I ended up just adding the following code to the atom matching function (after
moving it and copies of the substructure code that call it to a new library to
avoid other internal RDKit stuff calling the modified code):
int a1n = a1->getAtomicNum();
int a2n = a2->getAtomicNum();
// dummy
Hello,
I have put together another Chembience release (0.2.3): update of RDKit to
version 2018.03.*4, *Postgres to version 10.5, and Django to 2.1
https://github.com/chembience/chembience
https://twitter.com/markussitzmann/status/1035629283736264704
Best,
Markus
On Sun, Jun 10, 2018 at 4:41
Hi,
I am also very interested in measures of ligand flexibility. There has been
a post about a new descriptor 3 days ago that might be more "descriptive"
than the largest number of contiguous rotatable bonds.
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08196.html
best,
Hi Jim,
I have updated the gist to fix the bug that Andrew pointed out (thanks!).
That’s what happens when you write code while still in bed because you can’t
sleep :-/
Cheers,
p.
> On 31 Aug 2018, at 16:56, James T. Metz wrote:
>
> Paolo,
>
> Thank you for writing the
On Aug 31, 2018, at 15:27, Axel Pahl wrote:
> on Linux, using Anaconda, RDKit and Python 3.6, I always need to additionally
> install cairocffi via pip:
Thanks Axel.
When I tried it out, I figured out the more likely problem - I was using
jupyter from a non-conda virtualenv.
My problem
Hi Andrew,
on Linux, using Anaconda, RDKit and Python 3.6, I always need to
additionally install cairocffi via pip:
pip install cairocffi
Kind regards,
Axel
On 31.08.2018 15:05, Andrew Dalke wrote:
On Aug 31, 2018, at 11:58, Andrew Dalke wrote:
I am unable to see an inline structure
On Aug 31, 2018, at 11:58, Andrew Dalke wrote:
> I am unable to see an inline structure depiction in the Jupyter notebook, nor
> in the JupyterLab notebook, tested with both the Python 2 and Python 3
> kernels, and rdkit.__version__ '2018.03.1'.
I've narrowed it down to the Cairo code.
I ran
Hi all,
I am unable to see an inline structure depiction in the Jupyter notebook, nor
in the JupyterLab notebook, tested with both the Python 2 and Python 3 kernels,
and rdkit.__version__ '2018.03.1'.
I installed miniconda and RDKit on my Mac using:
curl -O
On Aug 31, 2018, at 07:41, Paolo Tosco wrote:
> this gist should do what you need:
Unless I misinterpreted what Jim is looking for, I don't think that returns the
contiguous rotatable bonds in a small molecule.
In the following there are only two rotatable bonds:
>>> mol =
Hi Thomas,
you are right; here's a better solution:
https://gist.github.com/ptosco/f499c7a8ced9c38067d36565ebd693f4
Please note that if you have more than 99 atoms with the same element
there will be duplicate atom names - you can easily write a small
function that uses letters in addition
Hi Paolo,
thanks a lot - this helps, but I just realized that your solution deletes the
atom name...
the pdb format should be
HETATM1C1 MOL 1 -1.011 0.850 -0.017 0.00 0.00 C
However, what I now get is:
HETATM1 MOL 1 -1.011 0.850 -0.017 0.00
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