Thanks Rocco! I just used AllChem.GenerateDepictionMatching2DStructure() with
a custom SMILES string as the template depiction for each resonance
structure. Due to the alternating double bonds switching places between the
two resonance structures, FindMCS did not seem to provide a SMARTS string
as
Instead of arbitrarily generating 2D coordinates (which can have any
orientation), you probably want to use
GenerateDepictionMatching2DStructure() to generate coordinates which match
a common orientation for a substructure.
See http://www.rdkit.org/docs/GettingStartedInPython.html#drawing-molecule
Hi,
I would like to visualize the following resonance structures in the same
orientation (i.e. the same atomic coordinates), however, the image on the
right appears to be drawn upside down compared to the image on the left,
while the element names (e.g. N, O, and F) in both images are right side
up
RDkit Discussion Group,
I note that RDkit can perform Butina clustering. Given an SDF ofsmall
molecules I would like to cluster the ligands, but obtain additionalinformation
from the clustering algorithm. In particular, I would like to obtainthe
cluster number and Tanimoto distance from th
Hi Paul
OK I think I see the reason why the readline installed by miniconda3 is not
available on my OS (Ubuntu 18.04.1 LTS):
ian@ian-VPCF24C5E:~> python
Python 3.6.5 |Anaconda, Inc.| (default, Apr 29 2018, 16:14:56)
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more in
On 18/09/2018 19:45, Ian Tickle wrote:
Hi all, I'm finding that the line recall/edit function is broken in the Python 3.6.5 interpreter from
miniconda3 installation of RDKit, i.e. the arrow keys just type out the escape sequences.
If I use miniconda2 instead it's fine. Also line recall/edit wo
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