[Rdkit-discuss] Strange behaviour for GetSubstructMatches with dative bonds

The following finds no matches: m = Chem.MolFromSmiles('C1P->[Zr+3]<-1') m.GetSubstructMatches(Chem.MolFromSmarts('C1P->[Zr+3]<-1’)) But all these work: m.GetSubstructMatches(Chem.MolFromSmiles('C1P->[Zr+3]<-1’)) m.GetSubstructMatches(Chem.MolFromSmarts('[*]->[Zr+3]’)) m =

[Rdkit-discuss] Bug in ResonanceMolSupplier?

Why does ResonanceMolSupplier only give me one resonance structure for O[NH+]=[C-]NC when O[NH+]=[CH]NC gives me two structures? Is that a bug? Best regards, Jan ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net

Re: [Rdkit-discuss] Problems reading XYZ file

Hi Gustavo raw_mol = Chem.MolFromXYZFile('acetate.xyz') mol = Chem.Mol(raw_mol) rdDetermineBonds.DetermineBonds(mol,charge=-1) Best regards, Jan On 7 Apr 2023, at 22.57, Gustavo Seabra mailto:gustavo.sea...@gmail.com>> wrote: Hi everyone, I'm having difficulties using

Re: [Rdkit-discuss] Understanding and visualizing counts fingerprints using GetHashedMorganFingerprint

Here’s code to draw the on-bit fragments in the hashed Morgan fingerprints. mol = Chem.MolFromSmiles('CCC') bi = {} cfp = AllChem.GetHashedMorganFingerprint(mol, 2, nBits=1024, bitInfo=bi) on_bits = [x for x in bi] prints = [(mol, x, bi) for x in on_bits] Draw.DrawMorganBits(prints, molsPerRow=4,

Re: [Rdkit-discuss] SMARTS definition for basic nitrogen

Hi Axel Have a look at https://github.com/jensengroup/protonator Best regards, Jan On 6 Oct 2022, at 12.09, Axel Pahl mailto:axelp...@gmx.de>> wrote: Dear RDKitters, does someone have a good SMARTS definition for basic nitrogen (aliphatic and aromatic), which they would be able to share?

Re: [Rdkit-discuss] RDKit in Google Colab

!pip install rdkit-py No need to use anaconda for Colab RDKit installation anymore! Best regards, Jan On 3 Aug 2022, at 15.40, Eduardo Mayo mailto:eduardomayoya...@gmail.com>> wrote: Hello, I have used RDKit in a Google collab before (a few months ago). However, when I tried today, I got

Re: [Rdkit-discuss] RDKit in Google Colab

Wups. !pip install rdkit-pypi Sent from my iPhone On 3 Aug 2022, at 15.47, Jan Halborg Jensen wrote:  !pip install rdkit-py No need to use anaconda for Colab RDKit installation anymore! Best regards, Jan On 3 Aug 2022, at 15.40, Eduardo Mayo mailto:eduardomayoya...@gmail.com>>

Re: [Rdkit-discuss] rdkit & Coordination chemistry on Mg

Hi Marco You can define dative bonds like this: C1CO->[Fe+2](O)(<-OC1)(<-O)(<-O)(<-O) Best regards, Jan On 22 Mar 2022, at 15.07, Marco Stenta mailto:marco.ste...@gmail.com>> wrote: You don't often get email from marco.ste...@gmail.com. Learn why this is

Re: [Rdkit-discuss] rdkit & Coordination chemistry on Mg

nything wrong here? cheers, m rdmol = Chem.MolFromSmiles('C1CO->[Fe+2](O)(<-OC1)(<-O)(<-O)(<-O))=O', sanitize=True) # case 1 coordinate bonds assert rdmol is not None print(rdmol) Il giorno mar 22 mar 2022 alle ore 15:13 Jan Halborg Jensen mailto:jhjen...@chem.ku.dk>> ha s

Re: [Rdkit-discuss] generating smiles using RDKit

This package might do the trick: https://doi.org/10.26434/chemrxiv-2021-gt5lb On 8 Dec 2021, at 11.02, Gyro Funch mailto:gyromagne...@gmail.com>> wrote: [You don't often get email from gyromagne...@gmail.com. Learn why this is important at

Re: [Rdkit-discuss] XYZ to mol ???

Hi Have a look at https://github.com/jensengroup/xyz2mol and https://github.com/rdkit/UGM_2020/blob/master/Presentations/C%C3%A9dricBouysset_From_RDKit_to_the_Universe.pdf Best regards,

[Rdkit-discuss] Some of the fingerprint bit rendering code not working

Some of the fingerprint bit rendering code in this tutorial is no longer working with 2020.09.01 https://rdkit.blogspot.com/2018/10/using-new-fingerprint-bit-rendering-code.html Draw.DrawMorganBit(epinephrine,589,bi) works, but tpls = [(epinephrine,x,bi) for x in fp.GetOnBits()]

[Rdkit-discuss] Some basic questions about binary fingerprints

I am trying to relate the reliability of ML models trained using binary fingerprint to the presence of on-bits, i.e. comparing the on-bits in a molecule in the test set to the on-bits in the training set. But I am getting some strange results The code is here so I will just summarise.

Re: [Rdkit-discuss] Problems with conda intall on Google Colab (2)

Hi Kazu You need to restart runtime, then the import statement will work If you don’t need the very latest version you can also use !time conda install -q -y -c conda-forge rdkit=2020.09.02 The following is much faster than a conda install but currently that only gives you 2020.03 !pip install

Re: [Rdkit-discuss] Problems with conda install on Google Colab

th… It might not be possible to control how native libraries are loaded. Matt On 14 Dec 2020, at 14:08, Jan Halborg Jensen mailto:jhjen...@chem.ku.dk>> wrote: My conda install script in Colab https://colab.research.google.com/drive/1cAuW02_9r3wFylijGP8rvOUa1-omVwpP?usp=sha

[Rdkit-discuss] Problems with conda install on Google Colab

My conda install script in Colab https://colab.research.google.com/drive/1cAuW02_9r3wFylijGP8rvOUa1-omVwpP?usp=sharing stopped working with the last 1-2 days. I now get the following error ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by

Re: [Rdkit-discuss] How many bonds of a Type in a molecule

mol.GetSubstructMatches(Chem.MolFromSmarts(‘[*]=[*]’)) Should find all double bonds between non-aromatic atoms. If you want to include those Chem.Kekulize(mol) first. On 8 Dec 2020, at 15.01, José Emilio Sánchez Aparicio mailto:joseemilio.sanc...@uab.cat>> wrote: Dear all, I need to find how

Re: [Rdkit-discuss] Incorrect gold particle placement

One option is to use AllChem.MMFFOptimizeMolecule(mol3D, ignoreInterfragInteractions=False), but I am not sure MMFF can handle Au. Another option is to define the Au-S bond ('C(C1C(C(C(C(O1)S[Au])O)O)O)O’) and use AllChem.UFFOptimizeMolecule(mol3D) Best regards, Jan On 1 Dec 2020, at 13.36,

Re: [Rdkit-discuss] Define identical atoms in SMARTS pattern

Thanks you to David, Ivan, and Hao for the very useful answers. Best regards, Jan > On 24 Jul 2020, at 15.51, Jan Halborg Jensen wrote: > > Is there a way to find a [C]([#X])[#X] pattern, where X=X, that finds C(C)C, > C(O)O, C(F)F, etc., but not C(C)O, etc.? > >

[Rdkit-discuss] Define identical atoms in SMARTS pattern

Is there a way to find a [C]([#X])[#X] pattern, where X=X, that finds C(C)C, C(O)O, C(F)F, etc., but not C(C)O, etc.? Best regards, Jan ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net

Re: [Rdkit-discuss] substructure matching

I get both to be True using version 2020.03.04 On 21 Jul 2020, at 14.08, Quoc-Tuan DO mailto:quoctuan...@greenpharma.com>> wrote: Hello, I am not very familiar with smiles/smarts and find the following results quite puzzling: >>> patt = >>>

Re: [Rdkit-discuss] Problem with AllChem.EmbedMolecule and/or MMFFOptimizeMolecule

The 3D structure of the first molecule looks fine to me: https://colab.research.google.com/drive/1V-KkS4tMfbD5UNIs5tyQewZnYtq7yQ7i?usp=sharing What version of RDKit are you using? On 12 Jul 2020, at 07.00, Wojtek Plonka mailto:plon...@plonkaw.com>> wrote: Dear Greg, All, (I tried sending the

Re: [Rdkit-discuss] Random structure generator based on chemical formula?

I whipped up something quick and dirty: https://colab.research.google.com/drive/18esebASwEfPviu-zn9xIs1fwmED-7Yi3?usp=sharing On 13 Jun 2020, at 10.54, theozh mailto:the...@gmx.net>> wrote: Dear RDKit-Community, is there maybe a way with RDKit to generate random (but valid) molecules with a

Re: [Rdkit-discuss] Random structure generator based on chemical formula?

As Nils mentioned this is not trivial. There is a program that does this (molgen.de) but I believe it’s commercial. Have a look at DOI 10.1002/anie.200462457 and reference 7 in that paper. It’s even more difficult if you only want realistic, i.e. stable and synthetically accessible, molecules.

Re: [Rdkit-discuss] IsBondRotatable() ?

Here’s some code. I found the first SMARTS string somewhere (can’t take credit for that) and added the two others (I think): https://github.com/jensengroup/get_conformations/blob/4f3c5ef47f66708defc64196c94e427a956b8f15/get_conformations.py#L16 On 30 May 2020, at 13.38, Tim Dudgeon

Re: [Rdkit-discuss] create a cations

Hi Shani This should work rxn = AllChem.ReactionFromSmarts('[C:1]=[C:2]>>[*:1][*+:2]') m = Chem.MolFromSmiles('CC(C)C1=CC[C@H]2C(=C1)CC[C@@H]3[C@@]2(3(C)C)C') ps = rxn.RunReactants((m,)) mols = [x[0] for x in ps] Best regards, Jan On 2 Feb 2020, at 11.34, Shani Levi

Re: [Rdkit-discuss] Interactive plots in Jupyter notebooks

Hi Chris Iwatobipen had this example using d3js https://iwatobipen.wordpress.com/2019/01/19/plot-chemical-space-with-d3js-based-library-rdkit-chemoinformatics/ I made a simple version here https://colab.research.google.com/drive/11rmBtA6nBgJIp_V_i_tafvffE5ZdY5Uz https://youtu.be/ORKOoLHc-Xg

[Rdkit-discuss] Turn off warning in Huckel calculations.

I am using the new Huckel feature to find bonded atoms using bond orders (https://github.com/jensengroup/xyz2mol : xyz2AC_huckel). This means I am doing a calculation in a mol object with no bonds based xyz coordinates I read in, including hydrogens. A calculation on water gives the following

Re: [Rdkit-discuss] Converting Bond Order Matrices to SMILES format

Hi Pablo Have a look at the BO2mol subroutine in https://github.com/jensengroup/xyz2mol/blob/master/xyz2mol.py Best regards, Jan On 2 Dec 2019, at 10.58, Pablo Ramos mailto:pablo.ra...@covestro.com>> wrote: Hello everybody, Bond Order matrices represent the connectivity between atoms in a

Re: [Rdkit-discuss] Molecules not rendere in Dataframe

Hi again, Since I thought it might be a Colab problem I also posted the question on Stackoverflow, and got an answer from Oliver Scott https://stackoverflow.com/questions/58656572/problem-using-addmoleculecolumntoframe-on-google-colab/58690736#58690736 "Seems like this is a problem with all

Re: [Rdkit-discuss] Molecules not rendere in Dataframe

I posted basically the same question on Friday. I thought it was a Google Colab problem, but apparently it is a more general problem. On 4 Nov 2019, at 19.47, Markus Heller mailto:mhel...@admarebio.com>> wrote: Hi, In a Jupyter notebook, the following code does not show renderings of the

[Rdkit-discuss] Problem using AddMoleculeColumnToFrame on Google Colab

I’d been using AddMoleculeColumnToFrame on Google Colab with no problem. After not using it for about 1 month I just discovered that it stopped working, i.e. the images are not showing up in the data frame (see below). Any ideas? The most likely explanation is that something changed on Google

Re: [Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule

Hi Mike This should work DF[‘HAC’] = [Chem.Lipinski.HeavyAtomCount(mol) for mol in DF[‘Molecule’]] Best regards, Jan On 31 Oct 2019, at 10.16, Mike Mazanetz mailto:mi...@novadatasolutions.co.uk>> wrote: Hi RDKit Gurus, I’ve followed the docs and created a molecule column in my Pandas

[Rdkit-discuss] Tanimoto and fingerprint representation

When using GetMorganFingerprintAsBitVect I get the “expected” Tanimoto score mol1 = Chem.MolFromSmiles('CCC') mol2 = Chem.MolFromSmiles('CNC') fp1 = AllChem.GetMorganFingerprintAsBitVect(mol1,2,nBits=1024) fp2 = AllChem.GetMorganFingerprintAsBitVect(mol2,2,nBits=1024)

Re: [Rdkit-discuss] SMILES to graphs

You can get an adjacency matrix with the function GetAdjacencyMatrix: mol = Chem.GetMolFromSmiles(‘C’) am = Chem.rdmolops.GetAdjacencyMatrix(mol) > On 16 Jul 2019, at 21.06, Navid Shervani-Tabar wrote: > > Hello, > > I was wondering if it is possible to generate graph representations

Re: [Rdkit-discuss] Conformer generation with torsion restraints/frozen atoms

Dear Angelica Here are a couple of codes that may be of interest. They don’t do exactly what you want, but maybe they can give you some ideas. https://github.com/jensengroup/get_conformations https://github.com/jensengroup/TS_conf_search Best regards, Jan On 3 Apr 2019, at 00.58, Angelica

Re: [Rdkit-discuss] Is there any way to protonate a molecule?

Here’s some more general code Best regards, Jan smiles_list = ["CCO","CCS","CC=O","Cc1ccncc1",'NCC(C)=C','CC(N)=N','o11'] reaction_list = ['[C;H2:1]=[C,N:2]>>[CH3:1][*+:2]','[C;H1:1]=[C,N:2]>>[CH2:1][*+:2]','[C;H0:1]=[C,N:2]>>[CH1:1][*+:2]',

[Rdkit-discuss] energy of conformers not matching

The following code gives 63.50505459068998 66.40551367349616 I don’t understand why the two numbers are not the same Any tips would be appreciated Thanks, Jan smiles = "c1ccc(cc1)OCCNC[C@@H](c2ccc(c(c2)CO)O)O" #CONF_107 mol = Chem.MolFromSmiles(smiles) mol = Chem.AddHs(mol) m

Re: [Rdkit-discuss] issues with explicit / implicit valence

I’ve written a program that does this: https://github.com/jensengroup/xyz2mol You need to set "charged_fragments = False” to work with radicals Best regards, Jan On 15 Nov 2018, at 15:05, Peter St. John mailto:peterc.stj...@gmail.com>> wrote: Makes sense, apologies for the lack of details --

Re: [Rdkit-discuss] organometallics?

Here’s a modest step in the right direction https://www.wildcardconsulting.dk/useful-information/how-to-solve-problems-with-coordinate-bonds-in-rdkit/ Best regards, Jan On 13 Sep 2018, at 15:14, Greg Landrum mailto:greg.land...@gmail.com>> wrote: Hi Michal, Though the RDKit theoretically has

Re: [Rdkit-discuss] enumeration of smiles question

This blogpost links to two other ones that may have done that (haven’t read them carefully): https://baoilleach.blogspot.com/2018/06/cheminformatics-for-deep-learners.html Best regards, Jan On 06 Aug 2018, at 11:57, Guillaume GODIN mailto:guillaume.go...@firmenich.com>> wrote: Dear Greg,

Re: [Rdkit-discuss] 3D structure generator

Dear Jahn I've written som code that might be useful to you. More info here http://proteinsandwavefunctions.blogspot.com/2017/12/tsconfsearch-conformer-search-for.html Best regards, Jan From: Jahn Nitschke [jahn.nitsc...@uni-konstanz.de] Sent: Friday,

Re: [Rdkit-discuss] ReactionFromSmarts on bimolecular systems

ave a second fragment there -greg On Mon, Jun 25, 2018 at 5:10 AM Jan Halborg Jensen mailto:jhjen...@chem.ku.dk>> wrote: The following code returns ‘CC’, i.e. the COC molecule is removed. I had a look at the documentation for RunReactants and do not see a way to change this. Is there a

[Rdkit-discuss] ReactionFromSmarts on bimolecular systems

The following code returns ‘CC’, i.e. the COC molecule is removed. I had a look at the documentation for RunReactants and do not see a way to change this. Is there any way to get the code to return ‘COC.CC’? Thanks, Jan mol = Chem.MolFromSmiles('COC.C=C') rxn_smarts =

Re: [Rdkit-discuss] convert a smiles file to a xyz file

Have a look at write_xtb_input_file in this module: https://github.com/jensengroup/take_elementary_step/blob/master/write_input_files.py The xtb input is simple an xyz file with some additional lines below if the molecule is charged. You can simply those lines in the code. Best regards, Jan

Re: [Rdkit-discuss] problems with EmbedMol

nesday, February 28, 2018 8:53:59 AM To: Jan Halborg Jensen Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] problems with EmbedMol Hi Jan, It took me much longer than it should have to figure this one out... The bounds matrix that is returned by GetMoleculeBoundsMatrix()

[Rdkit-discuss] problems with EmbedMol

The following code works fine with ethane (CC) but for propane (CCC) or anything else I get the following error ValueError: could not embed matrix Any ideas or solutions would be appreciated Best regards, Jan from rdkit import Chem from rdkit.Chem import AllChem from rdkit.Chem.Pharm3D import

Re: [Rdkit-discuss] Finding possible reaction products

One option is to construct a library of reaction SMARTS for common chemical reactions. Another, more exhaustive, approach is enumerate all possible connectivity matrices and convert them to molecules See DOI: 10.1039/C7SC03628K and https://github.com/jensengroup/xyz2mol I am working on

[Rdkit-discuss] atom mapping using GetSubstructMatch

I am trying to map atoms in one molecule to those of another using GetSubstructMatch, but have a problem with molecule pairs like the two below The problem is that GetSubstructMatch ignored the H on the n, so that the protonated “n" in mol1 is mapped to the deprotonated “n” in mol2, and vice

[Rdkit-discuss] changing atomic charges with ReactionFromSmarts

The following code changes the bond order correctly but does not change the charges accordingly Any idea what I am doing wrong? Thanks, Jan def clean_charges(mol): rxn_smarts = ['[N+:1]=[*:2]-[O-:3]>>[N:1]-[*:2]=[O:3]'] for smarts in rxn_smarts: rxn =

Re: [Rdkit-discuss] edge matrix

ond encoding in the Adjacency matrix as well to have an exact structure i.e. Double bonds => 2, triple bonds =>3, aromatic bonds =>1.5. But in principal it’s only what you need. BR, Guillaume De : Jan Halborg Jensen Date : jeudi, 18 janvier 2018 à 10:59 À : GVALMTGG Cc : Mario Lovrić, RDK

Re: [Rdkit-discuss] edge matrix

Is there a function for the reverse process, i.e. getting a molecule object from an adjacency matrix? Best regards, Jan On 17 Jan 2018, at 17:19, Guillaume GODIN > wrote: Dear Mario, There is a adjacency matrix available:

[Rdkit-discuss] RDKit and Binder

has anyone experience sharing RDKit scripts using https://mybinder.org/ ? If so, could you share an example? Best regards, Jan -- Check out the vibrant tech community on one of the world's most engaging tech sites,

[Rdkit-discuss] Problems with coordMap in EmbedMultipleConfs

The following code should produce 5 conformers of c1c1CCC” where the coordinates of the benzene ring is the same. But it doesn’t. What I am doing wrong? Best regards, Jan from rdkit import Chem from rdkit.Chem import AllChem template_smiles = "c1c1" template =

[Rdkit-discuss] Rigid 3D alignment of molecule to fragment

Is there a way to rigidly align a 3D molecule to a fragment? I want to compare several conformations by aligning a rigid part of the molecule Best regards, Jan -- Check out the vibrant tech community on one of the

[Rdkit-discuss] Problem with reading/writing files?

The following code 1. energy-minizes a molecule and computes the energy 2. writes to coordinates to an sdf file, 3. reads it in and re-computes the energy But the two energies are off by 4 kcal/mol Any idea what I am doing wrong? Best regards, Jan from rdkit import Chem from rdkit.Chem

[Rdkit-discuss] Atom mapping

I just came across this paper http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00764 which presents an variant of the Fewest Bonds First with Constructive Count Vector method by Crabtree and Mehta (https://dl.acm.org/citation.cfm?id=1498697) Has anyone implemented anything similar in with RDKit?

[Rdkit-discuss] remove H using ReactionFromSmarts (i.e. creating radicals)

Is it possible to remove hydrogens using ReactionFromSmarts, for example changing Cc1c1 to [CH2]c1c1? I can do it using ReplaceSubstructs but I am trying to write more general code that also does other transformations that are better done with ReactionFromSmarts. I can also create

[Rdkit-discuss] Conformational search not "converging" to low energy conformation

The code below shows the lowest energy found for 6 different protomers defined by the smiles strings below as a function of number of conformers. Even with 2000 conformers I am not getting convergence to within 1 kcal/mol for comp109_1=2. Is this expected? Any advice or tips appreciated

Re: [Rdkit-discuss] RDkit Molecule Fragmenter

I was also searching for this functionality earlier For what it’s worth here’s some *very* simple code I hacked together to do fragmentation. The focus is aromatic heterocycles, but it could be more general by, for example '[c,n]-[*]’ -> ‘[R]-[*]’ and ring = Chem.MolFromSmarts(‘[R]’) instead

[Rdkit-discuss] FW: ReplaceSubstructs changes chirality

Also newmol = AllChem.ReplaceSubstructs(m, patt1, patt2, useChirality=True) doesn't help From: Jan Halborg Jensen Sent: Saturday, May 27, 2017 3:11 PM To: rdkit-discuss@lists.sourceforge.net Subject: ReplaceSubstructs changes chirality The code below

[Rdkit-discuss] ReplaceSubstructs changes chirality

The code below protonates select nitrogen atoms using ReplaceSubstructs but in some cases the chirality is changed, despite the fact that I used MolToSmiles(xx,isomericSmiles=True) Any help appreciated Output C[C@]1(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)N=C(N)OCC1(F)F [NX2;H0] [NH+]