2D Structure Drawing
dimensionality & information content of representations; integrating a 2D editor into Rowan; robust interdimensional interfacing
Rowan aims to be a powerful, affordable, and elegant design tool that enhances the abilities of scientists working with molecules. While some of our users are experts in computational methods and 3D file editing, many still prefer to think about chemistry in 2D on the tried-and-true whiteboard, a pad of paper, or a purpose-built piece of software. Today, we're excited to be adding 2D structure drawing and robust 2D-3D interfacing to Rowan.
Molecular Representations
Molecules can be represented in string format (SMILES / SMARTS) that store connectivity information, as 2D pictures, and in full 3D coordinate form.
These different representations each have advantages and disadvantages—and most folks are trained to think in 2D, even though some important properties are very 3D dependent (like chirality):
1D string representations like SMILES are compact and easy for computers to work with, but aren't very intuitive for chemists and don't capture the structure of the underlying object very well. At Rowan, we almost always convert SMILES strings to 2D or 3D representations right away.
3D molecular structures are the most physical, and 3D coordinates are often needed for specific applications. Torsional scans only make sense in 3D, for instance, as do tasks like protein–ligand docking. But generating 3D coordinates from a 2D structure is non-trivial: finding the lowest energy conformers can become very challenging for complex molecules, even with low-cost methods like NNPs. Furthermore, some molecular properties are measured only over conformer ensembles, making it easier and more natural to work with 2D representations.
Through the path we’ve taken to get here (QM first), Rowan was built with 3D applications in mind—but as we seek to build a comprehensive toolkit, 3D stops being the only format that makes sense. For instance, some of our recent workflows (like solubility prediction and ADME/Tox modeling) operate on 2D representations. Today, we're excited to share some updates about how we're building 2D support into all aspects of Rowan.
Drawing in 2D
Many great 2D molecular editors have been built over the years. To add robust and battle-tested 2D drawing capabilities to our platform, we’ve chosen to integrate EPAM’s Ketcher, an open-source chemical structure editor, into Rowan. We’re very grateful to everyone who has contributed to building such a powerful piece of open-source software.
To draw a 2D structure in Rowan, you can now select the “Draw 2D” option from Rowan’s list of input options.
This will open the Ketcher interface inside the Rowan platform, allowing for easy 2D drawing. To save a new structure (or to save edits to an existing structure), click “Save” in the top right of the modal. To reject changes, click “X” and then confirm that you’d like to reject your changes.
Once you’ve drawn a 2D structure, you can convert from 2D to 3D by clicking the “Convert to 3D” cube button. 3D structures can be converted back to 2D as well using the corresponding “Convert to 2D” smiley-face button.
This process is powerful but not completely bullet-proof, as some 3D representations cannot be unambiguously mapped onto 2D representations. The reverse problem can also be difficult for large structures. We’re working on developing and improving our own algorithms to make both of these operations more robust—in the meantime, we’re curious to hear about any failures.
2D-Native Workflows
We launched our first 2D-only workflow recently, solubility prediction, and we have plans to support more workflows that are natively 2D.
When submitting a workflow in Rowan, if you have a structure selected in the wrong representation, the row will be highlighted and display this error:
Moving forward, we plan to closely integrate 2D and 3D features into Rowan, and we’d love to hear what would be most helpful. If you have an idea for how to make Rowan more intuitive or powerful, please let us know at contact@rowansci.com.