[Rdkit-discuss] RDKit Valences

Dear all, I tried to load a periodate from its smiles (I think these are correct), but it failed as according to rdkit, Iodine cannot have a valence of 7. However, it can when stabilised with oxygens (at least from what I recall from my undergraduate course!). In [23]: Chem.MolFromSmiles('[

Re: [Rdkit-discuss] Has3D?

Hi Dimitri, 3D geometry information for rdkit `Mol`s is stored as `Conformer`s. These can be accessed with the `GetConformer` method, which takes a confId as an argument. If you have loaded the molecule from a mol/sdf file, there should be a single conformer with ID 0, with the coordinates fro

Re: [Rdkit-discuss] where to find I-State of atoms

Hi Guillaume et al., First of all, I’d like to recommend “Molecular Descriptors for Cheminformatics” (http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527318526.html) as a slightly more up to date version of the Handbook of Molecular Descriptors, and a truly excellent resource in this area.

[Rdkit-discuss] Cartridge fingerprint customisation & IPython integration

Dear all, I’m new here, so to introduce myself, I’m currently a 1st year PhD student under Andreas Bender at the Unilever Centre for Molecular Informatics in Cambridge. I’ve got an install of the rdkit head on Mac OS X Mavericks using Eddie Cao’s homebrew formula (thanks!), and a functioning in

Re: [Rdkit-discuss] conda recipes for the RDKit

Dear all, Further to Riccardo’s email, I’ve built boost and rdkit binaries for OS X using conda, which may be installed using `conda install -c https://conda.binstar.org/richlewis rdkit`. These are *highly* experimental, but at least one of my colleagues has obtained a functional rdkit modul

Re: [Rdkit-discuss] Deep Copy of Molecule

Hi Dave, I actually came across this perculiarity yesterday! I think the problem is that the copy built-in module only works properly with Python objects, and rdkit Mol objects are really C++ objects (I’m sure someone else can give a better explanation). The solution that seemed to work for me

Re: [Rdkit-discuss] Problem building recent revisions on Windows

Hi Greg, I see rdkit currently uses Travis CI, but have you considered also using a Windows specific CI server like appveyor in addition? It is free for open source projects, and may guard against problems such as that seen in this thread in future development. I thin