Re: [Rdkit-discuss] Question about source code to do energy minimization with UFF or MMFF94 force field

Hi Srdjan, > On Sep 11, 2024, at 11:12, Srdjan Pusara wrote: > I would like to ask is it possible to find source code how these [UFF] > interaction terms were implemented? The RDKit source code is available at https://github.com/rdkit/rdkit/tree/master . Use the green button labeled "<> Cod

[Rdkit-discuss] Question about source code to do energy minimization with UFF or MMFF94 force field

Hello, I have seen that Rdkit can return force field parameters between group of atoms (bond_params = rdForceFieldHelpers.GetUFFBondStretchParams(mol, 6, 1),angle_params = rdForceFieldHelpers.GetUFFAngleBendParams(mol, 0, 1, 2) etc). I would like to ask is it possible to find source code ho

Re: [Rdkit-discuss] Question of substructure "neighborhood"

Hi Joey, I think the most straightforward way to do this is to use GetNeighbors() on all atoms. See below for an example: from rdkit import Chem mol=Chem.MolFromSmiles("O1COc2c1ccc(CC(NC)C)c2") substruct=Chem.MolFromSmarts("c1c1") a=mol.GetSubstructMatch(substruct) print("substructure benzene

[Rdkit-discuss] Question of substructure "neighborhood"

Dear RDKit experts, Substructure search is working well these days. RDKit is wonderful. For subsequent QM calcs., I would like to get the "next atom over" or the "one-atom-neighborhood" surrounding a substructure. The result would be something bigger than the original substructure with open v

Re: [Rdkit-discuss] question on complexity of cannonization

On Jun 16, 2023, at 03:15, S Joshua Swamidass wrote: > In graph theory, a planar graph is a graph that can be embedded in the plane, > i.e., it can be drawn on the plane in such a way that its edges intersect > only at their endpoints. In other words, it can be drawn in such a way that > no edg

Re: [Rdkit-discuss] question on complexity of cannonization

Planar graphs are... In graph theory , a *planar graph* is a graph that can be embedded in the plane

Re: [Rdkit-discuss] question on complexity of cannonization

On 16/06/2023 03:49, S Joshua Swamidass wrote: Incidentally, I came across this O(log N) canonization algorithm for planar graphs: https://arxiv.org/pdf/0809.2319.pdf I wonder if this algorithm can be adapted for chemistry? Molecules are usually planar, but I believe they occasionally are "near

Re: [Rdkit-discuss] question on complexity of cannonization

On Jun 15, 2023, at 20:49, S Joshua Swamidass wrote: > > And what (generally speaking) is the algorithm used by rdkit? Do we know it's > complexity? https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00543 "Get Your Atoms in Order—An Open-Source Implementation of a Novel and Robust Molecular Can

Re: [Rdkit-discuss] question on complexity of cannonization

Well, if I'm recalling correctly, a highly symmetric structure like buckminsterfullerene takes a long time to canonicalize. I don't know what the formal definition of a planar graph is, but I would guess it's not what chemists mean when they say a molecule is planar. -P. On Thu, Jun 15, 2023 at

Re: [Rdkit-discuss] question on complexity of cannonization

Incidentally, I came across this O(log N) canonization algorithm for planar graphs: https://arxiv.org/pdf/0809.2319.pdf I wonder if this algorithm can be adapted for chemistry? Molecules are usually planar, but I believe they occasionally are "nearly" planar, by which I mean planar graphs plus a

Re: [Rdkit-discuss] question on complexity of cannonization

Andrew, Thanks! According to wikipedia (and my recollections of algorithms class)... "The problem is not known to be solvable in polynomial time nor to be NP-complete , and therefore may be in the computatio

Re: [Rdkit-discuss] question on complexity of cannonization

On Jun 15, 2023, at 18:20, S Joshua Swamidass wrote: > It's well known that the graph-isomorphism problem is NP While P is contained in NP, I don't think that's the NP you mean. I suspect you may be thinking of subgraph isomorphism, which is NP-hard. Graph isomorphism may be quasi-polynomial ti

[Rdkit-discuss] question on complexity of cannonization

Hello, I had a theoretical question I thought the RDkit team might have some insight on. It's well known that the graph-isomorphism problem is NP, which means that for some examples run-time will be worse than polynomial using known algorithms. This problem is connected to molecule canonization.

Re: [Rdkit-discuss] Question on substructure search

, Joey (J) Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Question on substructure search CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Joey, You

Re: [Rdkit-discuss] Question on substructure search

Patrick Walters > *Sent:* Tuesday, June 13, 2023 5:54 PM > *To:* Storer, Joey (J) > *Cc:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] Question on substructure search > > > > * CAUTION:* This email originated from outside of the organization. Do > n

Re: [Rdkit-discuss] Question on substructure search

Hi Joey, You can get the intended result like this pat = Chem.MolFromSmarts("*=C1*C=C*1") mol = Chem.MolFromSmiles("C=C1SC=CS1") mol.HasSubstructMatch(pat) Pat On Tue, Jun 13, 2023 at 4:49 PM Storer, Joey (J) via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > Hi RDKit masters, >

[Rdkit-discuss] Question on substructure search

Hi RDKit masters, rdkit.__version__ = 2023.03.1 I am trying to match structures with a double bond in a 5-membered ring. [cid:image001.png@01D99E14.494E8F00] Then checking if this works in the sulfur case: [cid:image002.png@01D99E14.494E8F00] [cid:image003.png@01D99E14.494E8F00] Thanks for

Re: [Rdkit-discuss] Question about tautomer hash

Hi Greg, Actually, sorry I forgot I had another question. How about cis/trans immines? I would expect them to have different tautomer hashes but they don't e.g. m1 = Chem.MolFromSmiles('C\\N=C\\C') m2 = Chem.MolFromSmiles('C/N=C\\C') h1 = RegistrationHash.GetMolLayers(m1) h2 = RegistrationHash.G

Re: [Rdkit-discuss] Question about tautomer hash

Hi Greg, Thanks very much, I suspected as much! Susan On Thu, Jan 12, 2023 at 5:45 AM Greg Landrum wrote: > Hi Susan, > > The current version of the tautomer hash doesn't do keto-enol tautomerism > (your first example). It would be worthwhile for us to add this as an > option, but it's not cur

Re: [Rdkit-discuss] Question about tautomer hash

Hi Susan, The current version of the tautomer hash doesn't do keto-enol tautomerism (your first example). It would be worthwhile for us to add this as an option, but it's not currently available. -greg On Wed, Jan 11, 2023 at 3:04 PM Susan Leung wrote: > Hi all, > > > > I am trying out the ne

[Rdkit-discuss] Question about tautomer hash

Hi all, I am trying out the new registration hash and have a question about the tautomer hash. I think these two molecules (m1 and m2) should have the same tautomer hash but they are different. However, molecules m3 and m4 have the same hash. Please can you explain? import rdkit from rdkit i

[Rdkit-discuss] Question Regarding General SMARTS Query to Describe Reaction Sites for Reactants and Products

Dear RDKit Community, I hope you are all doing well! Before I state the specifics of my question, I want to thank Dr. Gregory Landrum for creating and developing (and maintaining) RDKit, and other users of RDKit who have contributed directly in some form to the continual development and main

[Rdkit-discuss] Question on tautomer standardization on RDKit

Dear all, I have a question on tautomer standardization using RDKit. Is that a way to turn off the aromatization of ring system when generating the tautomer enumerator? For example, [cid:image002.png@01D87FEA.150F03D0] • [cid:image003.png@01D87FEA.150F03D0] [cid:image004.png@01D87FEA.1E10EC5

Re: [Rdkit-discuss] Question matching substructures from SMARTS with explicit hydrogens

Glad it works for you. As Greg pointed out to someone else today, it’s marginally more efficient to do [#6] than [C,c] and likewise for nitrogen. But it’s always a trade off between speed and legibility/maintainability. If speed is of the essence and you’re running on millions of compounds it might

Re: [Rdkit-discuss] Question matching substructures from SMARTS with explicit hydrogens

Ahh! Thank you so much, to both of you. Yes, the different meaning of H in the various contexts was tripping me up. Also, DescribeQuery() was definitely a function that I needed for debugging this solo. Thank you. I will keep that in mind in the future. I found that this smiles (S4) is exactly w

Re: [Rdkit-discuss] Question matching substructures from SMARTS with explicit hydrogens

A minor correction: [H] by itself *is* valid and means a hydrogen atom. The Daylight docs say as much in section 4.1. But in other contexts it means a hydrogen count, so to be safe, always using #1 to mean a hydrogen atom can be a good practice. If you are ever in doubt about how RDKit is interpre

Re: [Rdkit-discuss] Question matching substructures from SMARTS with explicit hydrogens

Hi Adam There are a number of issues here. The key one, I think, is a misunderstanding about the meaning of H in SMARTS. It means "a single attached hydrogen", and is a qualifier for another atom, it cannot be used by itself. So [*H] is valid, [H] isn't. See the table at https://www.daylight.co

[Rdkit-discuss] Question matching substructures from SMARTS with explicit hydrogens

Hello, I have a baffling case where I am trying to match substructures on two ligands for the goal of aligning them. I have two ligands; one is a 6-chloroindole (6CI) and the other is a para-chloro toluene (PCT). I am attempting to use the following SMARTS (S1) to match them: '[C,c]1(Cl)[C,c][C,

[Rdkit-discuss] Question: Explaining bits from Morgan Fingerprints

Dear RDKit community, I am trying to explain the Explaining bits from Morgan Fingerprints as described in the RDKit getting started guide here ( http://www.rdkit.org/docs/GettingStartedInPython.html#explaining-bits-from-morgan-fingerprints ). I want to get the SMILES for each bit from morgan FP o

Re: [Rdkit-discuss] question about morgan bits

Great. Thanks, Greg. Best wishes, Wendong On Fri, Mar 12, 2021 at 2:55 PM Greg Landrum wrote: > > On Fri, Mar 12, 2021 at 7:48 AM Wendong Wang > wrote: > >> PS. By the way, how did you index all the atoms when you draw the >> molecule? >> > > MolDraw2D has a drawing option to add atom indices.

Re: [Rdkit-discuss] question about morgan bits

On Fri, Mar 12, 2021 at 7:48 AM Wendong Wang wrote: > PS. By the way, how did you index all the atoms when you draw the > molecule? > MolDraw2D has a drawing option to add atom indices. If you're using the RDKit in Jupyer with IPythonConsole, you can do: IPythonConsole.drawOptions.addAtomIndices

Re: [Rdkit-discuss] question about morgan bits

Hi Wendong, The morgan fingerprint algorithm removes redundant atom environments (environments which contain exactly the same atoms/bonds). For example, when looking at valine: [image: image.png] The environments with radius 2 which are centered on atoms 5 and 6 are redundant with the environment

[Rdkit-discuss] question about morgan bits

Greetings, I have a question about morgan fingerprints. The code is pasted at the end of the email, and please see the attached images for the results. For valine molecule, the radius is set to be 2. The dictionary (atom index, radius) shows all the substructures of all atoms with radius 0 as fing

Re: [Rdkit-discuss] Question about ECFP fingerprints when using multiprocessing and chiralty

Thanks a bunch Greg for the very helpful explanation! Things make more senses now. On Wed, May 20, 2020 at 12:51 AM Greg Landrum wrote: > Hi Hao, > > Good question! I had to do a bit of digging to figure that out > > Here's what's going on: > The Morgan fingerprint code uses CIP codes when you s

Re: [Rdkit-discuss] Question about ECFP fingerprints when using multiprocessing and chiralty

Hi Hao, Good question! I had to do a bit of digging to figure that out Here's what's going on: The Morgan fingerprint code uses CIP codes when you set useChirality=True Atomic CIP codes are stored as an atomic property When you use the multiprocessing module everything ends up being pickled and s

[Rdkit-discuss] Question about ECFP fingerprints when using multiprocessing and chiralty

Hello, This was a very strange bug that I saw. I was getting inconsistent fingerprints using GetMorganFingerprint with useChirality=True, when I used multiprocessing vs when I ran serially on rdkit 2017.09.1 and 2018.03.2. It seems to have been fixed in the latest version. Woo! I was just wonderin

Re: [Rdkit-discuss] Question on chirality

Thank you very much Jan, this in fact fixed the issue. I just had to add " AllChem.EmbedMolecule(mol)". Best, Navid On Fri, Sep 13, 2019 at 5:49 AM Jan Holst Jensen wrote: > Hi Navid, > > I am not familiar with the paper you mention, but I believe that the > problem is caused by non-isomeric i

Re: [Rdkit-discuss] Question on chirality

Hi Navid, I am not familiar with the paper you mention, but I believe that the problem is caused by non-isomeric input SMILES. Below is an Alanine read in from molfile, with coordinates. It has a chiral center with "S" configuration. When you output it as non-isomeric SMILES and read it back

[Rdkit-discuss] Question on chirality

Hello, In the paper: "Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals", authors introduce chirality as an atom feature input to analyze QM9 dataset. I was trying to recreate this atom feature as following > Chirality: (categorical) R, S, or not a Chiral center

[Rdkit-discuss] Question regarding Chemical Features module on RDKit

Hello, I have a question regarding Chemical Features module on RDKit. I realized that for molecule with SMILES representation "OC1CC1O" from QM9 dataset, using the code fdefName = os.path.join(RDConfig.RDDataDir,'BaseFeatures.fdef') factory = ChemicalFeatures.BuildFeatureFactory(fdefName) mol = C

Re: [Rdkit-discuss] Question about bond aromaticity change detection

8][cH:19]1)[N:26]1[CH2:25][c:23]2[c:22]([cH:21][cH:20][o:24]2)[CH2:28][CH2:27]1 > " > > Kind regards, > Hasic Haris, MSc > Tokyo Institute of Technology > ------ > *From:* Greg Landrum > *Sent:* 20 April 2019 06:43 > *To:* Haris Hasic > *Cc:* rdkit-discus

Re: [Rdkit-discuss] Question about bond aromaticity change detection

cH:12][cH:13]3)[S:14][CH2:15][CH2:16][S:17]2)[cH:18][cH:19]1)[N:26]1[CH2:25][c:23]2[c:22]([cH:21][cH:20][o:24]2)[CH2:28][CH2:27]1" Kind regards, Hasic Haris, MSc Tokyo Institute of Technology From: Greg Landrum Sent: 20 April 2019 06:43 To: Haris Hasic Cc:

Re: [Rdkit-discuss] Question about bond aromaticity change detection

HI Hasic, The products of reactions are not sanitized, which means that aromaticity perception has not been run. Try calling Chem.SanitizeMol on the reaction products and see if that helps. -greg On Fri, Apr 19, 2019 at 12:51 PM Haris Hasic wrote: > Hello guys, > > I'm a artificial intelligen

[Rdkit-discuss] Question about bond aromaticity change detection

Hello guys, I'm a artificial intelligence major, so I don't know a lot about aromaticity definitions in chemistry but since I'm doing some research in that field I run into a weird problem with identifying the aromatic bonds. I initialize the reaction as follows: rxn = "O[C:1](=[O:2])[c:3]1[c

[Rdkit-discuss] Question about (generic) Murcko frameworks

Hi there, is it normal to get, for the same set of smiles, more generic Murcko frameworks that normal frameworks? When running this: ### Generate framework for a SMILES, handling for errors def framecheck(s): try: return Chem.MolToSmiles(ms.GetScaffoldForMol(Chem.MolFromSmiles(s)))

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

Many thanks to everyone who contributed to this thread. The conclusion that I'm going to take from this is that, at the moment, it's probably best if I keep doing the RDKit builds and distributing them via the rdkit conda channel. I'll keep an eye on things and maybe we can reconsider this decision

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

I think this demonstrates one drawback of conda-forge right now: it's best to go 'all in' on conda-forge for all packages or you run the risk of a broken environment. In this Mac example, I think the issue may just be due to minor discrepancies between the recipes on the conda-forge and rdkit

[Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

t Discuss <mailto:rdkit-discuss@lists.sourceforge.net>>, RDKit > Developers List <mailto:rdkit-de...@lists.sourceforge.net>> > Subject: [Rdkit-discuss] [Question] Ok to switch to conda-forge for > RDKit builds? > Message-ID: ><mailto:CAD4fdRQD

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

So I'm certainly fine with a conda-forge only option, I don't happen to use the rdkit channel version. But I'll point out that I'm in the minority: comparing downloads of recent versions on https://anaconda.org/rdkit/rdkit/files vs https://anaconda.org/conda-forge/rdkit/files shows that the rdkit c

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

On 10/18/2018 11:20 AM, Greg Landrum wrote: > we're drifting a bit from the purpose of this thread, so I will give quick > answers: > > On Thu, Oct 18, 2018 at 6:00 PM Eric Jonas wrote: > >> Would there also be a pip install option ? Building from GitHub master >> is... Challenging. >> > > Thi

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

Note that it makes a difference whether you do "conda install -c conda-forge rdkit" or "conda install conda-forge::rdkit". The latter will pull in less packages from conda-forge. I'm on Linux, using a somewhat recent environment which has mostly default channel packages + rdkit::rdkit + openbabel:

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

we're drifting a bit from the purpose of this thread, so I will give quick answers: On Thu, Oct 18, 2018 at 6:00 PM Eric Jonas wrote: > Does being in conda-forge mean the package will eventually make it to the > mainline conda repo? > I doubt it, but that's not a question I can really ansewr.

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

Does being in conda-forge mean the package will eventually make it to the mainline conda repo? I just have memories (admittedly from when dinosaurs walked the earth) of upgrading a package from rpmforge and having it brick my Linux machine. And I still sometimes see a conda-forge install change a

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

Ok for me too. De : Markus Sitzmann Date : jeudi, 18 octobre 2018 à 17:52 À : Greg Landrum Cc : RDKit Discuss Objet : Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds? I am happy with conda forge :-). And thanks for the great work. Markus On Thu, Oct 18, 2018 at

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

I am happy with conda forge :-). And thanks for the great work. Markus On Thu, Oct 18, 2018 at 5:46 PM Greg Landrum wrote: > Um, guys, there are some interesting side conversations starting here, but > can we please keep this thread on the "is it ok for me to stop doing builds > on the RDKit ch

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

Um, guys, there are some interesting side conversations starting here, but can we please keep this thread on the "is it ok for me to stop doing builds on the RDKit channel" question? This is important to me (and possibly the community), so I'd like the keep the discussion as simple and uncluttered

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

Hmm, isn't that the problem with any build/dependency automation tool and hard to fix in a generic way? If you are really very dependent on a specific version of a software you have to be very careful with the environment it sits in while you do "carefree" updates only in a carefree environment :-)

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

On Thu, 18 Oct 2018 16:42:37 +0200 Greg Landrum wrote: > - create a new conda environment that includes an rdkit-channel RDKit > install > - uninstall the RDKit from that > - install the RDKit from the conda-forge channel The concern here is you have a working setup with a bunch of conda-forge

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

On Thu, Oct 18, 2018 at 2:21 PM Eric Jonas wrote: > Greg, I'm all for anything that makes the release process on developers > easier; my main question is : With conda-forge, how hard is it to install > just _one_ package without having everything else (say numpy, pandas, etc) > upgraded to the la

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

Date : jeudi, 18 octobre 2018 à 14:21 À : Greg Landrum Cc : "rdkit-discuss@lists.sourceforge.net" , "rdkit-de...@lists.sourceforge.net" Objet : Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds? Greg, I'm all for anything that makes the rele

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

Greg, I'm all for anything that makes the release process on developers easier; my main question is : With conda-forge, how hard is it to install just _one_ package without having everything else (say numpy, pandas, etc) upgraded to the latest conda-forge version? I've had situations in the past wh

[Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

Dear all, TL;DR: Now that RDKit builds are available on conda-forge, I would like to stop doing builds on the rdkit conda channel. I'm looking for feedback about that here. Thanks to the persistence of Peter St John and Matt Swain, the RDKit is now available on conda-forge: https://anaconda.org/c

[Rdkit-discuss] question about fixing a BRICS "bug"

Dear all, An interesting question came up in github ( https://github.com/rdkit/rdkit/issues/2036): The molecule CNC1CCC(c2ccc(Cl)c(Cl)c2)c2c12 [image: image.png] is not split by the BRICS code even though you might expect the bonds between the tetralin ring and both the 6 ring and the amine to

Re: [Rdkit-discuss] question on rdRGroupDecomposition

On Wed, May 16, 2018 at 4:24 AM Patrick Walters wrote: > > Don't expend a lot of effort on this. > I'm primarily curious to understand why this isn't behaving as we expect it to. It's either a bug or something that should be documented. > I ended up writing my own implementation of R-group dec

Re: [Rdkit-discuss] question on rdRGroupDecomposition

Hi Greg, Don't expend a lot of effort on this. I ended up writing my own implementation of R-group decomposition. Pat On Tue, May 15, 2018 at 10:00 PM Greg Landrum wrote: > Hi Pat, > > This one has me stumped. > @Brian: do you understand what's going on here or should I fire up the > debugger

Re: [Rdkit-discuss] question on rdRGroupDecomposition

Hi Pat, This one has me stumped. @Brian: do you understand what's going on here or should I fire up the debugger? -greg On Mon, May 14, 2018 at 4:24 AM Patrick Walters wrote: > Hi All, > > I'm hoping someone can help me with rdRGroupDecomposition. I'd like to be > able to specify specific R

[Rdkit-discuss] question on rdRGroupDecomposition

Hi All, I'm hoping someone can help me with rdRGroupDecomposition. I'd like to be able to specify specific R-group locations AND match cases where R=H. The example below illustrates what I'm talking about. When RGroupDecompositionParameters.onlyMatchAtRGroups = True, cases where R == H are skip

Re: [Rdkit-discuss] Question regarding 3D pharmacophores

Greg, Once again - many thanks. I admit to making my solution way harder, 'cos I'm an idiot: I was deleting all conformers but the one I needed. Your solution is much more elegant (and safer!). This now works flawlessly for me. Best, Andy On Tue, Oct 31, 2017 at 2:06 AM, Greg Landrum wrote: >

Re: [Rdkit-discuss] Question regarding 3D pharmacophores

On Mon, Oct 30, 2017 at 10:14 PM, Andy Jennings wrote: > > Next question on this topic, as I can't find it from digging into various > sources. > > The solution you pointed me to works very well. I'm now expanding it to > compare the 'color' between two conformations from different molecules. I >

Re: [Rdkit-discuss] Question regarding 3D pharmacophores

Hi Greg, Next question on this topic, as I can't find it from digging into various sources. The solution you pointed me to works very well. I'm now expanding it to compare the 'color' between two conformations from different molecules. I cannot, however, see how to do this. Is there an option suc

Re: [Rdkit-discuss] Question regarding 3D pharmacophores

On 10/21/2017 01:58 AM, Andy Jennings wrote: Hi, I'm curious if anyone has figured out a way to compare two molecules based upon their pharmacophore similarities. Specifically, I want to compare 2 molecules in their _absolute_ locations, and not simply see if they have 2 pharmacophores that m

Re: [Rdkit-discuss] Question regarding 3D pharmacophores

Greg, Outstanding - thanks! This looks to be as close to what I wanted as I could have dared hope. I had no idea where to even begin looking. Fine work. Very fine. Best, Andy On Fri, Oct 20, 2017 at 5:21 PM, Greg Landrum wrote: > Assuming I'm understanding correctly what you're asking for, th

Re: [Rdkit-discuss] Question regarding 3D pharmacophores

Assuming I'm understanding correctly what you're asking for, the RDKit actually has code for doing exactly this. That's the good news. The bad news is that there's pretty much no documentation for it. Since it's kind of interesting code (at least I think so) and it came up in an earlier conversati

[Rdkit-discuss] Question regarding 3D pharmacophores

Hi, I'm curious if anyone has figured out a way to compare two molecules based upon their pharmacophore similarities. Specifically, I want to compare 2 molecules in their _absolute_ locations, and not simply see if they have 2 pharmacophores that match well via a translation/rotation. From what I

Re: [Rdkit-discuss] Question about pKa prediction using RDKit

anks! > > On Mon, Oct 16, 2017, 3:37 PM Bennion, Brian wrote: > >> Hello Jacob, >> >> Have you received any offline replies to this post? >> >> brian >> >> >> -- >> *From:* Jacob D Durrant >> *Sent:* Th

Re: [Rdkit-discuss] Question about pKa prediction using RDKit

to this post? > > brian > > > -- > *From:* Jacob D Durrant > *Sent:* Thursday, October 12, 2017 10:21:46 PM > *To:* rdkit-discuss@lists.sourceforge.net > *Subject:* [Rdkit-discuss] Question about pKa prediction using RDKit > > I've been struggling to implement the SM

Re: [Rdkit-discuss] Question about pKa prediction using RDKit

Hello Jacob, Have you received any offline replies to this post? brian From: Jacob D Durrant Sent: Thursday, October 12, 2017 10:21:46 PM To: rdkit-discuss@lists.sourceforge.net Subject: [Rdkit-discuss] Question about pKa prediction using RDKit I've

[Rdkit-discuss] Question about pKa prediction using RDKit

I've been struggling to implement the SMARTS-based pKa prediction algorithm outlined by Crippen here: http://pubs.acs.org/doi/abs/10.1021/ci8001815 This same method has been mentioned elsewhere on this forum: https://sourceforge.net/p/rdkit/mailman/message/27318424/ ; http://rdkit-discuss.narkive.

Re: [Rdkit-discuss] Question on how to create mol from fragmented mol

Dear Ling, This Jupyter notebook shows two possible different approaches to accomplish this: https://gist.github.com/ptosco/f60d7fc122001c7f72e99bc66748c47b HTH, cheers p. On 10/05/17 11:12, Lingtjien hong wrote: I want to implement the following algorithm using RDkit - given an atom - bre

[Rdkit-discuss] Question on how to create mol from fragmented mol

I want to implement the following algorithm using RDkit - given an atom - break the bonds between this atom and its neighbor(s) - create new mol types/variables from the neighboring fragments example: R1-C-R2 - given atom C - return two mol types/variables R1 and R2 (not C) How can I achieve th

Re: [Rdkit-discuss] Question about WedgeMolBonds

(or by means of an optional argument :-) ) -P. Sent from a cell phone. Please forgive brvty and m1St@kes. On Feb 26, 2017 00:36, "Greg Landrum" wrote: > > > On Sat, Feb 25, 2017 at 7:23 PM, John Mayfield < > john.wilkinson...@gmail.com> wrote: > >> Is there something that the compute2DCoord

Re: [Rdkit-discuss] Question about WedgeMolBonds

On Sat, Feb 25, 2017 at 7:23 PM, John Mayfield wrote: > Is there something that the compute2DCoords() is doing that makes it a >> dependency for WedgeMolBonds() > > > Yes, calculating 2D coordinates. Look at these two molecules, they are the > same but the atoms have been positioned differently i

Re: [Rdkit-discuss] Question about WedgeMolBonds

> > Is there something that the compute2DCoords() is doing that makes it a > dependency for WedgeMolBonds() Yes, calculating 2D coordinates. Look at these two molecules, they are the same but the atoms have been positioned differently in 2D and hence the wedging needs to be different. Therefore y

[Rdkit-discuss] Question about WedgeMolBonds

Hi, I am using WedgeMolBonds() to label converted 3D->2D conformations, roughly: // ... read in 3D mol assignChiralTypesFrom3D(mol); assignStereochemistry(mol,true,true); WedgeMolBonds(mol,&mol.getConformer()); compute2DCoords(...) However, this does not produce an accurate result. In

Re: [Rdkit-discuss] Question about generating configurational isomerism

Worked great! Thanks for your help, Pavel. On Sat, Jan 28, 2017 at 1:52 AM Pavel Polishchuk wrote: > Hi Jacob, > > you need to call AssignStereochemistry with force=True parameter > Chem.AssignStereochemistry(mol, force=True) > > Pavel. > > On 01/28/2017 05:43 AM, Jacob Durrant wrote: > > I'

Re: [Rdkit-discuss] Question about generating configurational isomerism

Hi Jacob, you need to call AssignStereochemistry with force=True parameter Chem.AssignStereochemistry(mol, force=True) Pavel. On 01/28/2017 05:43 AM, Jacob Durrant wrote: I'm trying to set the configuration of a molecule with a double bond, but it doesn't seem to be working. Here's my cod

[Rdkit-discuss] Question about generating configurational isomerism

I'm trying to set the configuration of a molecule with a double bond, but it doesn't seem to be working. Here's my code: === from rdkit.Chem import AllChem from rdkit import Chem from rdkit.Chem.rdchem import BondStereo # Make a molecule with a double bond, no stereo specified (cis or

Re: [Rdkit-discuss] Question about how 3D flag is set

Hi, The current behavior of the Mol file reader is to set the dimensionality based on what the Mol file itself says. So if it says "3D", the "is3D" flag is set to true. If the flag says "2D" the flag is set to false. There's no attempt to determine whether or not this is actually correct (though f

[Rdkit-discuss] Question about how 3D flag is set

Dear all, I need to discriminate molecules with 2D or 3D coordinates. I have a question regarding how RDKit decides if a molecule read from SDF is 2D or 3D. I have a 2D molecule with, for reasons, the "software line" (2nd line in MolBlock) does not end with '2D' or '3D' but with '0D'. For te

Re: [Rdkit-discuss] Question about CreateDifferenceFingerprintForReaction

Dear Nadine, Thank you for your reply with the code examples. I understood the reason of low similarity in my code. Your mail is very informative for me. Best regards, Takayuki 2016年7月27日(水) 3:34 Nadine Schneider : > Hi Takayuki > > The reason why this happens is that the > CreateDifferenceFing

Re: [Rdkit-discuss] Question about CreateDifferenceFingerprintForReaction

Hi Takayuki The reason why this happens is that the CreateDifferenceFingerprintForReaction function takes the whole structure of the molecules of a reactions into account. This means it generates AtomPair FPs with a path length up to 30 bonds for the reactants and products and then builds the diff

[Rdkit-discuss] Question about CreateDifferenceFingerprintForReaction

Dear rdkitters, I want to analyse and build prediction model about reaction or matched molecular pair ( molecular transformations ). I found new function named CreateDifferenceFingerprintForReaction. So, I tried to use the function to do it. But I confused following result. I defined three reacti

Re: [Rdkit-discuss] Question about Run Reaction

Hi Taka, Yes, you need to sanitize every product molecule, after each step. Best wishes, Michal On 7 February 2016 at 01:58, Taka Seri wrote: > Hi Michal, > > Thank you for your quick and kind response. > I tried to sanitize mol according to your advice. > And my code worked fine ! > Thanks you.

Re: [Rdkit-discuss] Question about Run Reaction

Hi Michal, Thank you for your quick and kind response. I tried to sanitize mol according to your advice. And my code worked fine ! Thanks you. ;-) By the way, If I want to run several reaction steps. Do I need to sanitize each molecules? # reactiontest.py from rdkit import Chem from rdkit.Chem

Re: [Rdkit-discuss] Question about Run Reaction

Hi Taka, You have to call SanitizeMol() on the product(s) explicitely. The error is caused by the reactants not being 'sanitized'. Best wishes, Michal On Saturday, 6 February 2016, Taka Seri wrote: > Dear RDKitters, > > I have question about rdkit reaction function. > I want to generate molecule

[Rdkit-discuss] Question about Run Reaction

Dear RDKitters, I have question about rdkit reaction function. I want to generate molecules using several reaction steps. I referred rdkit blog post, and wrote following code. But second step of reaction caused error. I could not difference about mol and mol2 object. I wonder if anyone could help

Re: [Rdkit-discuss] question on MatchedPairs

> > If what you are looking for is information about what type of atom > [*:1] is in the original molecule, I think you can probably figure > it out based on the additional info that's present in the output > from Jameed's code. > > For example, here's one of the output lines from an indexing.

Re: [Rdkit-discuss] question on MatchedPairs

On Wednesday, August 27, 2014, wrote: > > I'm using Jameed's wonderful code for a matched pair analysis. > > Given such a transformation string "[*:1]C>>[*:1][H]" > => How do I check if [*:1] is an aromatic or an aliphatic atom? > > > I fear that this can only be done by going back into the origi

Re: [Rdkit-discuss] question on MatchedPairs

Hi Paul, The 'anchored' fingerprint by the attachment point is how I've done it in the past too. It can give you more granularity than the simple aromatic/non-aromatic classification. It's easy to do it with RDKit but I don't have the snippet at hand. Cheers, George Sent from my gPad On 2

Re: [Rdkit-discuss] question on MatchedPairs

> > Dear RDKitters, > > I'm using Jameed's wonderful code for a matched pair analysis. > > Given such a transformation string "[*:1]C>>[*:1][H]" > => How do I check if [*:1] is an aromatic or an aliphatic atom? > > > I fear that this can only be done by going back into the original > data/outp

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