[Rdkit-discuss] Building RDKit Java Wrappers

2019-11-05 Thread Jenny h
Dear all, First of all sorry for the spam in case you received the mail earlier, but since I so far did not see it on the list I assumed it got somehow stuck in some spam filter. I wanted to use the RDKit Java wrappers to just learn and play around with RDKit in Java (and maybe one day be able

Re: [Rdkit-discuss] Explicit H in substructure searches

2019-11-05 Thread Greg Landrum
Paolo's answer was completely correct, but there's an additional point that's worth mentioning here. Hs are often included in query molecules with the intent of restricting possible valence states of atoms, not because the user is actually interested in matching Hs. In this case you can use the

Re: [Rdkit-discuss] SMARTS Query Normalization?

2019-11-05 Thread Greg Landrum
On Mon, Nov 4, 2019 at 5:33 PM Webster Homer < webster.ho...@milliporesigma.com> wrote: > We are currently using Mol files, they’re large especially when > urlencoded, > That's a point. They tend to be less problematic when embedded in a POST query, but that has a different set of issues

Re: [Rdkit-discuss] Building RDKit Java Wrappers

2019-11-05 Thread Paolo Tosco
Hi Jenny, -- Could NOT find Boost (missing: serialization) (found suitable version "1.65.1", minimum required is "1.56.0") it looks like CMake found your Boost installation but either the serialization library was not built or possibly was not built for the same architecture (32-bit vs

[Rdkit-discuss] Explicit H in substructure searches

2019-11-05 Thread Markus Heller
Hi, I'm trying to understand how to properly use explicit hydrogens in substructure searches. Below is an example. I would like to find all molecules that contain my query with hydrogens at the nitrogens, and I thought I was on the right track ... Why does the first query with the explicit

Re: [Rdkit-discuss] Explicit H in substructure searches

2019-11-05 Thread Paolo Tosco
Hi Markus, I tried to put together a comprehensible explanation in his gist: https://gist.github.com/ptosco/1088937ce332bd66c999a2a5fbc855b3 Please also refer to the following threads on the mailing list: https://sourceforge.net/p/rdkit/mailman/message/29679834/

Re: [Rdkit-discuss] Molecules not rendere in Dataframe

2019-11-05 Thread Jan Halborg Jensen
Hi again, Since I thought it might be a Colab problem I also posted the question on Stackoverflow, and got an answer from Oliver Scott https://stackoverflow.com/questions/58656572/problem-using-addmoleculecolumntoframe-on-google-colab/58690736#58690736 "Seems like this is a problem with all