Cards & Table
Cards and Table are the two main tools to explore the chemical space. They are highly customizable.
By using the "More..." menu in either molecule view, users can easily:
- Export molecules of interest (as a CSV, SDF or Makya Dataset);
- Rescore selected molecules using a Scorer;
- Set the Core that is used as a reference for molecule alignment.
Cards
Cards put a focus on the molecule view. Scores that are displayed below the molecules can be customized and molecule order can be sorted based on these scores.
Table
Table puts a focus on the scores associated with each molecule. The table can be customized, with columns being moved around or used to sort molecules.
Switch between Cards and Table
To switch between the two visualization modes, use the toggle in the molecule view top bar.
Molecule Details
To view the details of a specific molecule, you can either:
- Select a compound of interest and click the Molecule Details sidebar:
- Click on the eye button, either in Card or Table view:
The Molecule Details sidebar will open, allowing users to verify the characteristics of or interact directly with the selected molecule, for example:
- In the Details tab:
- Check the scores of the molecule, and optionally, compare them to a Reference Molecule;
- Scroll through the molecules;
- Copy the SMILES, set the molecule as a Reference, add the molecules to the trash, access the retrosynthetic analysis (in Spaya), or export the molecule as a PNG (in the contextual menu);
- Leave a comment as an internal note or for collaborators to see;
- In the 3D View tab:
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See the 3D conformation and list of interactions for the molecule;
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- In the Generation Tree tab:
- See the step-by-step generation tree through which the algorithm found the molecule, identifying the specific building blocks and steps that were used.
Reference Molecule
For efficient comparison and exploration of the chemical space, Makya lets users specify a reference molecule. All molecules are systematically compared to the reference, similarity is calculated and the reference is highlighted in plots.
To add a reference molecule, click the focus icon on the molecule card or select "Set as reference molecule" in the contextual menu associated with the molecule. Similarity will be automatically computed and displayed.
Set Core (Alignment)
For consistent visual analysis, Makya lets users align molecule representations to a common substructure. The substructure can be a structure set during the generation setup, a user fragment, or the Maximum Common Substructure.
To do so, click on the "Set Core" option in the "More..." menu and specify the alignment structure. Alignment will be computed and the molecular view will be updated.