Re: [Rdkit-discuss] proper technical term for generating virtual compounds with rdkit and smarts

Hello Brian, On Fri, 25 Sep 2020 05:19:14 + "Bennion, Brian via Rdkit-discuss" wrote: > I have a paper in review and is intended for a large audience that has > synthetic chemists, biologist and comp chem. > One reviewer had issues with the term in-silico syntheses. > I used rdkit and

Re: [Rdkit-discuss] changes in chirality in rdkit?

Hello Brain, > The original smiles string > "OC[C@@H]1O[C@H](Cn2c(N33)nnc2[C@@H]2OCCC2)CC1" > > after conversion with rdkit > "OC[C@H]1CC[C@@H](Cn2c([C@H]3CCCO3)nnc2N22)O1" After visualisation it seems to me that both smiles represent the same structure (stereochemistry is the same,

Re: [Rdkit-discuss] Code efficiency improvement

On Wed, 18 Dec 2019 22:54:04 -0500 "topgunhaides ." wrote: > For large and flexiable molecules, will need a lot more than 10K (like > 100K) to try to cover the entire conformational space. In such case useExpTorsionAnglePrefs=True, useBasicKnowledge=True can make your conformational set less

Re: [Rdkit-discuss] Clearing isotope info

On Wed, 11 Dec 2019 10:53:47 + Tim Dudgeon wrote: > I'm wanting to write isomeric smiles that does not include isotope > information. I also had sytuation when I need to generate smiles with either isotopes or stereochemistry but not both. Maybe it is worth to add two options to

Re: [Rdkit-discuss] MolToSmiles preserve atom order

On Mon, 18 Nov 2019 16:40:28 + David Cosgrove wrote: > Point taken. I don’t think you’d be able to get RDKit to spit such SMILES > strings out unless you tortured it pretty hard, however. Export smiles with arbitrary given atom order is diffrent problem. Normally working with mol object you

[Rdkit-discuss] MolToSmiles preserve atom order

Hi all, Is there any way to preserve atom order from Mol object during exporting to smiles? I tried MolToSmiles with rootedAtAtom=0 and canonical=False options but it not always prevent oryginal order. I know I can use _smilesAtomOutputOrder to map old indices to new one in canonical smiles but

Re: [Rdkit-discuss] stereochemical atom order

On Thu, 6 Jun 2019 11:16:49 +0200 Greg Landrum wrote: > The order is definitely not the simple numerical order. Look at the results > that I sent again. Ok I see it now, C(5) CHI_TETRAHEDRAL_CW: 4 6 0 is not numerical order :) Ok, now I understand this. Thx Rafał

Re: [Rdkit-discuss] stereochemical atom order

Greg, thx for answer > In the RDKit the chiral order is determined by the order of the atom's > bonds. Here's a bit of code showing how to get the neighboring atoms in the > correct order: Your code tells that atom.GetBonds() return correct order, but the order is simple numerical order and

[Rdkit-discuss] stereochemical atom order

Hi all, Is it possible to get stereochemical atom order around chiral center? To be more verbose: in smiles/smarts chirality (@ or @@) is determined by atom order which is not exactly the same as atom idxes in mol. The difference may appear in ring-containing compounds, according to

[Rdkit-discuss] multiThreads OptimizeMoleculeConf with constraint?

Hello all, Is it possible to optimize multiple conformation with constraint using more that one thread (core)? I have following code: Chem.rdDistGeom.EmbedMultipleConfs(mol, numConfs=100, numThreads=10) ffps = ChemicalForceFields.MMFFGetMoleculeProperties(mol) ff =

[Rdkit-discuss] fast hydrogen count in molecule

Hello group, Is there any fast way to count all hydrogen atoms in molecule? The only idea which I have is: sum([atom.GetTotalNumHs() for atom in mol.GetAtoms() ]) which probably is not the most optimal because it require iteration over atom at python end. For all other atoms I found such

Re: [Rdkit-discuss] nitro-compounds from smarts

Curt & Greg, Thx for clarification. > But it's not clear to me why you would need to query in this way. in my code I use(d) smarts as a smiles with extra features ("regex", atom numbering). As far as I remember I had some problem with smiles and therefore decided to switch to smarts. Now I

Re: [Rdkit-discuss] nitro-compounds from smarts

Greg, Thx for answer, but it is still unclear for me. You wrote: > So, the short answer to your question is: "yes". You will need to rewrite > your SMARTS queries so that nitro groups are expressed consistently. If you > want those queries to match what the RDKit's molecule processing code >

[Rdkit-discuss] nitro-compounds from smarts

hi all, Is it possible to read smarts with nitro group in form 'N(=O)(=O)'? Here is the context of my question: The example below shows that there is some problem with nitro group and MolFromSmarts: >>> m1=Chem.MolFromSmiles('c1c1[N+](=O)[O-]') >>>

Re: [Rdkit-discuss] Kekulizing thiazoles

On Tue, 17 Jan 2017 16:52:36 + Chris Arthur wrote: > ValueError: Sanitization error: Can't kekulize mol In most case I have 'Can't kekulize mol' error for hetorocycle with hydrogen on nitrogen and smiles which have not explicite hydrogen on N. Exempli gratia:

Re: [Rdkit-discuss] Generating all stereochem possibilities from smile

On Thu, 8 Dec 2016 23:21:24 -0800 James Johnson wrote: > Hello all, I am trying to generate R and S from: CCC(C)(Cl)Br > > Below is the code for making the smi to mol file. Can someone give me some > guidance to generate all sterochem possibilities? There are two ways

[Rdkit-discuss] uff atomic partial charge

Hi all, How can I get atomic partial charged used by UFF? In original paper is stated that "Partial charges are obtained using the recently published QEq charge equilibration scheme" as described in http://pubs.acs.org/doi/pdf/10.1021/j100161a070. Is RDKit follow this scheme? Regards, Rafał

[Rdkit-discuss] gromacs force field and topology from SMILES

Dear all, 1. I want to generate gromacs topology with force field parameters from SMILES. RDKit has two FFs so this should be easy task at least for this two force fields. Bond and angle parameters can be simply take from Get*BondStretchParams and Get*StretchBendParams, but vdW and torsian

[Rdkit-discuss] embedMolecule - optimal bond and angle values

Dear all, As far as I know Chem.rdDistGeom.EmbedMultipleConfs function uses set of experimental (or optimal) values for bond length and angle to constructs 3d structure. Are there any function to get those optimal values or deviation from the optimal values for particular conformer? Quick

Re: [Rdkit-discuss] getting started in C++

On Mon, 9 May 2016 15:03:51 +0200 Greg Landrum wrote: > Though it would be nice to have better documentation for getting started > with the RDKit in C++, that would be even more time consuming than creating > the Python docs. It's unlikely to happen unless someone either

[Rdkit-discuss] getting started in C++

Hello, Is there any how-to, tutorial or other such documentation for RDKit in C++? For Python there is very nice http://www.rdkit.org/docs/GettingStartedInPython.html intoduction. Is there anything similar for C++ API? The only similar resource I found is Code/Demos/RDKit/ in source code which

[Rdkit-discuss] two versions of RDKit in one python program - static compilation?

Hello, I have python program which uses RDKit and: some functions in the program require old version of RDKit (don't ask me why), and some other (my code) in the program requires current version of RDKit. My problem is how to combine two different versions of RDKit in one python program. I

Re: [Rdkit-discuss] assign E/Z information to double bond and write to SMILES

On Wed, 13 Apr 2016 10:52:47 +0200 Greg Landrum wrote: > The RDKit does determine E/Z labels for double bonds. Here's a simple > In [4]: m.GetBondWithIdx(0).GetStereo() > Out[4]: rdkit.Chem.rdchem.BondStereo.STEREOE Thank you for comment. My input SMILES does not

[Rdkit-discuss] assign E/Z information to double bond and write to SMILES

Hello, Is there any way to assign information about double bond configuration (E or Z) and export the structure (with E/Z information) as a SMILES? I want to find the most stable E/Z-isomer for given SMILES and I wonder to know how much RDKit can help me. Regards, Rafal

[Rdkit-discuss] UFF Angle Bend force constant

Dear all, I try to reproduce UFF's Kijk (bend force constant). In source code in the file Code/ForceField/UF/AngleBend.cpp I found calcAngleForceConstant function. Equations in this function are the same as in UFF Paper (JACS from 1992), however results obtained from this function (equations)