Ahh! Thank you so much, to both of you.
Yes, the different meaning of H in the various contexts was tripping me up.
Also, DescribeQuery() was definitely a function that I needed for debugging
this solo. Thank you. I will keep that in mind in the future.
I found that this smiles (S4) is exactly what I
needed: '[C,c]1(Cl)[C,c][C,c]([N,n,C,c,#1])[C,c]([C,c])[C,c]([#1])[C,c]1'.
Cheers,
Adam
On Tue, Mar 1, 2022 at 4:32 AM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:
> A minor correction: [H] by itself *is* valid and means a hydrogen atom.
> The Daylight docs say as much in section 4.1. But in other contexts it
> means a hydrogen count, so to be safe, always using #1 to mean a hydrogen
> atom can be a good practice.
>
> If you are ever in doubt about how RDKit is interpreting a SMARTS,
> I recommend making use of the DescribeQuery function which provides a tree
> representation of a query atom or bond. For example (comments added):
>
> >>> mol = Chem.MolFromSmarts('[H][N,H][N,#1]')
>
>
> >>> print(mol.GetAtomWithIdx(0).DescribeQuery()) # [H]
>
> AtomAtomicNum 1 = val # [H] interpreted as a hydrogen atom
>
> >>> print(mol.GetAtomWithIdx(1).DescribeQuery()) # [N,H]
>
> AtomOr
> AtomType 7 = val
> AtomHCount 1 = val # H interpreted as a hydrogen count
> # Overall query atom means "an aliphatic nitrogen OR (any atom with one
> hydrogen)!
>
> >>> print(mol.GetAtomWithIdx(2).DescribeQuery()) # [N,#1]
>
> AtomOr
> AtomType 7 = val
> AtomAtomicNum 1 = val # "#1" is atomic number, therefore a hydrogen
> atom.
> # Overall query atom means "an aliphatic nitrogen OR a hydrogen"
>
> One non-obvious convention in the DescribeQuery output is that AtomType
> implies aliphatic when the value is a normal atomic number, or aromatic if
> the atomic number is offset by 1000. For example, [n] is "AtomType 1007".
>
> Hope you find this approach useful in the future.
>
> Ivan
>
> On Tue, Mar 1, 2022 at 6:33 AM David Cosgrove <davidacosgrov...@gmail.com>
> wrote:
>
>> Hi Adam
>> There are a number of issues here. The key one, I think, is a
>> misunderstanding about the meaning of H in SMARTS. It means "a single
>> attached hydrogen", and is a qualifier for another atom, it cannot be used
>> by itself. So [*H] is valid, [H] isn't. See the table at
>> https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html. If you
>> want to refer to an explicit hydrogen, you have to use [#1]. However, that
>> will only match an explicit hydrogen in the molecule, not an implicit one.
>> Thus c[#1] doesn't match anything in c1ccccc1. If you have read in a
>> molecule from a molfile, for example, that has explicit hydrogens then you
>> will be ok.
>>
>> Further to that, your SMARTS strings, at least as they have appeared in
>> gmail, which may have garbled them, are incorrect. In S1, the brackets
>> round [N,n,H] make it a substituent, so it will not match the indole
>> nitrogen. Also, it would probably be better as [N,n;H], which would be
>> read as "(aliphatic nitrogen OR aromatic nitrogen) AND 1 attached
>> hydrogen." The [N,n,H] will match a methylated indole nitrogen which I
>> imagine is not what you want. Similar remarks apply to S2. A SMARTS that
>> matches both 6CI and PCT
>> is [C,c]1(Cl)[C,c][C,c;H][C,c]([C,c])[C,c;H][C,c]1, but that won't match
>> the H atoms themselves if you want to use them in the overlay, and it also
>> won't work in the aliphatic case of, for example, ClC1CCC(C)CC1 because
>> there the carbon atoms have 2 attached hydrogens. If you really do want
>> it to match aliphatic cases as well, then you will need something
>> like
>> [C,c]1(Cl)[$([CH2]),$([cH])][$([CH2]),$([cH])][C,c]([C,c])[$([CH2]),$([cH])][$([CH2]),$([cH])]1
>> which is quite a mouthful. The carbons at the 2,3,5 and 6 positions on the
>> ring are specified as either [CH2] or [cH].
>>
>> Jupyter notebook can be really useful for debugging SMARTS patterns like
>> this. The one I used was variations of
>> ```
>> from rdkit import Chem
>> from IPython.display import SVG
>> mol = Chem.MolFromSmiles('C1=CC(=CC2=C1C=CN2C)Cl')
>> qmol = Chem.MolFromSmarts('[C,c]1(Cl)[C,c][C,c][C,c]([C,c])[C,c][C,c]1')
>> print(mol.GetSubstructMatches(qmol))
>> mol
>> ```
>> which prints the numbers of the matching atoms and also draws the
>> molecule with the match highlighted.
>> Regards,
>> Dave
>>
>>
>> On Tue, Mar 1, 2022 at 1:43 AM Adam Moyer <atom.mo...@gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I have a baffling case where I am trying to match substructures on two
>>> ligands for the goal of aligning them.
>>>
>>> I have two ligands; one is a 6-chloroindole (6CI) and the other is a
>>> para-chloro toluene (PCT).
>>>
>>> I am attempting to use the following SMARTS (S1) to match
>>> them: '[C,c]1(Cl)[C,c][C,c]*([N,n,H])*[C,c]([C,c,H])[C,c]([H])[C,c]1'.
>>> For some reason S1 only finds a match in 6CI.
>>>
>>> When I use the following SMARTS (S2) I only match to PCT as expected:
>>> '[C,c]1(Cl)[C,c][C,c]*([H])*[C,c]([C,c,H])[C,c]([H])[C,c]1'.
>>>
>>> How can S1 not match PCT? S1 is strictly a superset of S2 because I am
>>> using the "or" operation. Do I have a misunderstanding of how explicit
>>> hydrogens work in RDKit/SMARTS?
>>>
>>> Lastly when I use the last SMARTS (S3) I am able to match to both, but I
>>> cannot use that smarts due to other requirements in my
>>> project: '[C,c]1(Cl)[C,c][C,c][C,c]([C,c,H])[C,c]([H])[C,c]1'
>>>
>>> Thanks!
>>> Adam
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
>>
>> --
>> David Cosgrove
>> Freelance computational chemistry and chemoinformatics developer
>> http://cozchemix.co.uk
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
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>>
>
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