I have a question for the RDKit community that regards count-based RDKit
fingerprints. During a test, I have noticed that the compound *C1C1 has
a similarity (Euclidean) different than 1 against either [H]C1C1
or C1C1. So, I am wondering, how does RDKit encode starred atoms? I
thought
Bond(bidx, eidx)
> for atom_idx in sorted(ai_to_remove, reverse=True):
> rwmol.RemoveAtom(atom_idx)
> Chem.SanitizeMol(rwmol)
> return rwmol.GetMol()
> remove_selected_hs(mol_h, hs_to_remove)
> [image: image.png]
> Cheers,
> p.
>
> On Thu, Dec 2, 2021
Hi all,
I have been working on a library that computes properties for molecules
where hydrogens are explicit. These properties are then saved into a
dictionary where keys are indices, then I am using the dictionary to depict
these properties on their corresponding hydrogens - also according to
> set of new coordinates for your molecule.
>
> I hope I interpreted your needs correctly!
>
> Cheers,
> p.
>
>
> On Thu, Jan 13, 2022 at 2:05 PM Gianmarco Ghiandoni
> wrote:
>
>> Hi all,
>>
>> Quick question: I have noticed that when I read a
Hi all,
Quick question: I have noticed that when I read a compound from an SDF/Mol
file where all coordinates are already defined, the embedding process
changes the conformation of the RDKit mol object, hence coordinates are not
preserved:
import rdkit
cdk2_path = os.path.join(data_path,
rdkit.org/docs/cppapi/structRDKit_1_1MolDrawOptions.html#a6cf64fa7c9f2c08870914430f6a46282>
>
> e.g.
> IPythonConsole.drawOptions.annotationFontScale = 0.7
>
> The default scale is 0.5.
>
> Cheers,
> p.
>
>
> On Mon, Mar 28, 2022 at 2:31 PM Gianmarco Ghian
ue
> d2d.DrawMolecule(Chem.MolFromSmiles("c1n1"))
> d2d.FinishDrawing()
> SVG(d2d.GetDrawingText())
> [image: image.png]
>
> Cheers,
> p.
>
> On Mon, Mar 28, 2022 at 5:03 PM Gianmarco Ghiandoni
> wrote:
>
>> Hello Paolo,
>>
>> Thanks for
Hi all,
I am using RDKit to set calculated values to atoms as shown below and I
would like to know whether it is possible or not to change the font size to
make it slightly bigger.
# For each atom, set the property "atomNote" to a index+1 of the atom
atom.SetProp("atomNote",
Hi all,
I am writing a function that removes atoms with only one bond and can be
applied recursively in order to find the scaffold of a molecule. The
function works in most cases but I have observed that, when aromatic rings
are involved, it produces a loss of information. This is an example:
>
> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>
> rwmol
>
> [image: image.png]
>
> Using Chem.RWMol as a context manager will allow you commit the changes
> only when you are done, so you won't invalidate atom and bond iterators
> along the way.
>
> Cheers,
>
ze import rdMolStandardize
>
> uc = rdMolStandardize.Uncharger()
>
> Chem.MolToSmiles(uc.uncharge(Chem.MolFromSmiles("[CH+]1C2C2CC2C12")))
>
> 'C1CCC2CC3C3CC2C1'
>
>
> Cheers,
> p.
>
>
> On Fri, Apr 8, 2022 at 4:16 PM Gianmarco Ghi
Hello all,
I've been testing the Python module from rdkit.Chem import RegistrationHash for
some time now and I would like to use it in Java too. I browsed the RDKit
repository but I could not find it implemented in C++, and therefore, not
available in the Java JARs.
Am I missing it from
t regards,
> -greg
>
>
> On Thu, Sep 7, 2023 at 1:17 PM Gianmarco Ghiandoni
> wrote:
>
>> Hello all,
>>
>> I've been testing the Python module from rdkit.Chem import
>> RegistrationHash for some time now and I would like to use it in Java
>> too.
Hi all again,
I wonder whether there is a way in RDKit to neutralise the charges of
compounds such as "[C+]1C2C2CC2C12". Specifically, in my case I am
dealing with only carbon sequences.
Thanks,
--
*Gianmarco*
___
Rdkit-discuss mailing list
empty space around the
> molecule (the default is 0.05, and it's the fraction of the width/height of
> the image) such that there's enough room to show the whole annotation.
> It's a bit of a kludge, but it might work.
>
> Dave
>
> On Wed, May 4, 2022 at 4:20 PM Gianmarco Ghiandoni
sh. I assume it's related
> to https://github.com/rdkit/rdkit/discussions/5195. I'll fix it over the
> weekend, and hopefully it'll show up in the next patch release.
> Dave
>
>
> On Fri, May 6, 2022 at 1:07 PM Gianmarco Ghiandoni
> wrote:
>
>> Hi Dave,
>>
&
Hi all,
I am using rdkit_pypi==2021.9.4 to generate visualisation of compounds with
their atomic hydrogen bond strengths. In particular, I am using this
function to produce an SVG string:
d2d = rdMolDraw2D.MolDraw2DSVG(fig_size[0], fig_size[1])
d2d.drawOptions().annotationFontScale = 0.7
Hi all,
Anyone can help with this matter?
Thanks,
On Tue, 17 Jan 2023 at 13:03, Gianmarco Ghiandoni
wrote:
> Hi all,
>
> I have come across an issue while embedding structures with
> stereochemistry configurations that presumably lead to clashes between
> atoms:
>
> f
Hello all,
I have come across an unexpected behaviour by RDKit when reading MOL blocks
of the same compound in V2000 and V3000 formats. In particular, RDKit seems
to perceive the stereochemistry of the compound differently depending on
the format.
The original compound is a V3000 tab:
Hi all,
I have come across an issue while embedding structures with stereochemistry
configurations that presumably lead to clashes between atoms:
from rdkit import Chem
from rdkit.Chem import AllChem
smiles="C1N[C@@H]2CO[C@H]1C2"
m = Chem.MolFromSmiles(smiles)
mh = Chem.AddHs(m)
t; rdkit-discuss@lists.sourceforge.net>
> *Sent:* 19 January 2023 17:54
> *To:* Ling Chan ; Gianmarco Ghiandoni <
> ghiandon...@gmail.com>
> *Cc:* RDKit
> *Subject:* Re: [Rdkit-discuss] Embedding of molecules with incorrect
> stereochistry assignment
>
>
>
> A
Hello RDKit community,
I normally do not use this channel to promote my own research, however, I
thought it was a good idea to share a piece of my work with you this time.
Myself and a colleague recently published a paper on calculating
hydrogen-bond strengths and free energy of hydrations from
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