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Many chemical reactions I've tried recently have returned no products, and have also not thrown any errors in their execution. Here is an example:
```
rs = '[H:9][O:1][C:2]([H:10])([*:11])[C:3]([H:4…
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SMILES Strings with explicit hydrogens present and double bond geometry specified lose the double bond geometry when importing to RDKit ROMol object with default sanitization.
e.g. If we use, where w…
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The only difference is that `SmallMoleculeTopologyProposal` adds a `molecule_smiles` property but I don't think this is ever used.
My understanding was that there should be an `old_metadata` and `new…
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Currently, `SmallMoleculeSetProposalEngine` takes `receptor_topology` in the constructor.
Since the `current_topology` is passed into every `propose()` call, it would give us much more flexibility if…
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We have to make some decisions about how we tell YANK what we want it to do.
To be specific, we need to tell it:
- What input to use for the **ligand**, which might be a mol2 file, SDF file, IUPAC or…
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Right now, saved models can only be evaluated on train/test data. In order to use models to make useful predictions, models should be able to make predictions on input compounds (perhaps input as a cs…
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There are a couple of rows without structures on the Google spreadsheet
https://docs.google.com/spreadsheets/d/1Rvy6OiM291d1GN_cyT6eSw_C3lSuJ1jaR7AJa8hgGsc/edit#gid=510297618
MMV669543
MMV669849
MMV…
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@tscmacdonald to perform a literature survey and determine:
1. Best synthetic routes to Daraprim
2. Possible routes with UG/High School 'friendly' reagents
3. Analogs tested against toxoplasmosis, mal…
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We need to complete the dataset in the Master Sheet for OSM Series 1 compounds before we submit the relevant paper in the near future. The dataset will allow readers of the paper to browse the series …
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Today we received the green light from MMV to submit Paper 1, which is really exciting. There are just a few loose ends.
So, the Datatset. I think we’ve finished adding all the data we have for Serie…