Re: [Rdkit-discuss] HasSubstructureMatch using query atom list with hydrogen

2022-07-22 Thread Paolo Tosco 
Hi Susan,

adding explicit hydrogens is an expensive operation that you normally try
to avoid unless you have to (e.g., because you need to deal with 3D
molecule coordinates).
I would rather change the query in order to use implicit H queries, e.g.
something like:

q = Chem.MolFromSmarts('[$([#6;H0](-[#17])-[#17]),$([#6;H1]-[#17])]')
m = Chem.MolFromSmiles('ClC(C)(C)Cl')
print(m.HasSubstructMatch(q))
True

m = Chem.MolFromSmiles('CC(C)(C)Cl')
print(m.HasSubstructMatch(q))
False

m = Chem.MolFromSmiles('CC(C)Cl')
print(m.HasSubstructMatch(q))
True

Cheers,
p.

On Fri, Jul 22, 2022 at 12:58 PM Susan Leung  wrote:

> Sorry I replied too soon, just another quick question.
>
> I am trying to use the postgres cartridge. Is there any function to add
> hydrogens to the molecules once in the database? Or should this be done as
> a preprocessing step beforehand? E.g. I have a .smi or .sdf should all the
> molecules already have explicit hydrogens?
>
> Thanks,
>
> Susan
>
> On Fri, Jul 22, 2022 at 11:51 AM Susan Leung 
> wrote:
>
>> Ah, great thanks Paolo!
>>
>> On Fri, Jul 22, 2022 at 11:44 AM Paolo Tosco 
>> wrote:
>>
>>> Hi Susan,
>>>
>>> If you use [#1] in your SMARTS query, for your molecule to match there
>>> should be a real hydrogen atom in your molecule graph, while in your
>>> molecule you only have implicit hydrogens, unless you explicitly add them
>>> calling Chem.AddHs():
>>>
>>> print(Chem.AddHs(m).HasSubstructMatch(q))
>>> True
>>>
>>> Cheers,
>>> p.
>>>
>>> On Fri, Jul 22, 2022 at 12:13 PM Susan Leung 
>>> wrote:
>>>
 Hi all,



 I am trying to do substructure search using query atom lists, but I am
 seeing unexpected behaviour when I have hydrogen in my query atom list…



 import rdkit

 print(rdkit.__version__)

 from rdkit import Chem



 >>2022.03.2



 ## having carbon in the query atom list seems to work as expected

 q = Chem.MolFromSmarts('[#17,#6]-[#6]-[#17]')

 m = Chem.MolFromSmiles('ClCCl')

 print(m.HasSubstructMatch(q))

 m = Chem.MolFromSmiles('CCCl')

 print(m.HasSubstructMatch(q))



 >>True

 >>True



 ## having hydrogen in the query atom list doesn't work as expected

 q = Chem.MolFromSmarts('[#17,#1]-[#6]-[#17]')

 m = Chem.MolFromSmiles('ClCCl')

 print(m.HasSubstructMatch(q))

 m = Chem.MolFromSmiles('CCl')

 print(m.HasSubstructMatch(q))



 >>True
 >>False



 Best wishes,



 Susan
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Re: [Rdkit-discuss] HasSubstructureMatch using query atom list with hydrogen

2022-07-22 Thread Susan Leung 
Sorry I replied too soon, just another quick question.

I am trying to use the postgres cartridge. Is there any function to add
hydrogens to the molecules once in the database? Or should this be done as
a preprocessing step beforehand? E.g. I have a .smi or .sdf should all the
molecules already have explicit hydrogens?

Thanks,

Susan

On Fri, Jul 22, 2022 at 11:51 AM Susan Leung  wrote:

> Ah, great thanks Paolo!
>
> On Fri, Jul 22, 2022 at 11:44 AM Paolo Tosco 
> wrote:
>
>> Hi Susan,
>>
>> If you use [#1] in your SMARTS query, for your molecule to match there
>> should be a real hydrogen atom in your molecule graph, while in your
>> molecule you only have implicit hydrogens, unless you explicitly add them
>> calling Chem.AddHs():
>>
>> print(Chem.AddHs(m).HasSubstructMatch(q))
>> True
>>
>> Cheers,
>> p.
>>
>> On Fri, Jul 22, 2022 at 12:13 PM Susan Leung 
>> wrote:
>>
>>> Hi all,
>>>
>>>
>>>
>>> I am trying to do substructure search using query atom lists, but I am
>>> seeing unexpected behaviour when I have hydrogen in my query atom list…
>>>
>>>
>>>
>>> import rdkit
>>>
>>> print(rdkit.__version__)
>>>
>>> from rdkit import Chem
>>>
>>>
>>>
>>> >>2022.03.2
>>>
>>>
>>>
>>> ## having carbon in the query atom list seems to work as expected
>>>
>>> q = Chem.MolFromSmarts('[#17,#6]-[#6]-[#17]')
>>>
>>> m = Chem.MolFromSmiles('ClCCl')
>>>
>>> print(m.HasSubstructMatch(q))
>>>
>>> m = Chem.MolFromSmiles('CCCl')
>>>
>>> print(m.HasSubstructMatch(q))
>>>
>>>
>>>
>>> >>True
>>>
>>> >>True
>>>
>>>
>>>
>>> ## having hydrogen in the query atom list doesn't work as expected
>>>
>>> q = Chem.MolFromSmarts('[#17,#1]-[#6]-[#17]')
>>>
>>> m = Chem.MolFromSmiles('ClCCl')
>>>
>>> print(m.HasSubstructMatch(q))
>>>
>>> m = Chem.MolFromSmiles('CCl')
>>>
>>> print(m.HasSubstructMatch(q))
>>>
>>>
>>>
>>> >>True
>>> >>False
>>>
>>>
>>>
>>> Best wishes,
>>>
>>>
>>>
>>> Susan
>>> ___
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>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
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Re: [Rdkit-discuss] HasSubstructureMatch using query atom list with hydrogen

2022-07-22 Thread Susan Leung 
Ah, great thanks Paolo!

On Fri, Jul 22, 2022 at 11:44 AM Paolo Tosco 
wrote:

> Hi Susan,
>
> If you use [#1] in your SMARTS query, for your molecule to match there
> should be a real hydrogen atom in your molecule graph, while in your
> molecule you only have implicit hydrogens, unless you explicitly add them
> calling Chem.AddHs():
>
> print(Chem.AddHs(m).HasSubstructMatch(q))
> True
>
> Cheers,
> p.
>
> On Fri, Jul 22, 2022 at 12:13 PM Susan Leung 
> wrote:
>
>> Hi all,
>>
>>
>>
>> I am trying to do substructure search using query atom lists, but I am
>> seeing unexpected behaviour when I have hydrogen in my query atom list…
>>
>>
>>
>> import rdkit
>>
>> print(rdkit.__version__)
>>
>> from rdkit import Chem
>>
>>
>>
>> >>2022.03.2
>>
>>
>>
>> ## having carbon in the query atom list seems to work as expected
>>
>> q = Chem.MolFromSmarts('[#17,#6]-[#6]-[#17]')
>>
>> m = Chem.MolFromSmiles('ClCCl')
>>
>> print(m.HasSubstructMatch(q))
>>
>> m = Chem.MolFromSmiles('CCCl')
>>
>> print(m.HasSubstructMatch(q))
>>
>>
>>
>> >>True
>>
>> >>True
>>
>>
>>
>> ## having hydrogen in the query atom list doesn't work as expected
>>
>> q = Chem.MolFromSmarts('[#17,#1]-[#6]-[#17]')
>>
>> m = Chem.MolFromSmiles('ClCCl')
>>
>> print(m.HasSubstructMatch(q))
>>
>> m = Chem.MolFromSmiles('CCl')
>>
>> print(m.HasSubstructMatch(q))
>>
>>
>>
>> >>True
>> >>False
>>
>>
>>
>> Best wishes,
>>
>>
>>
>> Susan
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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Re: [Rdkit-discuss] HasSubstructureMatch using query atom list with hydrogen

2022-07-22 Thread Paolo Tosco 
Hi Susan,

If you use [#1] in your SMARTS query, for your molecule to match there
should be a real hydrogen atom in your molecule graph, while in your
molecule you only have implicit hydrogens, unless you explicitly add them
calling Chem.AddHs():

print(Chem.AddHs(m).HasSubstructMatch(q))
True

Cheers,
p.

On Fri, Jul 22, 2022 at 12:13 PM Susan Leung  wrote:

> Hi all,
>
>
>
> I am trying to do substructure search using query atom lists, but I am
> seeing unexpected behaviour when I have hydrogen in my query atom list…
>
>
>
> import rdkit
>
> print(rdkit.__version__)
>
> from rdkit import Chem
>
>
>
> >>2022.03.2
>
>
>
> ## having carbon in the query atom list seems to work as expected
>
> q = Chem.MolFromSmarts('[#17,#6]-[#6]-[#17]')
>
> m = Chem.MolFromSmiles('ClCCl')
>
> print(m.HasSubstructMatch(q))
>
> m = Chem.MolFromSmiles('CCCl')
>
> print(m.HasSubstructMatch(q))
>
>
>
> >>True
>
> >>True
>
>
>
> ## having hydrogen in the query atom list doesn't work as expected
>
> q = Chem.MolFromSmarts('[#17,#1]-[#6]-[#17]')
>
> m = Chem.MolFromSmiles('ClCCl')
>
> print(m.HasSubstructMatch(q))
>
> m = Chem.MolFromSmiles('CCl')
>
> print(m.HasSubstructMatch(q))
>
>
>
> >>True
> >>False
>
>
>
> Best wishes,
>
>
>
> Susan
> ___
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[Rdkit-discuss] HasSubstructureMatch using query atom list with hydrogen

2022-07-22 Thread Susan Leung 
Hi all,



I am trying to do substructure search using query atom lists, but I am
seeing unexpected behaviour when I have hydrogen in my query atom list…



import rdkit

print(rdkit.__version__)

from rdkit import Chem



>>2022.03.2



## having carbon in the query atom list seems to work as expected

q = Chem.MolFromSmarts('[#17,#6]-[#6]-[#17]')

m = Chem.MolFromSmiles('ClCCl')

print(m.HasSubstructMatch(q))

m = Chem.MolFromSmiles('CCCl')

print(m.HasSubstructMatch(q))



>>True

>>True



## having hydrogen in the query atom list doesn't work as expected

q = Chem.MolFromSmarts('[#17,#1]-[#6]-[#17]')

m = Chem.MolFromSmiles('ClCCl')

print(m.HasSubstructMatch(q))

m = Chem.MolFromSmiles('CCl')

print(m.HasSubstructMatch(q))



>>True
>>False



Best wishes,



Susan
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