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Hi,
Thanks for this project, it looks like it could be really helpful. Sorry if this is a stupid question but I was wondering, once I've tokenized a set of SMILES using the pre-trained SMILES model…
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C1C1 is used by Andrew Dalke in http://ctr.wikia.com/wiki/Chemistry_Toolkit_Rosetta_Wiki as an example of a SMILES error which ought to be caught and reported. OB converts it to CC (not even C=C, whic…
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```
def get_smiles(mol):
return Chem.MolToSmiles(mol, kekuleSmiles=True)
smiles = Chem.MolFragmentToSmiles(mol, atoms, kekuleSmiles=True)
```
Why does reading smiles require kekule forma…
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Get SMILES for PubChem Compount (here for aspirin CID 2244):
* https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/2244/JSON
Get AA sequence for a protein (check the sequence key)…
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https://github.com/Acylation/obsidian-chem
Run `npm install smiles-drawer`, and then declare it in the `global.d.ts` using the line `declare module 'smiles-drawer';`, then you'll have the smiles-dr…
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Hello,
how can I create a `VisualGraphDatasets` from a Pandas Dataframe containing smiles strings and a target?
Best, Kai
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Hi,
I am wondering if there is a straightforward way to use the get_most_stable_tautomer function as a standalone rdkit function that can be applied to a SMILES column in a pandas dataframe, for ex…
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How can I display reaction from smiles (e.g. CCO.C(=O)O>>C(=O)OCC )in Viewer2D? As I can see it is not possible to export/import it directly from smiles. My first idea is: a) export each mol to kcj, …
rmrmg updated
6 years ago
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When choosing to output the SMILES string for a molecule it will print out `*` instead of the respective element-symbols.
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### Bug Description
When generating mechanisms for surface reactions, there is a bug in the naming of the species in the output file. RMG used to replace the SMILES string of the species for example …