Re: [Rdkit-discuss] problem with substructure matching using SMARTS
Dear Greg,
Thanks a lot! This solves my problem.
Best wishes,
Michal
On 18 November 2013 10:27, Greg Landrum wrote:
> Dear Michal,
>
> On Mon, Nov 18, 2013 at 10:55 AM, Michal Krompiec
> wrote:
>>
>> 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]')
>> p2=Chem.MolFromSmarts('c2sccc2[H,F]')
>> print(mol.HasSubstructMatch(p1))
>> print(mol.HasSubstructMatch(p2))
>
>
> The problem is that an "H" in SMARTS normally doesn't mean what you think it
> does.
>
> You can see what's going on using MolToSmarts:
print(Chem.MolToSmarts(p1))
> c1:,-s:,-c:,-c:,-c:,-1-,:[#1]
print(Chem.MolToSmarts(p2))
> c1:,-s:,-c:,-c:,-c:,-1-,:[H1,F]
>
> In the second case, the H has been converted into a query for an atom that
> has exactly one H attached. The only time that the symbol "H" in a query is
> interpreted as "an atom with atomic number 1" is when it shows up as "[H]",
> as in your first example.
>
> The safest way to deal with H in SMARTS is to use [#1]:
p1=Chem.MolFromSmarts('c2sccc2[#1]')
p2=Chem.MolFromSmarts('c2sccc2[#1,F]')
print(mol.HasSubstructMatch(p1))
> True
print(mol.HasSubstructMatch(p2))
> True
>
> This is confusing, but it corresponds (at least I think it does) to the
> "spec" from Daylight:
> http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
>
> -greg
>
>
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Re: [Rdkit-discuss] problem with substructure matching using SMARTS
Dear Michal,
On Mon, Nov 18, 2013 at 10:55 AM, Michal Krompiec wrote:
> 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]')
> p2=Chem.MolFromSmarts('c2sccc2[H,F]')
> print(mol.HasSubstructMatch(p1))
> print(mol.HasSubstructMatch(p2))
>
The problem is that an "H" in SMARTS normally doesn't mean what you think
it does.
You can see what's going on using MolToSmarts:
>>> print(Chem.MolToSmarts(p1))
c1:,-s:,-c:,-c:,-c:,-1-,:[#1]
>>> print(Chem.MolToSmarts(p2))
c1:,-s:,-c:,-c:,-c:,-1-,:[H1,F]
In the second case, the H has been converted into a query for an atom that
has exactly one H attached. The only time that the symbol "H" in a query is
interpreted as "an atom with atomic number 1" is when it shows up as "[H]",
as in your first example.
The safest way to deal with H in SMARTS is to use [#1]:
>>> p1=Chem.MolFromSmarts('c2sccc2[#1]')
>>> p2=Chem.MolFromSmarts('c2sccc2[#1,F]')
>>> print(mol.HasSubstructMatch(p1))
True
>>> print(mol.HasSubstructMatch(p2))
True
This is confusing, but it corresponds (at least I think it does) to the
"spec" from Daylight:
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
-greg
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[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]')
p2=Chem.MolFromSmarts('c2sccc2[H,F]')
print(mol.HasSubstructMatch(p1))
print(mol.HasSubstructMatch(p2))
Best wishes,
Michal
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