[Rdkit-discuss] bug in rdMolTransforms.SetDihedralDeg?

=rdMolTransforms.GetDihedralDeg(mol.GetConformer(), a[0], a[1], a[2], a[3]) print(angle between atoms {}.format(a)+ is {}.format(angle)) Best wishes, Michal Krompiec -- October Webinars: Code for Performance Free Intel webinars

[Rdkit-discuss] UFF/MMFF atom types

Hello, Is Se defined in UFF and/or MMFF94? Apparently, molecules with selenophene moieties don't optimize in RDKit, and a warning appears in the log: UFFTYPER: Unrecognized atom type: Se2+2 Is it possible to define/modify the force field by hand? (for example, use the parametrs of S for Se)

Re: [Rdkit-discuss] MolFromXYZ?

of your molecule): tmp = Chem.MolFromPDBFile(yourfilename) template = Chem.MolFromSmiles(yoursmiles) mol = AllChem.AssignBondOrdersFromTemplate(template, tmp) I don't know if this is what you were looking for. Best, Sereina 2013/11/4 Michal Krompiec michal.kromp...@gmail.com Hello

[Rdkit-discuss] AllChem.ReplaceSubstructs

Hello, I have a question about AllChem.ReplaceSubstructs(mol, query,replacement). As I understand, it replaces 'query' pattern in 'mol' by 'replacement' fragment. It is clear which atom from 'mol' is the joining atom, but which is the joining atom in 'replacement'? The atom with index=0? Is it

Re: [Rdkit-discuss] AllChem.ReplaceSubstructs

in a molecule (i.e. to have a chosen atom at index 0)? Best wishes, Michal On 7 November 2013 11:38, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, I have a question about AllChem.ReplaceSubstructs(mol, query,replacement). As I understand, it replaces 'query' pattern in 'mol

[Rdkit-discuss] atom coordinates

Hello, In the Python API, is it possible to read the 3D coordinates of an atom (from a Mol object created from an SDF file with 3D coords)? Thanks, Michal -- November Webinars for C, C++, Fortran Developers Accelerate

Re: [Rdkit-discuss] atom coordinates

[0] for i in range(0, mol.GetNumAtoms()): pos = mol.GetConformer().GetAtomPosition(i) print '{0:12.4f}{1:12.4f}{2:12.4f}'.format(pos.x, pos.y, pos.z) Cheers, p. On 11/08/2013 01:01 PM, Michal Krompiec wrote: Hello, In the Python API, is it possible to read the 3D coordinates

[Rdkit-discuss] problem with substructure matching using SMARTS

Hello, Substructure matching with SMARTS behaves strangely sometimes - see code below. The pattern with [H] matches, but the pattern with [H,F] does not (both should match). from rdkit import Chem mol=Chem.MolFromSmiles('Clc2sccc2[H]') mol=Chem.AddHs(mol) p1=Chem.MolFromSmarts('c2sccc2[H]')

Re: [Rdkit-discuss] Minimising bits of molecules?

Dear Paolo, Is it possible to add also the option to freeze certain internal coordinates (I am particularly interested in freezing the dihedral angles)? Best wishes, Michal On 26 November 2013 18:09, Paolo Tosco paolo.to...@unito.it wrote: Dear James, I will try to get it done during the

Re: [Rdkit-discuss] Joining Fragments

Suppose we have 2 fragments, A and B, with free valences marked as some dummy atoms. For example, A=CH3* and B=HO*. We want a general method to combine A and B, in this example the result should be CH3OH. There are at least 3 ways to do it. 1. Use the trick from SMILIB: replace dummies with %11,

Re: [Rdkit-discuss] Joining Fragments

Dear Greg, But does CombineMols create any new bonds? What is the simplest/fastest way of joining two molecules (fragments) together? (i.e. is there anything simpler than using ReplaceSubstructs) Best wishes, Michal On 1 December 2013 04:40, Greg Landrum greg.land...@gmail.com wrote: This is

[Rdkit-discuss] distance matrix for non-bonded atoms

Hello, Is there any simpler (=faster) way of calculating the shortest distance between non-bonded atoms in a molecule? from rdkit import Chem from rdkit.Chem import AllChem from rdkit.Chem import rdMolTransforms import numpy mol=Chem.MolFromSmiles(Cc2ccsc2c1sccc1C) mol=Chem.AddHs(mol)

Re: [Rdkit-discuss] distance matrix for non-bonded atoms

| SM2 5NG T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter @ICRnews Facebook www.facebook.com/theinstituteofcancerresearch Making the discoveries that defeat cancer On 3 Dec 2013, at 15:56, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, Is there any

Re: [Rdkit-discuss] distance matrix for non-bonded atoms

for i in range(0, natom-1): for j in range(i+1,natom): if mol.GetBondBetweenAtoms(i,j)==None: dist=rdMolTransforms.GetBondLength(conf,i,j) if distminimum: minimum=dist print(minimum) On 3 December 2013 17:00, Michal Krompiec michal.kromp...@gmail.com wrote: Dear Nick, Thanks. I need

Re: [Rdkit-discuss] distance matrix for non-bonded atoms

Sorry for spamming the list. This is the correct version: from rdkit import Chem from rdkit.Chem import AllChem mol = Chem.MolFromSmiles('') mol=Chem.AddHs(mol) AllChem.EmbedMolecule(mol) AllChem.UFFOptimizeMolecule(mol) conf = mol.GetConformer() natom=mol.GetNumAtoms() conf=mol.GetConformer()

[Rdkit-discuss] SDWriter kekulizes by default

Hello, Is it possible to suppress kekulization by SDWriter? I get the following error on a call to SDWriter.write: ValueError: Sanitization error: Can't kekulize mol But some molecules can't be kekulized using RDKit's algorithm, even though they are otherwise 'correct'. I browsed the sources and

Re: [Rdkit-discuss] SDWriter kekulizes by default

it is not a bug in your code, unless you consider the fused thiadiazole ring aromatic. Best wishes, Michal On 5 December 2013 12:19, Greg Landrum greg.land...@gmail.com wrote: Hi Michal, On Thu, Dec 5, 2013 at 11:52 AM, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, Is it possible

[Rdkit-discuss] RDKit nodes in KNIME stopped working suddenly

Hello, We've been using the RDKit nodes in KNIME for quite a while without any problems. But suddenly they ceased to work on some computers, while still working on other ones. Tried with a fresh KNIME installation with latest RDKit nodes - same problem. What could be wrong? I pasted the

[Rdkit-discuss] sanitization removes Hs - is this expected?

Hello, I have just noticed this: Chem.MolToSmiles(Chem.MolFromSmiles([H]c1c([H])sc([H])c1[H])) 'c1ccsc1' Chem.MolToSmiles(Chem.MolFromSmiles([H]c1c([H])sc([H])c1[H],sanitize=False)) '[H]c1sc([H])c([H])c1[H]'

Re: [Rdkit-discuss] sanitization removes Hs - is this expected?

, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, I have just noticed this: Chem.MolToSmiles(Chem.MolFromSmiles([H]c1c([H])sc([H])c1[H])) 'c1ccsc1' Chem.MolToSmiles(Chem.MolFromSmiles([H]c1c([H])sc([H])c1[H],sanitize=False)) '[H]c1sc([H])c([H])c1[H]' Chem.MolToSmiles(Chem.RemoveHs

[Rdkit-discuss] RDKit fingerprints in Knime - operations on DenseBitVectorCell

Hello, I am trying to implement substructure searching with fingerprint-based screening in Knime, using RDKit fingerprints (I know that a database would be the preferred solution, but for some reasons I'd rather use Knime). In order to do this, I need an equivalent of

Re: [Rdkit-discuss] An ultimate way to compute 3D coordinates?

systems. That's why I switched to CORINA, btw. Best wishes, Michal Krompiec On 5 April 2014 18:05, JP jeanpaul.ebe...@inhibox.com wrote: I don't know about the ultimate way: but this works for me (to generate n conformers): writer = Chem.SDWriter('some_file.sdf') # add Hydrogens molH

Re: [Rdkit-discuss] An ultimate way to compute 3D coordinates?

On 5 April 2014 19:11, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: On 05/04/14 19:04, Michal Krompiec wrote: For example, it does not work well for long conjugated oligomers - sometimes it produces molecular knots instead of straight strands, and is quite slow for large systems. Can you

Re: [Rdkit-discuss] An ultimate way to compute 3D coordinates?

On 6 April 2014 05:36, Greg Landrum greg.land...@gmail.com wrote: Some substituted oligoarenes with at least 8 rings in the chain, not particularly fancy (I think the problem is related more to the length of the molecule than to the nature of the repeat units). I tried various options in the

Re: [Rdkit-discuss] portable PostgreSQL + RDKit cartridge?

simplify the lives of many ;) Best wishes, Michal On 28 August 2014 15:04, Jan Holst Jensen j...@biochemfusion.com wrote: On 2014-08-28 14:34, Michal Krompiec wrote: Hello, has anybody tried to compile a portable Windows binary of PostgreSQL with RDKit cartridge? There is a portable PostreSQL

Re: [Rdkit-discuss] portable PostgreSQL + RDKit cartridge?

, 2014, Michal Krompiec michal.kromp...@gmail.com wrote: Dear Jan, Thanks a lot. It remains a painstaking DIY job stil then. Greg: would it be possible to add the binary of the cartridge (compiled with, say, the latest PostgreSQL) to the binary Win32 distribution? It's definitely possible

Re: [Rdkit-discuss] tests failed on Cygwin

::getDihedralDeg(mol-getConformer(), 1, 3, 6, 8) actually is? It might just be a periodicity problem. Thanks for your collaboration, kind regards Paolo On 17/03/2015 14:48, Michal Krompiec wrote: Hello, I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current GitHub version). So

Re: [Rdkit-discuss] tests failed on Cygwin

it be? My suspicion is that it a wrong version of some dll is loaded, but how do I trace it? Best wishes, Michal On 17 March 2015 at 14:48, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current GitHub version). So far, everything

Re: [Rdkit-discuss] postgresql cartridge and fingerprints

Hi Greg, Thanks. I haven't started tests yet, so we'll see. Best wishes, Michal On 17 Mar 2015 15:08, Greg Landrum greg.land...@gmail.com wrote: Hi Michal, On Tue, Mar 17, 2015 at 3:02 PM, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, I understand that the index

[Rdkit-discuss] postgresql cartridge and fingerprints

Hello, I understand that the index for substructure searching is created by, for example: create index molidx on mols using gist(m) where m is the molecule column in mols table. Is this correct? How do I select the type of fingerprint used for the index? I just suspect that my dataset may

[Rdkit-discuss] building RDKit on Cygwin: rdBase not linked?

Hello, I am struggling to build RDKit on Cygwin, under 32-bit Windows 7, using gcc 4.9.2, boost 1.55 and python 2.7.8, with the standard options: cmake .. make make install The building itself did not raise any errors, but the python tests fail, for example: $ python -v -c 'from rdkit import

[Rdkit-discuss] tests failed on Cygwin

Hello, I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current GitHub version). So far, everything looked fine, but some tests failed: The following tests FAILED: 13 - testUFFForceField (OTHER_FAULT) 66 - testFMCS (SEGFAULT) 79 - pythonTestDbCLI (Failed) -

Re: [Rdkit-discuss] Oracle, pypl and rdkit

of substructure searching is done by rdkit. I think the same would be true of oracle. --- TJ O'Donnell On Thu, Mar 12, 2015 at 4:24 PM, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, has anybody tried to implement substructure searching in an Oracle database using PYPL

[Rdkit-discuss] RDKit on cygwin32: python silently crashes

Dear All, I know that building on Cygwin is not a popular topic here, but perhaps someone will have some ideas. I'm trying to build on 32-bit Cygwin under Windows 7 32-bit. The build seems successful and C tests are passed, but importing the python bindings causes python to crash silently: $

[Rdkit-discuss] cartridge: successful build on Cygwin 64-bit

Dear All, In case this may be useful to anybody in the future: RDKit (current github version) builds nicely on Cygwin 64-bit without any modifications (GCC 4.9.2, boost 1.55). The following tests fail: 13 - testUFFForceField (SEGFAULT) - rounding error 15 - pyForceFieldConstraints (Failed) -

Re: [Rdkit-discuss] sanitization removes Hs - is this expected?

Hi Greg, Thank you, this is exactly what I needed. On 2 April 2015 at 05:22, Greg Landrum greg.land...@gmail.com wrote: Skipping sanitization, as you propose, isn't going to help here: the kekulized form of the ring will not be converted to aromatic and you won't get the matches you are

[Rdkit-discuss] RDKit interactive table in Knime

Dear All, I have just found an interesting behaviour of the RDKit Interactive Table node in Knime. My workflow contains two such nodes and they contain pretty much the same data. If I hilite a molecule in one node, it is automatically hilited in the other one as well. I'm using KNIME 2.10.4 with

Re: [Rdkit-discuss] out-of-plane bends

approach, i.e. it minimizes only the methyl group in 2-methylthiophene while keeping the rest fixed, effectively pushing it back in plane. Would that work for you? Best, Paolo On 04/15/2015 10:57 AM, Michal Krompiec wrote: Hello, I'm trying to manipulate out-of-plane bends of substituents

[Rdkit-discuss] out-of-plane bends

Hello, I'm trying to manipulate out-of-plane bends of substituents attached to aromatic rings. Obviously, they should lie in the plane of the ring, but sometimes (after constrained optimization) they come slightly out of plane and there doesn't seem to be a way to push/rotate them back to the ring

Re: [Rdkit-discuss] sanitization removes Hs - is this expected?

added the feature to the cartridge and will check it in later today/tomorrow morning. -greg On Thursday, April 2, 2015, Michal Krompiec michal.kromp...@gmail.com wrote: Hi Greg, Thank you, this is exactly what I needed. On 2 April 2015 at 05:22, Greg Landrum greg.land...@gmail.com wrote

Re: [Rdkit-discuss] detect dihedral angles in a conformation

Hi Jose I have a similar problem, but I look for dihedrals between aromatic/unsaturated rings: rotatable_ring_bonds=Chem.MolFromSmarts("[!$(*#*)]-!@[!$(*#*)]") rotatable_matches=mol.GetSubstructMatches(rotatable_ring_bonds) rotatable=set() #set of sorted indices of the rotatable bonds for bond in

[Rdkit-discuss] UFF geometry optimization of lanthanide complexes

Hello, I was trying to generate 3D coordinates for an europium complex, [Eu(acac)3(phen)], with UFF, using RDKit nodes in KNIME (UFF is parametrized for lanthanides). Whereas the generation of coordinates seems to produce an almost sensible structure: [image: Inline images 3] subsequent geometry

Re: [Rdkit-discuss] UFF geometry optimization of lanthanide complexes

but I'm not quite sure. The corners of the code for dealing > with non-organic molecules are dark, dusty, and not particularly well > tested. > > Best, > -greg > > > > > On Mon, Sep 14, 2015 at 2:26 PM, Michal Krompiec < > michal.kromp...@gmail.com> wrote:

Re: [Rdkit-discuss] Question about Run Reaction

(mol2,) ) > uniq = set( [ Chem.MolToSmiles(x[0], isomericSmiles=True ) for x in ps2 ] > ) > print( uniq ) > --- > from shell > > $ python reactiontest.py > > {'Fc1ccc(F)cc1', 'Fc1(F)c1', 'Fc1c1F'} > > - &g

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

[Rdkit-discuss] canonical atom indexing

Hello, I need a "canonical" method for generating atom indices for a given molecule (with 3D coordinates, so the input is e.g. a mol file), for a molecular descriptor which should be invariant with respect to atom indexing. As I understand, canonical SMILES will give the same atom indices for

Re: [Rdkit-discuss] canonical atom indexing

; > [2,0,3,4,1,5,6,7] > > >>> > > Not that the output order is from the context of the output smiles string, > i.e. order[0] is the index of the original atom index that was the outputs > first atom and so on. I.e. order[output_atom_idx] = input_atom_idx > > On Thu

Re: [Rdkit-discuss] problems with installation on conda with python 3.5 32-bit

hopefully) be able to do "conda install -c > rdkit rdkit" now and have things work. I will try python 2.7 tomorrow. > > It turns out that this isn't much extra effort, so assuming this build > works I should be able to keep doing these. > > -greg > > > On Mon, Fe

Re: [Rdkit-discuss] problems with installation on conda with python 3.5 32-bit

g these again, > but I'm reluctant due to the amount of effort required. > How many users do you need to support who are stuck on 32bit machines? > > -greg > > > On Mon, Feb 20, 2017 at 2:18 PM, Michal Krompiec < > michal.kromp...@gmail.com > <javascript:_e(%7B%7D,'cvml','mic

Re: [Rdkit-discuss] errors with windows10 RDKit installation using conda

On Tuesday, 29 November 2016, Greg Landrum wrote: > > On Tue, Nov 29, 2016 at 5:17 PM, Bob Funchess > wrote: > > >> PS: All I really need is the C# wrappers; if those could be included in >>

Re: [Rdkit-discuss] UpdatePropertyCache() after RunReactants

You need to sanitize the products, just run Chem.SanitizeMol on each molecule. See http://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions : "the molecules that are produced by the chemical reaction processing code are not sanitized". Best, Michal On 12 January 2017 at 17:22,

Re: [Rdkit-discuss] Problem Installing RDKit

Dear Stephen, You have installed RDKit in the environment my-rdkit-env, you need to activate the environment in order to use it (btw, it seems that you installed it in "mr-rdkit-env"). But you can also install RDKit in the default environment: conda install rdkit -c rdkit Best wishes, Michal On

Re: [Rdkit-discuss] Jupyter Could not find environment: my-rdkit-env

Hi Germano, You can also install rdkit in the default environment: conda install -c rdkit rdkit Best, Michal On 29 June 2017 at 14:22, Germano Massullo wrote: > Hi there, I am experiencing some troubles in letting jupyter use rdkit > on Fedora 25 > I installed

Re: [Rdkit-discuss] How to match any halogen of a structure with any halogen of a substructure?

Hi Alexis, Try aromatic form instead of Kekule notation. Best, Michal On 17 May 2017 at 12:55, Alexis Parenty wrote: > Hi everyone, > > I am looking for substructure match between a smarts and a smiles, but I > want any heteroatom from the smarts to match any

Re: [Rdkit-discuss] HasSubstructMatch doesn't work as expected

I'm afraid it won't work in the general case (i.e. you can make it work for some classes of compounds, but not without unwanted side effects on others) if the aromaticity model of the other cartridge is different - and it seems to be the case here... On Wednesday, 13 September 2017, Michał

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

+1 vote for Symmetrizer. It would be very useful for preparing input for computational chemistry codes. Best, Michal Krompiec Merck KGaA On Mon, 15 Jan 2018 at 15:21, Jason Biggs <jasondbi...@gmail.com> wrote: > >- I've had this on my to-do list for a few months now,

Re: [Rdkit-discuss] UFF/MMFF atom types

a, 9 - 10125 Torino (Italy) > Tel: +39 011 670 7680 | Mob: +39 348 5537206 > Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it > http://open3dqsar.org | http://open3dalign.org > == > > > > On 5 Nov 2013, at 07:20,

Re: [Rdkit-discuss] RDKit and organometallics

Isn't this patch already incorporated in the master branch? On Tue, 13 Nov 2018 at 12:35, Malgorzata Werner < malgorzata.wer...@molecularhealth.com> wrote: > Hi Henrique, > > You could try using v3000 sd files. > > Here's a blog about this: >

[Rdkit-discuss] number of significant digits in molblock?

Hello, Is it possible to control the number of significant digits of XYZ coordinates? I am modifying coordinates of my molecules using SetAtomPosition but when I save them into an SDF it seems that the precision is limited to 4 digits after the decimal point (I'd like 10 instead...). Best wishes,

Re: [Rdkit-discuss] number of significant digits in molblock?

. C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 > M END > > >>> print(Chem.MolToMolBlock(m, forceV3000=True)) > > RDKit 2D > > 0 0 0 0 0 0 0 0 0 0999 V3000 > M V30 BEGIN CTAB > M V30 COUNTS 2 1 0 0 0 > M V30 BEGIN

Re: [Rdkit-discuss] number of significant digits in molblock?

6 digits seems perfectly fine for me. On Fri, 5 Oct 2018 at 14:26, Greg Landrum wrote: > > On Fri, Oct 5, 2018 at 2:42 PM Ivan Tubert-Brohman < > ivan.tubert-broh...@schrodinger.com> wrote: > >> In the newer "V3000", the atom line is not column-based, which I believe >> gives more freedom to

[Rdkit-discuss] Fingerprint collision and machine learning

Hi all, I have a slightly off-topic question. I'm trying to train a neural network on a dataset of small molecules and their melting points. I did get a not-so-bad accuracy with Morgan fingerprints, but I've realised that regardless of FP radius and bitvector length, several dozen molecules have

Re: [Rdkit-discuss] Fingerprint collision and machine learning

Hi Thomas, Radius 2, 2048 bits, 5200 data points. On Wed, 10 Oct 2018 at 13:13, Thomas Evangelidis wrote: > What's your bitvector length and radius? How many training samples do you > have? > > On Wed, 10 Oct 2018 at 13:51, Michal Krompiec > wrote: > >> Hi all, >&g

[Rdkit-discuss] organometallics?

anybody point me to a toolkit (or RDKit hack) that can handle these? Best, Michal Dr. Michal Krompiec Adjunct Professor School of Chemistry, University of Southampton Highfield, Southampton SO17 1BJ, UK and Head of Computational Modelling | Performance Materials | Early Research and Business

Re: [Rdkit-discuss] organometallics?

... and yet another example, bis-mu-dichloro-bis(allyl)dipalladium(II), drawn according to ChemAxon's instructions: https://docs.chemaxon.com/display/docs/How+to+draw+coordination+compounds Michal On Thu, 13 Sep 2018 at 14:45, Michal Krompiec wrote: > Hi Greg, > Thanks for your fast

Re: [Rdkit-discuss] organometallics?

them. > > If you have some examples you can share, I'd be happy to take a look to > see if I can suggest ways to read them in. > > Best, > -greg > > > On Wed, Sep 12, 2018 at 10:30 PM Michal Krompiec < > michal.kromp...@gmail.com> wrote: > >> Hello, &

Re: [Rdkit-discuss] organometallics?

ay be possible to add the ability > to directly parse and interpret this information; that would make things > easier and the drawings would be less crappy. > > -greg > > > > On Fri, Sep 14, 2018 at 10:55 AM Michal Krompiec < > michal.kromp...@gmail.com> wrote: > >>

[Rdkit-discuss] rotate a conformer around an axis?

Hello, I'd like to check if a particular axis is a C2 symmetry axis of a conformer. How do I rotate my conformer around an axis? (apart from extracting the coordinates into numpy, multiplying by a rotation matrix and updating the coordinates) Can TransformConformer function be used for this?

Re: [Rdkit-discuss] Using RdKit in Parallel

Dear Stamatia, If the molecules are processed completely independently by your code, it may be simpler to split the SDF into chunks (e.g. with csplit in a bash script) and then run separate instances of your python code on each chunk, wait until all are finished and finally collate the output.

Re: [Rdkit-discuss] rotate a conformer around an axis?

z axis. > > https://nbviewer.jupyter.org/github/iwatobipen/playground/blob/master/rotation_mol.ipynb > > Unfortunately molecule will not render on github but you can view molecule > if you run the code on your PC. > I hope this would be some of help. > > Best regards, > T

Re: [Rdkit-discuss] Bug with Calculation of aromatic rings?

It’s because the molecule with atom indices is a tautomer of the other one (H at the other N), hence different Kekule structure and different behaviour of the aromaticity perception code. Best, Michal On Wed, 6 Mar 2019 at 10:04, Colin Bournez wrote: > Hi Greg, > > Indeed it seems one bond is

[Rdkit-discuss] Chem.GetMolFrags and 3D coordinates

Hello, Let mol be a molecule with a conformer with 3D coordinates, consisting of 2 fragments. Chem.GetMolFrags(mol, asMols=true) returns these fragments as Molecule objects, but the 3D coordinates are lost. Is there any way to preserve them? Best, Michal

Re: [Rdkit-discuss] Chem.GetMolFrags and 3D coordinates

0 > 2 3 1 0 > 3 4 2 0 > 4 5 1 0 > 5 6 2 0 > 6 1 1 0 > 1 8 1 0 > 2 9 1 0 > 3 10 1 0 > 4 11 1 0 > 5 12 1 0 > 6 13 1 0 > 7 14 1 0 > 7 15 1 0 > 7 16 1 0 > M END > > > > Best, >

Re: [Rdkit-discuss] Calculating VDW interaction energy between two molecules

Dear Omar, Probably, but it is not trivial: you’d need to optimise geometries of a few 1:1 complexes and calculate average interaction energy. Why use rdkit for that? Michal On Tue, 11 Jun 2019 at 01:48, Omar H94 wrote: > Dear RDKit users, > Is there a way to calculate the VDW energy between

Re: [Rdkit-discuss] The "maxAttempts" option in "EmbedMultipleConfs"

It depends what you need it for, but if you want a more realistic conformational analysis instead, CREST is the tool of choice. https://xtb-docs.readthedocs.io/en/latest/crest.html Best, Michal On Tue, Dec 17, 2019 at 16:26 topgunhaides . wrote: > Hi guys, > > Can anyone tell me more about the

Re: [Rdkit-discuss] how to handle metallocenes?

Dear Mike, Try changing all metal-ligand bonds to "dative" or "ionic, and standardize afterwards (but disable adjusting of implicit Hs). This way, I was able to process (in KNIME) >99% of organometallics (incl. metallocenes) downloaded from Reaxys. Example snippet (which doesn't check the

Re: [Rdkit-discuss] Code efficiency improvement

n to slow things down, but not quite sure. > Any suggestions are very welcome! > > Best, > Leon > > > > > > > > On Wed, Dec 18, 2019 at 7:08 PM Michal Krompiec > wrote: >> >> Are you looking for the global minimum or an ensemble of conformers? Eit

Re: [Rdkit-discuss] Code efficiency improvement

Are you looking for the global minimum or an ensemble of conformers? Either way, this is already very fast. Bear in mind, however, that MMFF’s accuracy isn’t great for this type of tasks (see for example https://arxiv.org/pdf/1705.04308.pdf ). In other words, I don’t see a use case for generation

Re: [Rdkit-discuss] TIL: Mol objects having varying attributes depending on rdkit imports

pute2DCoords(m). And this won't work unless AllChem is loaded. Best, Michal Krompiec Merck KGaA On Wed, 23 Sep 2020 at 16:56, Rocco Moretti wrote: > Hi Norwid, > > There's a subtle but significant difference between the two examples: > > >>> AllChem.Compute2DCoor

Re: [Rdkit-discuss] TIL: Mol objects having varying attributes depending on rdkit imports

Uhm, you’re right. On Wed, Sep 23, 2020 at 7:46 PM Rocco Moretti wrote: > Python translates object.method() to method(object). > > > Well, yes and no. "Yes" in the sense that instance methods are internally > implemented equivalently to a free method which takes an instance as the > first

[Rdkit-discuss] PathToSubmol on atom indices?

Hello, I noticed this was discussed before and I'm wondering if anything's changed. Is it possible to extract a substructure from a molecule, based on atom indices? I understand that Chem.PathToSubmol does something similar, but takes bond indices. Best, Michal

Re: [Rdkit-discuss] PathToSubmol on atom indices?

msToUse": > > e.g. > > rdkit.Chem.rdmolfiles.MolFragmentToSmiles(mol, atomsToUse=[11,13,22,15]) > > Kangway > -- > *From:* Michal Krompiec > *Sent:* Thursday, June 4, 2020 10:45 AM > *To:* RDKit Discuss > *Subject:* [Rdkit-discuss] PathToSubmol on atom indices? > >

Re: [Rdkit-discuss] Incorrect gold particle placement

Dear Anthony, >From MMFF or UFF you shouldn’t expect reasonable structures of metal-containing compounds. If you need a quick and qualitatively OK method, I recommend xtb. Best wishes, Michal Krompiec, Merck KGaA On Tue, Dec 1, 2020 at 1:09 PM Anthony Nash wrote: > > Dear all, &g

[Rdkit-discuss] Dragon fingerprints?

Hello RDKitters, Are Dragon fingerprints (or something close) available in RDKit (or free codes that depend on RDKit)? I'm trying to reproduce results from one paper. Thanks, Michal Krompiec Merck KGaA ___ Rdkit-discuss mailing list Rdkit-discuss

Re: [Rdkit-discuss] Dragon fingerprints?

elps, > Nils > > Am 10.11.2020 um 23:11 schrieb Michal Krompiec: > > Hello RDKitters, > > Are Dragon fingerprints (or something close) available in RDKit (or free > > codes that depend on RDKit)? I'm trying to reproduce results from

[Rdkit-discuss] install on macosx with Python 3.8

;brew install rdkit", but then rdkit is unimportable in Python ("No module named 'rdkit'"). What am I doing wrong? I'm using brew 3.2.0 on MacOS 11.4 Thanks in advance, Michal Krompiec ___ Rdkit-discuss mailing list Rdkit-discuss@lists.s

Re: [Rdkit-discuss] install on macosx with Python 3.8

Thanks Maciek, Francois and Peter. A clean conda environment was all that was needed… Best, Michal On Fri, Jun 25, 2021 at 1:44 AM Francois Berenger wrote: > On 25/06/2021 02:57, Michal Krompiec wrote: > > Hello, > > Is it possible to install RDKit on MacOSX in a Python