[Rdkit-discuss] Use custom tautomer rules in Rdkit

Hi all, I've been using TautomerEnumerator recently. I'm wondering whether it is possible to use custom tautomer rules in RdKit. For example, the SMIRKS rules listed in *J. Chem. Inf. Model.* 2020, 60, 3, 1253–1275. Thanks, Best Regards, Changge Ji ___

[Rdkit-discuss] Valance Error on Aromatic N atoms.

Dear all, I met a problem with Aromatic N atoms. Here is the code: sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@ [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[#7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:[#6]:[#6]:[#6]:[#6]

Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

there any particular reason that you're calling updatePropertyCache on > the molecule? That's not an operation that's normally necessary. > > Best, > -greg > > > > On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji wrote: > >> Dear all, >> &

Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

for. Query-Query matching is different than Query-Atom matching. > > It's more common to look for ph4 features in molecules constructed from > SMILES or from a mol file. Is there a particular reason that you need to > use SMARTS? > > -greg > > > On Tue, Jul 11, 2017

Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

> > -greg > > > On Tue, Jul 11, 2017 at 1:41 PM, Greg Landrum > wrote: > >> Interesting use case. >> >> I can send some sample code for this later this afternoon. >> >> >> On Tue, Jul 11, 2017 at 11:43 AM, Chicago Ji >> wrote: >> >

Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

R: RDKit ERROR: RDKit ERROR: [16:07:15] Can't kekulize mol. Unkekulized atoms: 4 5 6 7 8 9 RDKit ERROR: --- On Wed, Jul 12, 2017 at 2:27 PM, Greg Landrum wrote: > > > On Tue, Jul 11, 2017 at 6:53 PM, Chicago Ji wrote: > >> Thanks a lot for you

[Rdkit-discuss] read sdf file without removing hydrogen atoms.

Dear RDkit Users, Rdkit would delete all hydrogen atoms when read in a sdf file. Since I want to use charge information of all atoms in sdf file, I want to keep all hydrogen atoms when readin. Is there something like Chem.SmilesParserParams() for sdfsupplier ? Many thanks for your help. Best, C

Re: [Rdkit-discuss] Compiling RDKit for Python 3.5

Dear Greg and RDKitters , I try to follow your instruction to install python3-rdkit on my laptop (Ubuntu 16.04). But I got the following error information: "../../../lib/libRDKitFilterCatalog.so.1.2018.09.1dev1: undefined reference to `boost::archive::text_iarchive_impl::load_override(boost::

[Rdkit-discuss] NDonor Smarts in BaseFeatures.fdef

Dear rdkit users, I'm trying to use rdkit to calculate pharmacophore patterns in molecules. I found that the code recognizes methylamide's N atom as a donor. For example, the N atom in CCN(C)C(=O)CC. I don't think this N atom can act as a hydrogen bond donor. This N atom can match the following

[Rdkit-discuss] How does rdkit cartridge work?

Hello, everyone. I find that rdkit cartridge is quite efficient in substructure searching. Is there any paper or similar paper that describes things behind rdkit cartridge? For example, what kind of substructures were indexed? Is there a way that the users can add custom defined fingerprints and