[Rdkit-discuss] CanonicalRankAtoms

Hi, I experimented a little bit with CanonicalRankAtoms and observed some unexpected results. I have two mols (actually sets of fragments): C[*].n[*].C[*].N[*] CC[*].CC[*].cn([*])c.CN([*])C In the first case, pairs of carbons and nitrogens are recognized as symmetrical [0, 2, 0,

[Rdkit-discuss] problems with alignment (py3Dmol + rdkit, jupyter notebook)

dear all i am trying to align molecules read from a *sdf file (list of conformers) against another molecule (reference - a crystal structure), also read from a *sdf file and make a nice 3d picture in jupyter notebook as shown in: http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/

Re: [Rdkit-discuss] scaffold distance algorithm

Well, I guess this means no. That leaves more fun for me... :-P -Axel On 23.03.2017 09:38, Axel Pahl wrote: > Dear fellow RDKitters, > > has someone by any chance tried to implement in RDKit the scaffold > distance algorithm by Jürgen Bajorath et al. (and would be willing to > share some code)?

Re: [Rdkit-discuss] interactive py3Dmol in jupyter notebook - not all py3Dmol.view() are visible

thank you! best regards, gosia 2017-03-28 16:12 GMT+02:00 Greg Landrum : > Ah got it. I think this is a 3dmol.js/py3dmol question, not an RDKit > question. > I'd suggest asking on the 3dmol.js issue tracker: https://github.com/ > 3dmol/3Dmol.js/issues > > On Tue, Mar 28,

[Rdkit-discuss] interactive py3Dmol in jupyter notebook - not all py3Dmol.view() are visible

hello, i'm using rdkit with py3Dmol in jupyter notebook, as in this example: http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/bl ob/master/notebooks/Trying%20py3Dmol.ipynb is there a limit of how many py3Dmol.view() frames can be in one notebook? i'm asking because it seems that jupyter

Re: [Rdkit-discuss] interactive py3Dmol in jupyter notebook - not all py3Dmol.view() are visible

Ah got it. I think this is a 3dmol.js/py3dmol question, not an RDKit question. I'd suggest asking on the 3dmol.js issue tracker: https://github.com/3dmol/3Dmol.js/issues On Tue, Mar 28, 2017 at 4:06 PM, gosia olejniczak < gosia.olejnic...@gmail.com> wrote: > dear Greg, > > thank you for your

Re: [Rdkit-discuss] interactive py3Dmol in jupyter notebook - not all py3Dmol.view() are visible

I may not have understood the question correctly: when I open that page all frames are active. On Tue, Mar 28, 2017 at 3:56 PM, gosia olejniczak < gosia.olejnic...@gmail.com> wrote: > hello, > > i'm using rdkit with py3Dmol in jupyter notebook, as in this example: >

Re: [Rdkit-discuss] interactive py3Dmol in jupyter notebook - not all py3Dmol.view() are visible

dear Greg, thank you for your prompt response, yes, that notebook works just fine, however if i try to call py3Dmol.view() many more times, only few windows appear (and they disappear as i scroll down to run cells below), example:

[Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster

Hi, rdkiters, ? ? Have you tried install rdkit from source? It's ok when I installed rdkit by conda in my PC. But when I tried installing it in a server in which I am only a user who cannot use "sudo" and the "python" is in a read-only directory. Here is my cmake

Re: [Rdkit-discuss] looking for feedback on new python API documentation format

Hi, Greg, Here are my comments. - Formatting - pdoc at a glance is certainly more handsome than epydoc - To my eye, there is a huge amount of wasted space in the pdoc documentation. - The line spacing is hugely disproportional to the font size - Maybe this

Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster

Hi, Andrew,     I did set the LD_LIBRARY_PATH and added the $conda/lib in it.        Today, I tried installing a new boost (1.60.0) myself with the following commands:```./bootstrap.sh ./b2 install ```        Interestingly, I colud not `make` successfully this time, with the several

[Rdkit-discuss] looking for feedback on new python API documentation format

Dear all, TL;DR I'd like to switch to a new system for generating the RDKit Python API documentation and I'd like some feedback. Please take a look at this possible API documentation format: http://rdkit.org/docs_temp/ and let me know if it looks like it looks as useful as the old API doc

Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster

I tried installing rdkit using conda install -c rdkit rdkit into the latest Anaconda2 in a RHEL5 linux cluster I have limited control over. I see exactly the same error when I try 'from rdkit import Chem.' I am running the same release of Anaconda2 on my PC and all is fine. If it is an

Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster

On Mar 28, 2017, at 17:56, 杨弘宾 wrote: > Have you tried install rdkit from source? It's ok when I installed rdkit > by conda in my PC. But when I tried installing it in a server in which I am > only a user who cannot use "sudo" and the "python" is in a read-only >