Dear Kangway,
Thank you very much!
M.
On Thu, Jun 4, 2020 at 6:56 PM Chuang, Kangway
wrote:
> Hi Michal,
>
> You can use rdkit.Chem.rdmolfiles.MolFragmentToSmiles (or related
> MolFragmentToSmarts) and specify an atom id list with "atomsToUse":
>
> e.g.
>
>
Hi Michal,
You can use rdkit.Chem.rdmolfiles.MolFragmentToSmiles (or related
MolFragmentToSmarts) and specify an atom id list with "atomsToUse":
e.g.
rdkit.Chem.rdmolfiles.MolFragmentToSmiles(mol, atomsToUse=[11,13,22,15])
Kangway
From: Michal Krompiec
Sent:
Hello, I noticed this was discussed before and I'm wondering if anything's
changed.
Is it possible to extract a substructure from a molecule, based on atom
indices? I understand that Chem.PathToSubmol does something similar, but
takes bond indices.
Best,
Michal
Dear Michal,
You can use
http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=path#rdkit.Chem.rdmolops.GetShortestPath
or
http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=distance#rdkit.Chem.rdmolops.GetDistanceMatrix
e.g.:
from rdkit import Chem
Hi,
I've never tried the RDKit PostgreSQL cartridge but I'm curious about it.
In particular I wonder how far have people pushed it in terms of
database size. The documentation gives examples with several million rows;
has anyone tried it with a couple billion rows? How fast are substructure
Hi Joey,
It looks like there's a dependency conflict in there somewhere that conda
is unable to resolve.
Unsurprisingly, it looks like at least part of the problem here is the
version of boost. The rapids environment that you are using has boost 1.70
installed (and that's probably a dependency
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