Yeah, this is exactly the case where using qmol_from_ctab() should help.
Below is a short example demonstrating this by querying my local ChEMBL
instance. Notice that the first form of the query, which uses
mol_from_ctab() matches what you describe: the results include amides,
esters, etc. The second query, which uses qmol_from_ctab(), only returns
molecules which have a ketone.
I hope this helps,
-greg
chembl_28=# select * from rdk.mols where m@>mol_from_ctab('aldehyde query
MJ192500
4 3 0 0 0 0 0 0 0 0999 V2000
-2.8123 1.5508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5267 1.1383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.2412 1.5508 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.5267 0.3133 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
2 4 2 0 0 0 0
2 3 1 0 0 0 0
M END
') limit 5;
molregno | m
----------+----------------------------------------------------------------
310993 | O=C(NO)c1cc(CS(=O)(=O)c2ccc(Cl)cc2)on1
310992 | O=C(NO)c1cc(CS(=O)(=O)c2cccc(Cl)c2)on1
318822 | CCC(NC(=O)C[C@H](N)C(=O)N1CCC[C@H]1C#N)c1ccccc1
310016 | O=C(CCNC(=O)c1ccccc1)NC1CCN(Cc2ccc(Cl)cc2)C1
319381 | CCOC(=O)/C=C/c1ccc(CN(C(=O)C2CCCCC2)c2cccc(/C=C/C(=O)OC)c2)cc1
(5 rows)
chembl_28=# select * from rdk.mols where m@>qmol_from_ctab('aldehyde query
MJ192500
4 3 0 0 0 0 0 0 0 0999 V2000
-2.8123 1.5508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5267 1.1383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.2412 1.5508 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.5267 0.3133 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
2 4 2 0 0 0 0
2 3 1 0 0 0 0
M END
') limit 5;
molregno |
m
----------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
284772 | COC(=O)NC1[C@H](C)O[C@@H](O[C@H]2C/C=C(\C)[C@@H]3C=C[C@@H]4[C@
@H](O)[C@@H](C)C[C@H](C)[C@H]4[C@]3(C)/C(O)=C3\C(=O)O[C@]4(CC(C=O)=C[C@H
](OC(C)=O)[C@H]4/C=C\2C)C3=O)CC1(C)[N+](=O)[O-]
284633 | COC(=O)NC1[C@H](C)O[C@@H](O[C@H]2C/C=C(\C)[C@@H]3C=C[C@@H]4[C@
@H](O[C@H]5CCCCO5)[C@@H](C)C[C@H](C)[C@H]4[C@]3(C)/C(O)=C3\C(=O)O[C@
]4(CC(C=O)=C[C@H](OC(C)=O)[C@H]4/C=C\2C)C3=O)CC1(C)[N+](=O)[O-]
284865 | COC(=O)NC1[C@H](C)O[C@@H](O[C@H]2C/C=C(\C)[C@@H]3C=C[C@@H]4[C@
@H](OCc5ccc(OC)cc5)[C@@H](C)C[C@H](C)[C@H]4[C@]3(C)/C(O)=C3\C(=O)O[C@
]4(CC(C=O)=C[C@H](OC(C)=O)[C@H]4/C=C\2C)C3=O)CC1(C)[N+](=O)[O-]
299586 | CC1(C)C2CC[C@]3(C)C(CC=C4C5CC(C)(C)[C@@H](OC(=O)c6ccccc6)[C@H
](OC(=O)/C=C/c6ccccc6)[C@]5(C=O)[C@H](O)C[C@]43C)[C@@]2(C)CC[C@@H]1O
317613 | Cn1cncc1C=O
(5 rows)
On Tue, Jul 20, 2021 at 11:55 PM Webster Homer <
webster.ho...@milliporesigma.com> wrote:
> I should have included the query. It looks like RD Kit is ignoring the H
> atom
>
> The user put in an explicit H
>
> ===========MOL file after this
>
> aldehyde query
>
> MJ192500
>
>
>
> 4 3 0 0 0 0 0 0 0 0999 V2000
>
> -2.8123 1.5508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>
> -3.5267 1.1383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>
> -4.2412 1.5508 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
>
> -3.5267 0.3133 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>
> 2 1 1 0 0 0 0
>
> 2 4 2 0 0 0 0
>
> 2 3 1 0 0 0 0
>
> M END
>
> =================MOL file above this
>
>
>
>
>
> *From:* Greg Landrum <greg.land...@gmail.com>
> *Sent:* Friday, July 16, 2021 11:38 PM
> *To:* Webster Homer <webster.ho...@milliporesigma.com>
> *Cc:* rdkit-discuss@lists.sourceforge.net
> *Subject:* Re: [Rdkit-discuss] Substructure search for an aldehyde
> returns ketones and acids
>
>
>
> *[WARNING – EXTERNAL EMAIL]* Do not open links or attachments unless you
> recognize the sender of this email. If you are unsure please click the
> button "Report suspicious email"
>
>
>
> Hi Webster,
>
>
>
> Without seeing an actual query I am inclined to believe that it’s not a
> bug. The problem is more likely a query which has not been drawn explicitly
> or an easily made mistake in the way the cartridge is being used.
>
>
>
> Assuming that the aldehyde queries have been drawn with an explicit H atom
> connected to the C (apologies for not showing this, I’m on my phone and
> don’t have a sketcher available), you should be calling the cartridge
> function qmol_from_ctab(), not mol_from_ctab(), before doing the query.
> qmol_from_ctab() will use the H to help define the query.
>
>
>
> If you’re doing this and still seeing incorrect search results, please
> share a query and the way you’re doing the search and we can try to help
> (or diagnose the bug if there is one)
>
>
>
> Best,
>
> -greg
>
>
>
>
>
> On Fri, 16 Jul 2021 at 17:53, Webster Homer <
> webster.ho...@milliporesigma.com> wrote:
>
> We use RDKit Postgresql cartridge as our substructure searcher. When a
> user sketches an aldehyde and submits the mol fle as the query. RD Kit
> returns aldehydes, but also returns ketones and acids. Is this a bug?
>
>
>
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