Hi,
Just a quick question. I start from correct geometries (generated with
ligprep) and I superpose many molecules on a reference ligand. The overlap
is very good but sometimes the aromatic rings are not planar due to the
restraints. How can I check automatically in batch mode that the atoms in
th
Thanks for the notebook Sereina!
Unfortunately when I run it I get different results. In your version, the
very first call to EmbedMolecule() returns 0, which presumably means that
embedding went OK.
*## Embed the molecule without HsAllChem.EmbedMolecule(m,
useExpTorsionAnglePrefs=True, useBa
Hi all,
I really like combination of rdkit and py3dmol and have been able to
replicate e.g. Greg's notebook here:
http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/blob/master/notebooks/Trying%20py3Dmol.ipynb
But I can't seem to get AllChem.EmbedMultipleConfs() to generate any valid
confo
On 2017-03-02 04:37, Guillaume GODIN wrote:
> Based on the precision of the coordinates (in rdkit sdf files it's 4
> digits) can we infer the precision on the PBF value based on that ?
Only if you *know* the values are actually accurate to 4 digits and not
e.g. were printed as "%.4f" just becaus
Guillaume,
Which test are you actually doing?
I would certainly always recommend adding some kind of tolerance value for
anything involving floating point values. This helps protect you from both
roundoff error and the precision of various file formats.
-greg
On Thu, Mar 2, 2017 at 11:37 AM, G
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