Any advice on getting RDKit to read in SDF files that use bond order '4' to
mark bonds as aromatic and don't have explicit hydrogen? For example,
imagine two fused heterocycles where the hydrogen isn't really known. I
have SDF files that just mark the bond orders as '4', aromatic, and don't
Hi Dr. Guillaume,
I played around with the ability to map a set of fragments to molecules a
couple months ago. The result of my experiments are here:
You give it a set of molecules and fragments you would like to have mapped.
It tries to find the smallest
What is the
trickiness and dangerousness of this API? And could we make an easy way to
enumerate bond stereo?
On Fri, Dec 9, 2016 at 5:44 PM, Brian Cole <col...@gmail.com> wrote:
> This has me quite curious now, how do we detect unspecified bond stereo
> chemistry in RDKit?
This has me quite curious now, how do we detect unspecified bond stereo
chemistry in RDKit?
m = Chem.MolFromSmiles("FC=CF")
for bond in m.GetBonds():
RMSD with auto-morph symmetries with hydrogens are crazy expensive to
calculate. Symmetry should be on by default, but without hydrogens. Would
even love to see the RMSD auto-morph symmetry code ignore trifluro type of
groups too as they dramatically increase the cost of the computation with
Is there a recommended way in RDKit to preserve hydrogens necessary for
representing cis/trans stereochemistry of imines?
For example, given the attached SDF I need to maintain explicit hydrogens
in the output SMILES string to maintain the imine cis/trans
You can use Chem.CanonicalRankAtoms to de-duplicate the SMARTS matches
based upon the atom symmetry like this:
def count_unique_substructures(smiles, smarts):
mol = Chem.MolFromSmiles(smiles)
ranks = list(Chem.CanonicalRankAtoms(mol, breakTies=False))
Here's an example of why this is useful at maintaining molecular
fragmentation inside your molecular representation:
>>> from rdkit import Chem
>>> smiles = 'F9.[C@]91(C)CCO1'
>>> fluorine, core = smiles.split('.')
>>> fragment = core.replace('9', '([*:9])')
> Somehow you got the code to generate a "9" for that ring closure, which is
> not something that RDKit does naturally, so we are only seeing a step in
> the larger part of your goal.
Certainly, but thousands of lines of Python doesn't fit in an email in an
easily digestible way. :-)
This is an extreme subtlety in the interpretation of SMILES atom
stereochemistry and I think a bug in RDKit. Specifically, I think the
following SMILES should be the same molecule:
It appears like Postgres 9.6+ supports parallel queries now to accelerate
Has anyone successfully got this to accelerate substructure queries with
the RDKit Postgres cartridge?
> The problem (and it's a sizable one) is that parallel queries don't use
> the index. Until parallel scans using GIST indices work, I don't think this
> is really going to help much.
> On Fri, Jun 1, 2018 at 12:04 AM Brian Cole wrote:
they should. Does a ::mol query on the same table parallelize? If
> it does but a ::qmol query does not maybe I forgot something in the SQL
> function definitions
> On Fri, 1 Jun 2018 at 15:43, Brian Cole wrote:
>> Hi Greg,
>> Are SMARTS searches with the
+1 to the MolVS project as well.
Perhaps an easy bite-size project is to incorporate the open source mae
parser code into core RDKit: https://github.com/schrodinger/maeparser
On Mon, Jan 15, 2018 at 9:08 PM, Francois BERENGER <
> On 01/16/2018 05:51 AM,
You can calculate the per-atom contributions to the surface area with
If you have the MOE SMARTS for "pure hydrogen bond acceptors", the
following is the Python I
ll stuck on is how to build RDKit's master branch
using conda. Changing `git_rev` in rdkit/meta.yaml didn't have the desired
On Wed, Dec 27, 2017 at 5:08 PM, Brian Cole <col...@gmail.com> wrote:
> Trying to 'conda build rdkit' as described in the
Trying to 'conda build rdkit' as described in the
https://github.com/rdkit/conda-rdkit README to no success. Are there any
OSX 'conda build' instructions tucked away somewhere?
It's currently failing on the cairo dependency:
-- Checking for one of the modules 'cairo'
CMake Error at
While Dr. Guillaume is correct, there are some ways to find known molecules
given the formula by hacking InChI strings.
For example just google search the formula with the InChI prefix, e.g.,
Little late to the party, but here is an RDKit implementation of a
contiguous rotatable bond count I wrote awhile ago:
Doesn't return the actual bonds like Paolo's does. But it does take into
account amides, triple bonds, and terminal
I would be interested, but not sure we would have such a large draw in the
Midwest as we would in Cambridge MA.
Potential idea would be to schedule it around the SciPy Conference?
Was thinking about checking that out this year.
ame #6: 0x7fff5fe23015 libdyld.dylib`start + 1
frame #7: 0x7fff5fe23015 libdyld.dylib`start + 1
(lldb) info threads
On Mon, Apr 16, 2018 at 1:11 PM, Brian Cole <col...@gmail.com> wrote:
> An issue like this was fixed in the past: https://github.com/
On Mon, Apr 16, 2018 at 1:20 PM, Brian Cole <col...@gmail.com> wrote:
> I can reproduce the problem, and the issue does appear to be different
> than the previous issue. Reproducible with the following on OSX:
> $ conda create -c rdkit -n rdkit_2017 rdkit pyt
An issue like this was fixed in the past:
Will see if I can reproduce this.
On Mon, Apr 16, 2018 at 12:09 PM, Patrick Walters
> Hi All,
> I installed the latest RDKit using
I know it has been talked about in the community that fingerprints are not
a way to obfuscate molecules for security, but I don't recall a paper
actually demonstrating actual reverse engineering a fingerprint into a
chemical structure. Does anyone know if such a paper
Thanks Andrew, very interesting and useful script!
Unfortunately it doesn't work on circular/ECFP-like fingerprints. It has
the requirement that the fingerprint be a substructure fingerprint as you
described. It seems the evolutionary/genetic algorithm approach is the
current state-of-the-art for
I'm trying to get a reaction SMARTS pattern to ignore chiral atoms and it
doesn't appear straightforward. First, it appears RDKit doesn't support
'!@' to indicate a non-chiral specified atom. I have to wrap this in a
recursive SMARTS to get it to work. For example:
In : mol =
My google search for 'rdkit python point3d' yielded the following as the
Which unfortunately now has a 404, page not found.
Was this an intentional reorganization of the documentation?
For your use-case #2 should suffice, "set STEREOCIS/STEREOTRANS tags +
manually set stereo atoms". This is what the EnumerateStereoisomers code
As to what is the 'ground truth', that is a more
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