Hi Chris,
There's an additional step performed during sanitization that recognizes
that the implicit H needs to be on the N. The steps of a normal full
molecular sanitization operation are documented here:
http://www.rdkit.org/docs/RDKit_Book.html#molecular-sanitization
The adjustHs() function
Hello,
As part of my workflow, I am attempting to generate a starting 3D structure
from a 2D representation loaded from an sdf file.
On certain structures I receive the following UFF errors when attempting to
minimize the structure.
[20:50:43] UFFTYPER: Unrecognized atom type: He1 (0)
Hi!
I'm running at an issue with implicit hydrogens on aromatic heteroatoms. I
am feeding the following sdf into a mol object:
Mrv16c5 10021719092D
28 31 0 0 0 0999 V2000
-2.90000.20760. C 0 0 0 0 0 0 0 0 0 0 0 0
-2.18710.62280. N
Hi
Some interesting differences in behaviour compared with my RDkit
installation. Using the ChEMBL SMILES (freshly downloaded now) -
Dear Ling,
This Jupyter notebook shows two possible different approaches to
accomplish this:
https://gist.github.com/ptosco/f60d7fc122001c7f72e99bc66748c47b
HTH, cheers
p.
On 10/05/17 11:12, Lingtjien hong wrote:
I want to implement the following algorithm using RDkit
- given an atom
-
I want to implement the following algorithm using RDkit
- given an atom
- break the bonds between this atom and its neighbor(s)
- create new mol types/variables from the neighboring fragments
example: R1-C-R2
- given atom C
- return two mol types/variables R1 and R2 (not C)
How can I achieve
Hi
Be aware that there is a problem with one of the azide groups in
CHEMBL592333 - in SMILES it's '-N=[NH+]-[NH-]' rather than '-N=[N+]=[N-].
This doesn't render the structure chemically invalid but it's probably
wrong.
What's the provenance of your SD file? It isn't the same as as a fresh
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