Great. Thanks, Greg.
Best wishes,
Wendong
On Fri, Mar 12, 2021 at 2:55 PM Greg Landrum wrote:
>
> On Fri, Mar 12, 2021 at 7:48 AM Wendong Wang
> wrote:
>
>> PS. By the way, how did you index all the atoms when you draw the
>> molecule?
>>
>
> MolDraw2D has a drawing option to add atom
On Fri, Mar 12, 2021 at 7:48 AM Wendong Wang
wrote:
> PS. By the way, how did you index all the atoms when you draw the
> molecule?
>
MolDraw2D has a drawing option to add atom indices.
If you're using the RDKit in Jupyer with IPythonConsole, you can do:
Hi Wendong,
The morgan fingerprint algorithm removes redundant atom environments
(environments which contain exactly the same atoms/bonds).
For example, when looking at valine:
[image: image.png]
The environments with radius 2 which are centered on atoms 5 and 6 are
redundant with the environment
Hi Ling,
The RDKit does not currently have such a function (at least not that I'm
aware of).
-greg
On Fri, Mar 12, 2021 at 6:13 AM Ling Chan wrote:
> Hello colleagues,
>
> Just wonder if there is any function to distinguish between a chair ring
> and a boat ring?
>
> Don't worry if there is
Hello colleagues,
Just wonder if there is any function to distinguish between a chair ring
and a boat ring?
Don't worry if there is no such utility. I can write my own geometry
detection. Just that I don't want to reinvent the wheel.
Thank you.
Ling
Greetings,
I have a question about morgan fingerprints. The code is pasted at the end
of the email, and please see the attached images for the results.
For valine molecule, the radius is set to be 2. The dictionary (atom index,
radius) shows all the substructures of all atoms with radius 0 as
Hello Goutam,
There are not even 30 atoms in your smiles string. This is because, for
example, [C@H] denotes one carbon atom. The H is there to describe the C.
It is not an atom in the smiles string.
Ling
Goutam Mukherjee 於 2021年3月11日週四 上午8:35寫道：
> Dear Members,
>
> I have found an error in
Dear Ivan,
Many thanks for your reply.
Yes, when I give 3D hydrogen added molecule as input (molecule.pdb) the
result remains the same.
Say, if I give benzene molecule (C1=CC=CC=C1) as an input, or other complex
molecule, it prints the correct atom rank no matter whether hydrogen atoms
are there
Hi Goutam,
The ring atoms reported by RDKit in your example are correct; you just need
to consider that the atom indexes correspond to the position of each atom
in the SMILES string. How could RDKit guess the index that the atom might
have in a PDB file that's not even being read in your example?
Dear Members,
I have found an error in RDKit output. I am not sure whether it is my
mistake.
I have a SMILES code of a molecule:
C[S+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=CN=C2N
the 3D coordinates of the molecule is attached here with.
*I ran the following command:*
Hi,
it seems that the answer to my initial question depends on how the
prescription:
"stereobonds between stereocenters should be avoided at all costs"
is followed.
Many thanks!
Jean-Marc
Le 10/03/2021 à 20:24, Ling Chan a écrit :
Hello Mark,
I thought you could depict it like the
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