Hi Francois,
there is no inherent limitation to small molecules n the RDKit MMFF94
implementation - you may assess the energy of systems of any size,
including protein ligand complexes, provided that all atom types in your
complex are defined in MMFF94.
Cheers,
p.
On Mon, Jan 30, 2023 at 2:38
Thomas -
Check out https://www.rdkit.org/docs/RDKit_Book.html#smarts-reference. It's
always hard to make a SMARTS expression that works for both implicit
hydrogen and explicit hydrogen ROMols. I think that you probably want:
[#6d1]
Which will match any carbon with non-hydrogen degree one,
Hi Thomas,
* in SMARTS just means "any atom".
[!H], for historical reasons, means "and atom without a single Hydrogen"
(i.e. it matches CH2 and CH3, but not CH)
You want [!#0], that is "not hydrogen"
-greg
On Mon, Jan 30, 2023 at 5:40 PM Thomas wrote:
> I thought that the wildcard * would
I thought that the wildcard * would match any atom except hydrogen, but
that's true unless hydrogens are explicit in the molecule
I have some patterns in the form of SMILES with wildcards and implicit
hydrogens. For example C* means "terminal carbons" only.
(" * " stands for any atom except
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