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)?
>
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, 2]
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/
blob/mast
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
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:
> http://nbviewer.jupyter.org/gi
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:
http://nbviewer.jupyter.org/github/gosiao/test_notebooks/blob/mast
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 prom
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, 2017 at 4:06 PM, gosia ol
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 command:`~applic/cmake/bin/
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
> directory.
Yes I have, and
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 LD_LIBRARY_
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
format:
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 errors
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
A first thing that's important to know and that may make all of this easier:
You can install the rdkit using conda even if you don't have write access
to the directory where anaconda python is installed.
If you follow the directions in the documentation and create an environment
to use the RDKit in
Hi Greg,
Here's my user case: usually I want to find out the details of a
certain class/function I already know of, but I may not have a clue to
which module that class/function belongs to. This is where the
alphabetical index of epydoc is often quite handy. Of course a proper
search within the doc
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