Re: [Rdkit-discuss] Mongo-RDKit Integration!

x. do we include different tautomers as duplicates?) > > I'll keep the other features you mentioned in mind going forward as > well—while they're not quite optimized yet, we can already support the > queries that you mention, ensure indices, and canonicalize SMILES. > >

Re: [Rdkit-discuss] Mongo-RDKit Integration!

Chris, That sounds like a great idea! Optimized similarity and substructure searches are hard to get right, and most libraries leave it as an exercise to the reader to choose the right fingerprinting and db structure. I think the hardest part will be figuring out a robust end-user experience. You'

Re: [Rdkit-discuss] MaxMin Picker and Python

Try using parentheses instead of square brackets. This converts lists to generators , which will take up almost no memory. Haven’t tested it, but here’s how it would impact your code: from rdkit import Chemfrom rdkit.Chem import AllChemfrom rdkit import Da

Re: [Rdkit-discuss] Chemical formula

If you’re using Python, I’d recommend using collections.Counter (part of the standard lib). It’s better than rolling out your own parser. In [1]: from rdkit import Chem In [2]: mol = Chem.AddHs(Chem.MolFromSmiles('C(=O)O')) In [3]: from collections import Counter In [4]: c = Counter(atom.GetSymbol

Re: [Rdkit-discuss] Fwd: Cartridge fingerprint customisation & IPython integration

I hadn't seen that. The 3D functionality is something that it would be very nice to have available in the notebook, and I think it's only fair to borrow some ipython ideas back from OpenBabel. ;-) Steal away :-) The viz runs off of this repo, which is al

Re: [Rdkit-discuss] looking for suggestions: github vs bitbucket vs google code

Seconding Markus - My biggest issue switching from svn to git was honestly the word "checkout". It means two different things between them, and I found myself doing stupid things all the time. Outside of that, and the weird "staging area" thing I never got a hold of but can be easily skipped, I did

Re: [Rdkit-discuss] looking for suggestions: github vs bitbucket vs google code

Github has a lot more features than its competitors, and they're growing rapidly. To help, look at a big project that's already using it (like three.js) to try to e