Hi Gabriele,
this has come up previously:
https://sourceforge.net/p/rdkit/mailman/message/36796385/
This gist
https://gist.github.com/ptosco/ba11e577a8c616b958c49e23cc42a5e3
shows a possible solution, provided that your molecules do not contain
Astatine, otherwise pick another unusual element.
Cheers,
p.
On 13/02/2020 14:01, Gabriele Macari wrote:
Hello everybody,
I have a list of molecular fragments generated with BRICS and
saved in PDB format. When I read them back with Chem.MolFromPDBlock()
RDKiT is unable to recognize the dummy atom * and throws a warning
(and no molecule is returned). Is it possible add custom atoms to the
PDB Parser? Or is there another workaround?
Thanks in advance,
Gabriele
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