Re: [Rdkit-discuss] Programatic access to the mol sanitation process results

2018-03-16 Thread Lukas Pravda 
That worker! Although I was too lazy to modify the actual class and used python 
package for that. If anyone would be interested the minimal code how not to 
mess the stderr while retaining the error message as a variable to work with, 
see below. It uses python streams and wurlitzer package 
https://github.com/minrk/wurlitzer

 

 

 

from rdkit import Chem

import io

from wurlitzer import pipes

 

mol = Chem.MolFromSmiles('CO(C)C', sanitize=False)

out_stream = io.BytesIO()

 

with pipes(stderr=out_stream):

    sanitization_result = Chem.SanitizeMol(mol, catchErrors=True)

    error_msg = out_stream.getvalue().decode('utf-8')

    print(error_msg)

 

 

Lukas 

 

From: Peter Gedeck <peter.ged...@gmail.com>
Date: Friday, 9 March 2018 at 15:02
To: Lukas Pravda <lpra...@ebi.ac.uk>
Cc: Greg Landrum <greg.land...@gmail.com>, <Rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Programatic access to the mol sanitation process 
results

 

Hello Lukas,

 

The file rdkit/TestRunner.py contains a class/context manager called 
OutputRedirectC. If I remember correctly, this allowed capturing these 
messages. It's not used anywhere in the RDkit code base, so it not work 
anymore. Anyway, give it a try and if it works, you can modify it to redirect 
the output into a variable or StringIO. 

 

Best,

 

Peter

 

 

On 9 Mar 2018, at 9:34 AM, Lukas Pravda <lpra...@ebi.ac.uk> wrote:

 

Hello Greg, 

 

I’m very sorry for the late reply. Thank you for the hint on disabling the log 
message, it works on my end. However, I was more interested in catching the 
other bit i.e. which part of the structure is wrong, rather than which part of 
the sanitization process failed. That is accessing the message ‘Explicit 
valence for atom # 1 O, 3, is greater than permitted’ in form to find out that 
it is the misbehaving oxygen which causes failure of the sanitization process. 
Perhaps piping the log information into a variable or something like that.

 

Best,

Lukas

 

 

 

From: Greg Landrum <greg.land...@gmail.com>
Date: Thursday, 22 February 2018 at 13:32
To: Lukas Pravda <lpra...@ebi.ac.uk>
Cc: RDKit Discuss <Rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Programatic access to the mol sanitation process 
results

 

Hi Lukas,

 

On Thu, Feb 22, 2018 at 1:14 PM, Lukas Pravda <lpra...@ebi.ac.uk> wrote:

Dear rdkiters,

 

I’m constructing molecules from scratch using python 3.5.4 and RDKit 2017.09.2 
and due to the variety of reasons some of them are violating general principles 
of chemistry in a way implemented in rdkit, so I’m getting information like:

 

Explicit valence for atom # 14 N, 4, is greater than permitted etc.

 

I wonder if there is a way how to retrieve this piece of information in a 
programmatic way. In order to work with it. Presently, rdkit only prints this 
out into terminal and Chem.SanitizeMol() only returns first sanitization flag 
with the issue. Ideally, I’d like no information to be printed into console, 
while keeping the log info ‘Explicit valence for atom # 14 N, 4, is greater 
than permitted’ preferably in a structured way (in a property/method?), in 
order to further deal with those erroneous cases.

 

At last part of this is pretty straightforward.

 

There are two parts: 

- making it so error messages don't go to the console 

- capturing the failed operation.

 

The first is a bit fragile (i.e. doesn't always work), so you will sometimes 
end up still seeing error messages (as here), but the second should be reliable:

 

In [30]: rdBase.DisableLog('rdApp.*')

 

In [31]: m = Chem.MolFromSmiles('c11',sanitize=False)

 

In [32]: Chem.SanitizeMol(m,catchErrors=True)

[14:29:37] Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 4

 

Out[32]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE

 

In [35]: 
Chem.SanitizeMol(Chem.MolFromSmiles('CO(C)C',sanitize=False),catchErrors=True)

[14:31:37] Explicit valence for atom # 1 O, 3, is greater than permitted

Out[35]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES

 

 

You can see that the return value indicates what went wrong in the sanitization.

 

I hope this helps,

-greg

 

 

 

 

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Re: [Rdkit-discuss] Programatic access to the mol sanitation process results

2018-03-09 Thread Peter Gedeck 
Hello Lukas,

The file rdkit/TestRunner.py contains a class/context manager called 
OutputRedirectC. If I remember correctly, this allowed capturing these 
messages. It's not used anywhere in the RDkit code base, so it not work 
anymore. Anyway, give it a try and if it works, you can modify it to redirect 
the output into a variable or StringIO. 

Best,

Peter


> On 9 Mar 2018, at 9:34 AM, Lukas Pravda <lpra...@ebi.ac.uk> wrote:
> 
> Hello Greg, 
>  
> I’m very sorry for the late reply. Thank you for the hint on disabling the 
> log message, it works on my end. However, I was more interested in catching 
> the other bit i.e. which part of the structure is wrong, rather than which 
> part of the sanitization process failed. That is accessing the message 
> ‘Explicit valence for atom # 1 O, 3, is greater than permitted’ in form to 
> find out that it is the misbehaving oxygen which causes failure of the 
> sanitization process. Perhaps piping the log information into a variable or 
> something like that.
>  
> Best,
> Lukas
>  
>  
>  
> From: Greg Landrum <greg.land...@gmail.com <mailto:greg.land...@gmail.com>>
> Date: Thursday, 22 February 2018 at 13:32
> To: Lukas Pravda <lpra...@ebi.ac.uk <mailto:lpra...@ebi.ac.uk>>
> Cc: RDKit Discuss <Rdkit-discuss@lists.sourceforge.net 
> <mailto:Rdkit-discuss@lists.sourceforge.net>>
> Subject: Re: [Rdkit-discuss] Programatic access to the mol sanitation process 
> results
>  
> Hi Lukas,
>  
> On Thu, Feb 22, 2018 at 1:14 PM, Lukas Pravda <lpra...@ebi.ac.uk 
> <mailto:lpra...@ebi.ac.uk>> wrote:
>> Dear rdkiters,
>>  
>> I’m constructing molecules from scratch using python 3.5.4 and RDKit 
>> 2017.09.2 and due to the variety of reasons some of them are violating 
>> general principles of chemistry in a way implemented in rdkit, so I’m 
>> getting information like:
>>  
>> Explicit valence for atom # 14 N, 4, is greater than permitted etc.
>>  
>> I wonder if there is a way how to retrieve this piece of information in a 
>> programmatic way. In order to work with it. Presently, rdkit only prints 
>> this out into terminal and Chem.SanitizeMol() only returns first 
>> sanitization flag with the issue. Ideally, I’d like no information to be 
>> printed into console, while keeping the log info ‘Explicit valence for atom 
>> # 14 N, 4, is greater than permitted’ preferably in a structured way (in a 
>> property/method?), in order to further deal with those erroneous cases.
>  
> At last part of this is pretty straightforward.
>  
> There are two parts: 
> - making it so error messages don't go to the console 
> - capturing the failed operation.
>  
> The first is a bit fragile (i.e. doesn't always work), so you will sometimes 
> end up still seeing error messages (as here), but the second should be 
> reliable:
>  
> In [30]: rdBase.DisableLog('rdApp.*')
>  
> In [31]: m = Chem.MolFromSmiles('c11',sanitize=False)
>  
> In [32]: Chem.SanitizeMol(m,catchErrors=True)
> [14:29:37] Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 4
>  
> Out[32]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE
>  
> In [35]: 
> Chem.SanitizeMol(Chem.MolFromSmiles('CO(C)C',sanitize=False),catchErrors=True)
> [14:31:37] Explicit valence for atom # 1 O, 3, is greater than permitted
> Out[35]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES
>  
>  
> You can see that the return value indicates what went wrong in the 
> sanitization.
>  
> I hope this helps,
> -greg
>  
>  
>  
>  
> --
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> engaging tech sites, Slashdot.org <http://slashdot.org/>! 
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Re: [Rdkit-discuss] Programatic access to the mol sanitation process results

2018-03-09 Thread Lukas Pravda 
Hello Greg, 

 

I’m very sorry for the late reply. Thank you for the hint on disabling the log 
message, it works on my end. However, I was more interested in catching the 
other bit i.e. which part of the structure is wrong, rather than which part of 
the sanitization process failed. That is accessing the message ‘Explicit 
valence for atom # 1 O, 3, is greater than permitted’ in form to find out that 
it is the misbehaving oxygen which causes failure of the sanitization process. 
Perhaps piping the log information into a variable or something like that.

 

Best,

Lukas

 

 

 

From: Greg Landrum <greg.land...@gmail.com>
Date: Thursday, 22 February 2018 at 13:32
To: Lukas Pravda <lpra...@ebi.ac.uk>
Cc: RDKit Discuss <Rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Programatic access to the mol sanitation process 
results

 

Hi Lukas,

 

On Thu, Feb 22, 2018 at 1:14 PM, Lukas Pravda <lpra...@ebi.ac.uk> wrote:

Dear rdkiters,

 

I’m constructing molecules from scratch using python 3.5.4 and RDKit 2017.09.2 
and due to the variety of reasons some of them are violating general principles 
of chemistry in a way implemented in rdkit, so I’m getting information like:

 

Explicit valence for atom # 14 N, 4, is greater than permitted etc.

 

I wonder if there is a way how to retrieve this piece of information in a 
programmatic way. In order to work with it. Presently, rdkit only prints this 
out into terminal and Chem.SanitizeMol() only returns first sanitization flag 
with the issue. Ideally, I’d like no information to be printed into console, 
while keeping the log info ‘Explicit valence for atom # 14 N, 4, is greater 
than permitted’ preferably in a structured way (in a property/method?), in 
order to further deal with those erroneous cases.

 

At last part of this is pretty straightforward.

 

There are two parts: 

- making it so error messages don't go to the console 

- capturing the failed operation.

 

The first is a bit fragile (i.e. doesn't always work), so you will sometimes 
end up still seeing error messages (as here), but the second should be reliable:

 

In [30]: rdBase.DisableLog('rdApp.*')

 

In [31]: m = Chem.MolFromSmiles('c11',sanitize=False)

 

In [32]: Chem.SanitizeMol(m,catchErrors=True)

[14:29:37] Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 4

 

Out[32]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE

 

In [35]: 
Chem.SanitizeMol(Chem.MolFromSmiles('CO(C)C',sanitize=False),catchErrors=True)

[14:31:37] Explicit valence for atom # 1 O, 3, is greater than permitted

Out[35]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES

 

 

You can see that the return value indicates what went wrong in the sanitization.

 

I hope this helps,

-greg

 

 

 

 

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Re: [Rdkit-discuss] Programatic access to the mol sanitation process results

2018-02-22 Thread Greg Landrum 
Hi Lukas,

On Thu, Feb 22, 2018 at 1:14 PM, Lukas Pravda  wrote:

> Dear rdkiters,
>
>
>
> I’m constructing molecules from scratch using python 3.5.4 and RDKit
> 2017.09.2 and due to the variety of reasons some of them are violating
> general principles of chemistry in a way implemented in rdkit, so I’m
> getting information like:
>
>
>
> Explicit valence for atom # 14 N, 4, is greater than permitted etc.
>
>
>
> I wonder if there is a way how to retrieve this piece of information in a
> programmatic way. In order to work with it. Presently, rdkit only prints
> this out into terminal and Chem.SanitizeMol() only returns first
> sanitization flag with the issue. Ideally, I’d like no information to be
> printed into console, while keeping the log info ‘Explicit valence for atom
> # 14 N, 4, is greater than permitted’ preferably in a structured way (in a
> property/method?), in order to further deal with those erroneous cases.
>
>
At last part of this is pretty straightforward.

There are two parts:
- making it so error messages don't go to the console
- capturing the failed operation.

The first is a bit fragile (i.e. doesn't always work), so you will
sometimes end up still seeing error messages (as here), but the second
should be reliable:

In [30]: rdBase.DisableLog('rdApp.*')

In [31]: m = Chem.MolFromSmiles('c11',sanitize=False)

In [32]: Chem.SanitizeMol(m,catchErrors=True)
[14:29:37] Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 4

Out[32]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE

In [35]:
Chem.SanitizeMol(Chem.MolFromSmiles('CO(C)C',sanitize=False),catchErrors=True)
[14:31:37] Explicit valence for atom # 1 O, 3, is greater than permitted
Out[35]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES


You can see that the return value indicates what went wrong in the
sanitization.

I hope this helps,
-greg
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