Dear Phuong,
you might just update the coordinates of the LigParGen PDB with the
aligned coordinates.
Cheers,
p.
On 08/23/18 18:23, Phuong Chau wrote:
Dear Paolo,
The new chemical chemical after alignment (UNK.pdb) file is in format
of RDKIT pdb file. Is it possible for the output in form
Thanks for the feedback and code example!
I understand that it works to make a third query mol using MCS that matches
both the original mols to then match with. However, this seems like overkill
(overly expensive) for this particular problem – as I understand it MCS can be
very expensive depen
Dear Paolo,
The new chemical chemical after alignment (UNK.pdb) file is in format of
RDKIT pdb file. Is it possible for the output in format of LIgParGen? I am
trying to run stimulation with the aligned chemical but it seems like it
can not read pdb file generated from RDKit.
Best,
Phuong Chau
Hi Kovas,
You have two fuzzy compounds that you try to match them, because our
intuition says that any atom notation [*:1] from m1 should match the
Fluorine [F:11] in m2 and any atom [*:14] in m2 should match Carbon [CH3:4]
in m1.
The issue here is that you create two query compounds from m1 and m
Dear Kovas,
It looks like GetSubstructMatch() only finds a match if the dummy atom
is in the query, not if it is in the molecule they you are matching the
query against.
This notebook present a possible solution off the top of my head:
https://gist.github.com/ptosco/a35ac28a14103b47096f6d6af
Dear Andrew,
My bad, excuse me fooling around.
Thanks for the clarification. I wanted to really make sure if also the
cartridge can be used for commercial purposes. I also reached the same
conclusions, but didn't know about the CC licenses for documentation hint.
Thanks for taking your time!
On Aug 23, 2018, at 07:18, Roman Bolzern wrote:
> Dear RDKittens,
I would prefer to not be called a 'kitten'.
> https://www.rdkit.org/docs/Cartridge.html#license, and at the bottom it says
> “This work is licensed under the Creative Commons Attribution-ShareAlike 4.0
> License”,
...
> Is “th
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