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Docs on draw_reaction usage #20

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jamesbraza merged 2 commits into from
Oct 23, 2025
Merged

Docs on draw_reaction usage #20

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62517bb
Fixed typo in visualization section
jamesbraza Oct 23, 2025
5d8986d
Added docs on draw_reaction
jamesbraza Oct 23, 2025
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15 changes: 14 additions & 1 deletion README.md
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Expand Up @@ -113,7 +113,7 @@ assert valid_mol_eval(valid_completion_smiles, partial_smiles)

### Visualization

If it helps, you can visualize the molecules:
If it helps, you can visualize molecules:
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```python
from ether0.data import draw_molecule
Expand All @@ -134,6 +134,19 @@ or in your terminal via `chafa valid_molecule.svg`

![valid molecule](docs/assets/valid_molecule.svg)

Similarly, one can visualize reactions:

```python
from ether0.data import draw_reaction

# Source: ether0-benchmark's test split's question 41251b01-7291-56a0-9030-ea51bab03a4c
rxn_smiles = "CC1CNCC1c1nc2c(cnn2C(C)C)c(=O)[nH]1.COc1ccc(C=O)cn1>>"

rxn_text = draw_reaction(rxn_smiles)
with open("reaction.svg", "w") as f:
f.write(rxn_text)
```

### Benchmark

Here is a sample baseline of
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