> It would be great if you (or your student) could create a github issue
for this, I will go ahead and take a look.
I will, thanks for looking into this.
On Thu, 15 Nov 2018 at 06:35, Greg Landrum wrote:
> Hi JP,
>
> I am able to reproduce this.
> It's not directly connected to the
Hi Peter,
Without seeing how you're building the molecule this one is a bit tricky to
help with.
If I start with a standard molecule and just adjust the valence count
things are fine:
In [22]: m = Chem.MolFromSmiles('CNC(C)C')
In [23]: m.GetAtomWithIdx(0).SetNumRadicalElectrons(1)
In [24]: mh
Hi Jim,
The biggest challenge here is likely to be the fact that the RKDit doesn't
have a Mol2 writer.
-greg
On Tue, Nov 13, 2018 at 7:05 PM James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> RDkit Discussion Group,
>
> Given a set of small molecules as a SDF
Hi JP,
I am able to reproduce this.
It's not directly connected to the standardization itself, since a
standardized molecule works fine with the embedding:
In [8]: omol = Chem.MolFromSmiles('C1=NN(C2=NC=NC(=O)[C@@H]21)[C@H]3[C@
@H]([C@@H]([C@H](O3)CO)O)O')
In [11]: nmol =
Hi:
I want to set timeout for the function named RunReactants, because sometimes I
found there needs over 10 minutes when running this function. For example:
>>import rdkit.Chem as Chem
>>from rdkit.Chem import AllChem
>>from rdkit.Chem import MolFromSmiles,MolFromSmarts
>>from
Hi Greg, thanks for the info. I hope that is in the roadmap.
Ali
On Tue, Nov 13, 2018 at 7:47 PM Greg Landrum wrote:
> Hi Ali,
>
> At the moment there are no pypi packages for the RDKit and it can only be
> installed using conda
>
> -greg
>
>
> On Tue, Nov 13, 2018 at 11:40 PM Ali Eftekhari
Dear Jose,
you need to AlignMol your conformers onto the original coordinates of
your constrained core using the mapped atoms as superimposition points.
In fact, the internal coordinates of the constrained core are preserved,
but the Cartesian coordinates may be different. An AlignMol()
Dear RDKitters,
I am writing a code to generate conformers of a given molecule constraining
some atoms to occupy fixed positions with the coordMap option. However, the
coordMap option does not see to work, as in the conformers generated the
constraint atoms are at very different positions in each
a.GetNumRadicalElectrons() does have the right number.
If it set all the atoms to not have implicit hydrogens with
for atom in mol.GetAtoms():
atom.SetNoImplicit(True)
then I still get a sanitization error with
>>> Chem.SanitizeMol(mol)
ValueError: Sanitization error: Explicit valence for
I have a molecule with radicals for which I'm trying to correct the bond
orders.
The mol block I have currently is shown below.
Ultimately it thinks the first carbon (which is supposed to have 2 explicit
hydrogens, 1 C-C bond, and 1 radical electron) has a valence of 5. So when
I try to call
Dear all,
Using the latest/greatest 2018.09.1.
I have an MSc student who is working on some targets in DUDE.
If we take some specific molecules from there (e.g. "C1=NN(C2=NC=NC(=O)[C@
@H]21)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O"), sanitize them using r
dMolStandardize.StandardizeSmiles(smiles),
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