[Rdkit-discuss] Pharmacophore matching

Dear all, I am new to working with the Pharm3D module and I have a question regarding pharmacophore matching: Is it possible to match a molecule to a pharmacophore that requires one atom to match to two different features (e.g. H-bond acceptor and donor)? Here is a dummy code example for a case

Re: [Rdkit-discuss] pharmacophore

On 30/03/2022 03:49, Patrick Walters wrote: One way to compare interactions (pharmacophores) in a binding site is to use interaction fingerprints. I've had a good experience with ProLIF. https://github.com/chemosim-lab/ProLIF Additionally, I know about all those open-source ones: - https://pha

Re: [Rdkit-discuss] pharmacophore

One way to compare interactions (pharmacophores) in a binding site is to use interaction fingerprints. I've had a good experience with ProLIF. https://github.com/chemosim-lab/ProLIF On Tue, Mar 29, 2022 at 6:26 AM Muhammad Akram wrote: > Hello Everybody, > > > > I am looking if there is a way t

Re: [Rdkit-discuss] pharmacophore

Hi Mu, The RDKit has code for identifying pharmacophoric points and calculating the distances between them, but there is no pharmacophore perception tool in the core RDKit. Best regards, -greg On Tue, Mar 29, 2022 at 12:25 PM Muhammad Akram wrote: > Hello Everybody, > > > > I am looking if t

[Rdkit-discuss] pharmacophore

Hello Everybody, I am looking if there is a way to extract a pharmacophore from co-crystallized ligand using RDKit. Thank you so much in advance. Kind Regards, Mu ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourcef

[Rdkit-discuss] Pharmacophore fingerprint search

Hello,I am trying to perform a pharmacophore similarity search using the RDKit implementation of the Pharmacophore fingerprint code.While reading the documentation, I came across this sentence:"In the RDKit scheme the bit ids in pharmacophore fingerprints are not hashed:"Does this mean each bit

Re: [Rdkit-discuss] Pharmacophore Fingerprints

Hi Antoine, |rdkit.Chem.Pharm2D.Generate.||Gen2DFingerprint()| expects a single molecule https://www.rdkit.org/docs/source/rdkit.Chem.Pharm2D.Generate.html?highlight=gen2dfingerprint#rdkit.Chem.Pharm2D.Generate.Gen2DFingerprint while you are passing a list of molecules: pharmacophorefps = Gene

[Rdkit-discuss] Pharmacophore Fingerprints

Hello, I am trying to generate a set of pharmacophore fingerprints in python using RDKIT from a list of SMILES (20k molecules) No matter what I do the script keeps throwing an error saying my code doesn't match the C++ signature. Here is a copy of my code as it stands right now from __future__

Re: [Rdkit-discuss] Pharmacophore atom typing for torsion or atom pair FP

This RDKit blog post uses some code from Nadine to provide SMARTS strings corresponding to standard Morgan ("ECFP") bits: http://rdkit.blogspot.com/2016/03/explaining-morgan-similarity.html At the moment it's not possible to do the same thing with the new fingerprinting code (that didn't get finis

Re: [Rdkit-discuss] Pharmacophore atom typing for torsion or atom pair FP

Here's a simple example that uses custom atom invariants based on the RDKit's usual pharmacophore features: https://gist.github.com/greglandrum/e28ef79e8e9f63e371de8a2c6829a691 On Thu, Jan 31, 2019 at 12:50 AM Lewis Martin wrote: > Thanks so much Greg! > > If I catch your drift, you are talking

Re: [Rdkit-discuss] Pharmacophore atom typing for torsion or atom pair FP

Hi Francois, If it helps, this is what Ive been using while playing with atom types: https://github.com/ljmartin/snippets/blob/master/snippet_atom_typing.ipynb The SMARTS codes were taken from down the bottom of this page https://www.rdkit.org/docs/GettingStartedInPython.html#chemical-features-an

Re: [Rdkit-discuss] Pharmacophore atom typing for torsion or atom pair FP

Hi, I have a related question: how to output the type of an atom in a molecule, if possible in a human-readable format; i.e. a human readable/understandable string rather than some (obscure) integer. I am interested to look at the atom types used by the ECFP and the FCFP fingerprints. Thanks a

Re: [Rdkit-discuss] Pharmacophore atom typing for torsion or atom pair FP

Yep, that's quite similar to what I'm working on. In fact, I'm probably going to borrow some of your example for mine. :-) On Thu, Jan 31, 2019 at 12:50 AM Lewis Martin wrote: > Thanks so much Greg! > > If I catch your drift, you are talking about the new fingerprint > generators from the google

Re: [Rdkit-discuss] Pharmacophore atom typing for torsion or atom pair FP

Thanks so much Greg! If I catch your drift, you are talking about the new fingerprint generators from the google summer of code. I took a look myself since I was curious. Here's a notebook demonstrating how I think it works: https://github.com/ljmartin/snippets/blob/master/snippet_fp_with_invaria

Re: [Rdkit-discuss] Pharmacophore atom typing for torsion or atom pair FP

Hi Lewis, This is a great chance to demonstrate some of the things that can be done with the new fingerprint generation code. It's going to take me a bit to put this together (it's all new enough that I'm still not quite "fluent"), but I will try to get an example put together over the next couple

[Rdkit-discuss] Pharmacophore atom typing for torsion or atom pair FP

Hi rdkitters, I'd like to compare the similarity of torsion/atom pair FPs using standard atomic numbering with those using pharmacophore types, like the 'CATS' atom typing developed by Gisbert Schneider, and hoped someone has some advice here. *CATS* is a pharmacophore atom typing system with these

Re: [Rdkit-discuss] pharmacophore align

Dear Greg and rdkit-discuss members. Thank you for your kindness. Your messages are very helpful for me. Thanks. Taka 2012/7/22 Greg Landrum : > Dear Taka, > > On Sun, Jul 22, 2012 at 12:20 AM, Taka Seri wrote: >> >> And I have one question. >> Can I get selected pharmacophore feature position

Re: [Rdkit-discuss] pharmacophore align

Dear Taka, On Sun, Jul 22, 2012 at 12:20 AM, Taka Seri wrote: > > And I have one question. > Can I get selected pharmacophore feature positions from AtomIds? > Or how can I get selected pharmacophore features from AtomIds? > From feature object, it is easy to do that by useing "feature.GetPos()"

Re: [Rdkit-discuss] pharmacophore align

Dear Greg, and rdkit-discuss members. Thank you for your advice. That code is very useful for me ! And I have one question. Can I get selected pharmacophore feature positions from AtomIds? Or how can I get selected pharmacophore features from AtomIds? >From feature object, it is easy to do that by

Re: [Rdkit-discuss] pharmacophore align

Dear Taka, On Thu, Jul 19, 2012 at 9:44 AM, Taka Seri wrote: > Dear all. > I have some questions about Pharmacophore. > I want to align molecules that from SDF files, by Pharmacophore. > At first, I set Pharmacophore by using "EmbedPharmacophore()" method. > And checked molecules by "EmbedPharma

[Rdkit-discuss] pharmacophore align

Dear all. I have some questions about Pharmacophore. I want to align molecules that from SDF files, by Pharmacophore. At first, I set Pharmacophore by using "EmbedPharmacophore()" method. And checked molecules by "EmbedPharmacophore()" method. Then, generated 3D structures by "EmbedPharmacophore(

Re: [Rdkit-discuss] Pharmacophore points and alignment

Hi Markus, On Tue, Jul 8, 2008 at 9:33 AM, markus wrote: > I want to align two molecules based on just the tips of some feature > direction arrows (a.k.a Projected Pharmacophor Points) > As to my understanding this problem should be solved in the same way, as > already coded in > $RDBASE/Python/C

[Rdkit-discuss] Pharmacophore points and alignment

Hi, I recently read into the Pharmacophore Alignment code of RDKit and have a question that may be ralated to my post allready discussed (cf. *Distance geometry / Graph theory Functions )* *