[Rdkit-discuss] https://en.wikipedia.org/wiki/Hansen_solubility_parameter

2016-12-08 Thread Guillaume GODIN
Dear all, I would like to know if you have an idea on how to determine the "real" fragment count in a molecule. I mean find one fragment with priority and remove it from the molecule and continue until the molecule was empty. the complex part is related to the proper enumaration of linear or

Re: [Rdkit-discuss] https://en.wikipedia.org/wiki/Hansen_solubility_parameter

2016-12-08 Thread Brian Cole
Hi Dr. Guillaume, I played around with the ability to map a set of fragments to molecules a couple months ago. The result of my experiments are here: https://github.com/coleb/fragment_mapper You give it a set of molecules and fragments you would like to have mapped. It tries to find the smallest

[Rdkit-discuss] Generating all stereochem possibilities from smile

2016-12-08 Thread James Johnson
Hello all, I am trying to generate R and S from: CCC(C)(Cl)Br Below is the code for making the smi to mol file. Can someone give me some guidance to generate all sterochem possibilities? The code would also need to work for 2 stereocenters such as: RR, RS, SR, SS or RE, RZ, SE, SZ etc. Thanks!

Re: [Rdkit-discuss] Handling SDF with 'aromatic' bonds?

2016-12-08 Thread Greg Landrum
First the thing I always have to say: According to the spec for mol blocks, aromatic bond orders are only supposed to be used for queries. Given the number of bogus mol files out there in the wild, the RDKit does actually still read these: In [49]: print(mb) RDKit 2D 6 6 0 0