What is the best way to swap 2 bonds that are attached to an atom without
changing the 3D coordinates of the other atoms.
As an example, I have a tetrahedral carbon with bonds 1, 2, 3 and 4. I want
to switch bonds 1 and 2, including relocating any atoms attached to the
other atom in those bonds,
mations/blob/4f3c5ef47f66708defc64196c94e427a956b8f15/get_conformations.py#L16
>
> On 30 May 2020, at 13.38, Tim Dudgeon wrote:
>
> Is there an easy way to ask whether a particular bond is rotatable?
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> Rd
I've noticed that when writing a 3D molfile that has been generated by
RDKit (in my case using AllChem.EmbedMolecule) and has chirality present
that the chiral flag is not set. At least it is not always set, I can't be
exactly sure. My exact scenario is to read a chiral SMILES, convert to 3D
using
>
> The code behaves this way because otherwise it would need to guess what
> the user intended (as well as how they interpret/use the chiral flag).
>
> -greg
>
>
> On Mon, Jul 13, 2020 at 1:28 PM Tim Dudgeon wrote:
>
>> I've noticed that when writing a 3D molfile th
The points in a featuremap seem to have a 'weight' property that is set to
1.0 as default.
When merging featuremaps with the CombineFeatMaps() the weight of the
merged points remains as 1.0. Is it possible to change this behaviour so
that the meged point has an increased weight? Either a weight
ConstrainedEmbed should be what you need. If it's saying that your molecule
doesn't match the core then that's where you need to look. Maybe the core
is not an exact substructure?
If you still have difficulties you could generate the MCS between the
structures and use that as the core.
Greg's blog
I'm needing to save a FeatMap to a file so that I can load it back later.
I've been using a pickle for this, but am now told that this will not be
permitted for security reasons.
Is there a better way to do this?
Thanks
Tim
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RDKit can read PDB files but is there any functionality to work with the
resulting molecule at the chain and residue level?
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I'm struggling to work out a stange core dump I'm getting when calculating
Morgan fingerprints from Java. This seems to happen with the
Release_2020_09 releases but not with the Release_2019_09 ones. It does not
happen when calculating RDKit fingerprints. The exact Java code involved is:
I'm wanting to pick the molecules in one set that are most similar to those
in a seed set.
Seems like I should be able to use the MaxMinPicker to do this by using a
function of (1 - tanimoto).
Would this work, or is there a better approach?
Thanks
Tim
Wondering if anyone had any thoughts on this core dump from Java.
What other info would be useful?
Tim
On Tue, Jan 12, 2021 at 12:55 PM Tim Dudgeon wrote:
> I'm struggling to work out a stange core dump I'm getting when calculating
> Morgan fingerprints from Java. This seems to
already tried, but it's worth checking
> anyway: can you force your web app to only run a single thread at a time?
> That shouldn't be a problem with the morgan fingerprinting code, but it's
> still worth the experiment.
>
> -greg
>
>
> On Tue, Feb 2, 2021 at 7:14 P
>>> parsers? Have they been sanitized?
>>>
>>> Another thing you might have already tried, but it's worth checking
>>> anyway: can you force your web app to only run a single thread at a time?
>>> That shouldn't be a problem with the morgan fingerprinting co
I have Python code to enumerate undefined chiral centres in a molecule.
Mostly this works fine, but for some constrained structures this can
generate stereochemistry that makes no sense. For
instance consider NC1CC2CCC1C2:
[image: #1 (2).png]
These two make sense:
[image: #2.png]
[image: #3.png]
le.
>
> -Brian
>
>
> On Sep 27, 2021, at 8:06 AM, Tim Dudgeon wrote:
>
>
> I have Python code to enumerate undefined chiral centres in a molecule.
> Mostly this works fine, but for some constrained structures this can
> generate stereochemistry that makes no s
I'm hitting problems when building from source on an Ubuntu system.
I've installed the dependencies (e.g. boost) using apt and think I have
everything set properly, but cmake is failing. Early on it says:
-- Found Boost:
/usr/lib/x86_64-linux-gnu/cmake/Boost-1.71.0/BoostConfig.cmake (found
I've found that a source of molecules that I use now has some smiles
that contain the * character, whereas earlier versions did not. This is now
causing downstream problems.
Whilst it would be pretty simple to check the smiles for * characters I
think there should be a more general solution here
I'm looking into the current status of techniques that use RDKit to perform
3D alignments based on shape (e.g. not using AlignMol()) and struggling to
find what the best tools are and the status of each.
The Open3D align tools are relatively straightforward to use, but in my
hands do not seem to
I'm trying to merge two molecules into one, and it looks like the
InsertMol() function is supposed to do this. But when I try the merged
molecule is messed up.
[image: image.png]
Am I doing the right thing?
Thanks
Tim
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and
> only sanitize at the end of the insertion process.
>
> Cheers,
> p.
>
> On Mon, Oct 25, 2021 at 1:15 PM Tim Dudgeon wrote:
>
>> I'm trying to merge two molecules into one, and it looks like the
>> InsertMol() function is supposed to do this. But when I try the
I am needing to access the text of each record of a SDF, as well as
creating a mol instance.
I was successfully doing this using SDMolSupplier.GetItemText().
Then I needed to switch to handling gzipped SD files, and SDMolSupplier can
only take a file name in its constructor.
ForwardSDMolSupplier
Chem.RemoveHs(mol) will remove all Hs.
Do you really want to only remove them from sp3 carbons?
On Tue, Oct 19, 2021 at 7:08 PM Alfredo Quevedo
wrote:
> Dear all,
>
> I am trying to figure out if there is a way to remove all hydrogens bond
> to sp3 carbons in my molecule?
>
> thanks in advance
I'm having problems building with Debian bullseye release.
Bullseye now has swig4.0, but RDKit build seems to require exactly 3.0.
Error is:
CMake Error at
/usr/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:165
(message):
Could NOT find SWIG: Found unsuitable version "4.0.2", but
Worked it out for myself.
I needed to use:
Chem.AddHs(mol, addCoords=True)
Doh!
On Tue, Dec 14, 2021 at 5:45 PM Tim Dudgeon wrote:
> I'm seeing lots of failures when minimising molecules using
> MMFFOptimizeMolecule.
> A large proportion of seemingly valid molecules seem to fail.
>
I'm seeing lots of failures when minimising molecules using
MMFFOptimizeMolecule.
A large proportion of seemingly valid molecules seem to fail.
Am I doing something stupid here?
Example:
from rdkit import Chem
from rdkit.Chem import AllChem
molblock = '''
RDKit 3D
5 4 0 0 0
I think you have to add a step that removes the quote marks if they are
present?
Tim
On Mon, Jan 10, 2022 at 10:15 AM James Wallace wrote:
> As the subject suggests, I'm trying to find a universal solution for
> reading CSVs via the SmilesMolSupplier (as the input setup could be single
> column
e's support for visualizing molecules from SMILES and CTAB, but
> currently no support for SDF properties out of the box.
>
> Cheers,
> p.
>
> On Thu, Mar 3, 2022 at 6:31 PM Tim Dudgeon wrote:
>
>> Is there a full list of the RDKit functionality that is available from
&g
Is there a full list of the RDKit functionality that is available from the
JavaScript bindings (
https://github.com/rdkit/rdkit/tree/master/Code/MinimalLib)? Maybe I'm
missing the obvious, but I can only find the examples e.g.
e the molecule and clear aromatic
> flags before starting to remove atoms, then sanitize:
>
> rwmol = Chem.RWMol(Chem.MolFromSmiles("c1c1"))
> Chem.Kekulize(rwmol, clearAromaticFlags=True)
> rwmol.RemoveAtom(0)
>
> Chem.SanitizeMol(rwmol)
> rdkit.Chem.rdmolops.Sa
I'm using mol.RemoveAtom(atom) to remove atoms from a molecule, and then
calling Chem.SanitizeMol(mol) at the end to clean up the molecule. Mostly
this works fine.
But when I delete atoms in an aromatic ring but leave a single ring atom
remaining in the molecule then the sanitize function fails:
;
> On Fri, Feb 11, 2022 at 3:49 PM Tim Dudgeon wrote:
>
>> Hi Greg,
>> yes, but my situation is that the X dimension is much larger than the Y
>> and most of the time things are aligned nicely. But not always. Here is an
>> example.
>> OC(C(=O)NC=1C=CC=
ch, among other things,
> addresses exactly the need that you describe through the baseFontSize
> parameter, which is currently not exposed to Python. The PR is almost ready
> for merging and it should become part of the March release.
>
> Cheers,
> p.
>
> On Wed, Feb 9, 20
I'm confused over how the font is chosen when drawing molecules.
There are MolDrawOptions.minFontSize and MolDrawOptions.maxFontSize
properties, and if I set them to the same value then that sized font is
used. But if I set max to a larger size than min then it's not clear what
font size will be
e
> default.")
> ```
> to $RDBASE/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp immediately after
> the analogous minFontSize entry
> HTH,
> Dave
>
>
>
> On Wed, Feb 9, 2022 at 10:31 AM Tim Dudgeon wrote:
>
>> OK, thanks. That's great to hear.
&g
At Dave Cosgrove's suggestion I raise this as a new topic, though it was
touched on briefly recently.
I'd like to know if it's possible to depict a molecule in a way that takes
into account the dimensions of the box it will appear in. In my case I have
a rectangle that is short and wide (aspect
.com/greglandrum/12b793b240d27e3c0899c9c6c62d4f30
>
> -greg
>
>
> On Fri, Feb 11, 2022 at 10:20 AM Tim Dudgeon
> wrote:
>
>> At Dave Cosgrove's suggestion I raise this as a new topic, though it was
>> touched on briefly recently.
>>
>> I'd like to know if it
I'm building RDKit from the latest code on the master branch.
The build is fine, but the python bindings seem broken:
>>> from rdkit import Chem
Traceback (most recent call last):
File "", line 1, in
File "/data/github/rdkit/rdkit/rdkit/__init__.py", line 6, in
from . import rdBase
And to clarify, the build completes OK. It's just that the Python
bindings don't work.
On Wed, Jan 26, 2022 at 2:42 PM Tim Dudgeon wrote:
> Yes, it sounds similar, but I'm not applying that fix (though on the
> Release_2021_09_4 tag I do also see that same problem).
> I'm just doin
lds
> fine for me too.
>
> Cheers,
> p.
>
> On Wed, Jan 26, 2022 at 2:58 PM Tim Dudgeon wrote:
>
>> I'm building RDKit from the latest code on the master branch.
>> The build is fine, but the python bindings seem broken:
>>
>> >>> from rdki
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