rdkit-discuss

[Rdkit-discuss] Suppress stdout and stderr in rdkit

[Gaetano C. <gca...@uc...>]

Hi there,

I wonder if there is an easy way to suppress the standard output and standard error from RDkit. For example:

from rdkit import Chem

smart = '[#6]1(:[#6]:[#6]:[#6]2:[#6](:[#6]:1):[#6]:[#6]:[#6]:[#6]:2)-[#8,#6]'

mol = Chem.MolFromSmarts(smart)

Chem.SanitizeMol(mol)

This will produce the warning message:

[15:52:25] Explicit valence for atom # 3 C, 5, is greater than permitted

I would like to suppress this message. Is there any way to do it?

Thanks,

Gaetano

Re: [Rdkit-discuss] Suppress stdout and stderr in rdkit

[Paolo T. <pao...@un...>]

Dear Gaetano,

you may try the following:

from rdkit import rdBase
rdBase.DisableLog('rdApp.error')

You may check the logging levels you wish to disable/enable in 
rdkit/RDLogger.py, or use a wildcard such as 'rdApp.*' to affect all 
levels at once.

Best,
Paolo

On 17/02/2016 23:54, Gaetano Calabro wrote:
> from rdkit import Chem
>
> smart = '[#6]1(:[#6]:[#6]:[#6]2:[#6](:[#6]:1):[#6]:[#6]:[#6]:[#6]:2)-[#8,#6]'
>
> mol = Chem.MolFromSmarts(smart)
>
> Chem.SanitizeMol(mol)

Re: [Rdkit-discuss] Suppress stdout and stderr in rdkit

[Gaetano C. <gca...@uc...>]

Hi Paolo,

Thanks a lot for your prompt reply. I ended up coding this:

from rdkit import Chem
from rdkit import RDLogger

smart = 
'[#6]1(:[#6]:[#6]:[#6]2:[#6](:[#6]:1):[#6]:[#6]:[#6]:[#6]:2)-[#8,#6]'

mol = Chem.MolFromSmarts(smart)

lg = RDLogger.logger()

lg.setLevel(RDLogger.CRITICAL)

try:
     Chem.SanitizeMol(mol)
except:
     print 'OK'


Ciao,

Gaetano


On 02/18/2016 01:09 AM, Paolo Tosco wrote:
> Dear Gaetano,
>
> you may try the following:
>
> from rdkit import rdBase
> rdBase.DisableLog('rdApp.error')
>
> You may check the logging levels you wish to disable/enable in 
> rdkit/RDLogger.py, or use a wildcard such as 'rdApp.*' to affect all 
> levels at once.
>
> Best,
> Paolo
>
> On 17/02/2016 23:54, Gaetano Calabro wrote:
>> from rdkit import Chem
>>
>> smart = 
>> '[#6]1(:[#6]:[#6]:[#6]2:[#6](:[#6]:1):[#6]:[#6]:[#6]:[#6]:2)-[#8,#6]'
>>
>> mol = Chem.MolFromSmarts(smart)
>>
>> Chem.SanitizeMol(mol)
>