Re: [Rdkit-discuss] Docker with (latest) rdkit+jupyter

Hi JP, From the Docker log you posted it is obvious that the build starts from the latest miniconda version which than will use python 3.6 as default, however one of the python packages still relies python 3.5. One thing you can try is to tell the conda install command in the docker script

Re: [Rdkit-discuss] How to create a list of molecules and iterate

Dear Maciek, Thanks for the help. This has solved my problem. Regards, Abhik On 2017-11-21 14:49, Maciek Wójcikowski wrote: Hi, Wrap the reader into a list() function: mols = list(SDMolSupplier('in.sdf')) Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl

Re: [Rdkit-discuss] Docker with (latest) rdkit+jupyter

I've got some dockerfiles that might be worth a look. https://github.com/InformaticsMatters/docker_jupyter Not sure if they will help. Tim On 21/11/2017 15:25, JP wrote: Yo RDKitters, I am running a CADD workshop for a group of MSc students and would like to show them some some RDKit

Re: [Rdkit-discuss] How to create a list of molecules and iterate

Hi, Wrap the reader into a list() function: > mols = list(SDMolSupplier('in.sdf')) Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-11-21 15:39 GMT+01:00 abhik : > Hi, > > I am running a similarity search process using rdkit where my query >

[Rdkit-discuss] Docker with (latest) rdkit+jupyter

Yo RDKitters, I am running a CADD workshop for a group of MSc students and would like to show them some some RDKit awesomeness. I thought the best way to do this is to use an rdkit enabled docker image + jupyter notebooks (they are comfortable with python). In preparation, I tried building the

[Rdkit-discuss] How to create a list of molecules and iterate

Hi, I am running a similarity search process using rdkit where my query consists of ~20 templates and my target consists of ~1000 molecules. How can I create a list (or any container) of molecules that I can iterate later. My present algorithm is read template create molecule > read target

Re: [Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

Hi Oops - typo! The chlorate and perchlorate oxygens should all be [O-]. I was copying by hand from a different computer... Regards, Chris On 21 November 2017 at 09:19, Paolo Tosco wrote: > Hi Chris, > > if the behaviour with chlorate and perchlorate is the one you report

[Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

Hi Sometime between 2014 and now there appears to have been a change in the way hypervalent halogen structures are handled. The old behaviour (involving some tweaking of atomic_data.cpp to allow the higher oxidation states) was to have a neutral halogen with double bonds to most of the oxygens,

Re: [Rdkit-discuss] Having trouble getting RDKIT to recognize LiAsF6

Hi A quick follow-up to my last message, w.r.t. halogens. The issue is not that higher oxidation state halogen ions can't be constructed at all, but they end up with bizarre charges on the halogen which are frequently not recognised by other software. Chris On 21 November 2017 at 08:22, Chris