side menu.
Hover over Molecule, then click Import New Molecules.
Under Import location, select a project or folder to house the molecules. You can also select a schema.
Select your import method from the drop-down menu.
If you’re using spreadsheet or .sdf, select Choose file. Select the file, then click Open.
If you’re using raw text, enter or paste the text into the window.
Click Next to upload the data, then click Next to validate it.
Note: If you’re importing from a spreadsheet, you can rely on a column of data representing chemical structure in SMILES or .mol file format; both must be in text/string format.
Supported file formats for chemical structure imports
Benchling supports many common and proprietary file formats. You can use the table below as a general reference to determine if a file type is supported, however, we’re continuously expanding our list of supported formats, so we always recommend first trying to upload your file into the importer, as it might not yet be included in this reference.
MDL MOLfiles V2000
Extended MOLfiles V3000
ChemAxon compressed MOLfile
MDL RXNfiles V2000
Extended reaction files V3000
MDL SD Files
MDL RG Files
ChemAxon Marvin Document (MRV)
Simplified molecular Input Line Entry Specification (SMILES)
.smi, .smiles, .cxsmiles
ChemAxon Extended SMARTS
.sma, .smarts, .cxsmarts
Chemical Markup Language (CML)
International Chemical Identifier (InChI)
Protein Data Bank
There are a variety of endpoints available through Capillary which can:
Bulk archive molecules
Bulk unarchive molecules
Bulk update molecules
Create bulk and single molecules
Get a molecule by API identifier
List all molecules
To learn more about these endpoints, visit the Molecules API documentation.
Can I create or import molecules with R-groups?
No. At this time, molecule entities don’t support ambiguous molecules containing R-groups.
Can I store multicomponent structures?
No. Multicomponent chemical structures can’t currently be stored as molecules. If you try to create a molecule with multiple components, an error displays.
Can I display salts on chemical structures?
Not yet. Currently, salts are automatically stripped from the file during conversion. The largest fragment of the original molecule by atom count is kept as the parent molecule, and all other fragments are treated as salts.
Salts can be saved in schema and custom fields when detected upon bulk import. They’re parsed and stored as a list of SMILES strings saved as a text field value.