Re: [Rdkit-discuss] Can't stifle warnings / logs

[Andrew Dalke]

Hi Cameron,

  While you are waiting for an answer about the proper way to silence errors, I 
can give you a work-around which will help with the metaphorical reams of 
teletype paper you are printing out.

However, it is a very crude solution. Basically, close the C/C++ stderr file 
descriptor, and tell Python to route its error messages to a new stderr.

# Copy the stderr descriptor
new_fd = os.dup(2)
# Close the original stderr
os.close(2)
# Tell Python about the new stderr
sys.__stderr__ = sys.stderr = os.fdopen(new_fd, "w", 0)


Here it is in context:

import os
import sys
from rdkit import Chem

print("Error?")
Chem.MolFromSmiles("Q") # error message

# Copy the stderr descriptor
new_fd = os.dup(2)
# Close the original stderr
os.close(2)
# Tell Python about the new stderr
sys.__stderr__ = sys.stderr = os.fdopen(new_fd, "w", 0)

print("Error again?")
Chem.MolFromSmiles("Q")  # No warning or error message.

This assumes that neither RDKit nor some other code at the C level write 
directly to file descriptor 2 assuming it's stderr. Otherwise there's a problem 
if you ever open up a new file and it's assigned fd 2. If you *really* want to 
be sure that C/C++ code doesn't write to stderr, and the above doesn't work, 
and you are on a Unix-like system, then add the following after the 
"sys.__stderr__ = .." line:

# Reroute the original descriptor number 2 to /dev/null
fd2 = os.open("/dev/null", os.O_WRONLY)
if fd2 != 2:
raise SystemExit("Unable to reroute file descriptor 2: %d\n" % (fd2,))


Andrew
da...@dalkescientific.com



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[Rdkit-discuss] Can't stifle warnings / logs

[Cameron Pye]

Hi There,

I'm a longtime rdkit user but a first time mailing list user.

One thing that has always haunted me is the warnings and errors that get
thrown whilst reading in a dirty sd file or smiles list. I've tried to no
avail to silence the warnings and errors many times and normally just live
with the endless scroll on my terminal but today I've finally had enough.

Any help would be appreciated!!

I've tried wrapping a ForwardSDMolSupplier with the following :

from io import StringIO
import sys
Chem.WrapLogs()

def silent_supplier(supplier):
sio = sys.stderr = StringIO()
for m in supplier:
sio = sys.stderr = StringIO()
if m is None:
continue
else:
yield m

but still get a stream of these sorts of errors:
[11:39:24]  S group DAT ignored on line 143364
[11:39:24] Can't kekulize mol.  Unkekulized atoms: 5 6 7 8 9 10 11 13 14

[11:39:24] ERROR: Could not sanitize molecule ending on line 143370
[11:39:24] ERROR: Can't kekulize mol.  Unkekulized atoms: 5 6 7 8 9 10 11
13 14

[11:39:24]  S group DAT ignored on line 145111
[11:39:24] Can't kekulize mol.  Unkekulized atoms: 3 4 5 6 26

[11:39:24] ERROR: Could not sanitize molecule ending on line 145117
[11:39:24] ERROR: Can't kekulize mol.  Unkekulized atoms: 3 4 5 6 26

[11:39:24]  S group DAT ignored on line 159380
[11:39:24] Can't kekulize mol.  Unkekulized atoms: 5 6 7 8 9 10 11 12 13

[11:39:24] ERROR: Could not sanitize molecule ending on line 159386
[11:39:24] ERROR: Can't kekulize mol.  Unkekulized atoms: 5 6 7 8 9 10 11
12 13
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Re: [Rdkit-discuss] mmpdb installation on windows using mingw

[Kramer, Christian]

Hi Markus,

thanks for pointing this out. The reason for that error message is that
signal.SIGPIPE is not available under windows. This seems to have slipped
below our radar, since we developed the code on Linux.

There is a simple solution to this: In the mmpdb file, one needs to
import os

and then change the error-causing line to:
if not os.name=="nt": signal.signal(signal.SIGPIPE, signal.SIG_DFL)

That solves the problem on my window laptop.

I will add this and update mmpdb in the repo asap.

Bests,
Christian


*Dr. Christian Kramer*

Computer-Aided Drug Design (CADD) Scientist


F. Hoffmann-La Roche Ltd

Pharma Research and Early Development
Bldg. 092/3.56 C

CH-4070 Basel


Phone +41 61 682 2471

mailto: christian.kra...@roche.com


*Confidentiality Note: *This message is intended only for the use of the
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contained in this message is prohibited.

On Fri, Sep 22, 2017 at 2:01 PM, Peter Gedeck 
wrote:

> Here is a relevant stackoverflow question.
>
> https://stackoverflow.com/questions/1948862/is-the-
> python-3-x-signal-library-for-windows-incomplete
>
> What happens if you comment out the code if you run on windows?
>
> Best
>
> Peter
> On Fri, Sep 22, 2017 at 7:25 AM Markus Metz  wrote:
>
>> Hello Christian:
>>
>> I am trying to install your program and get the following error message:
>>
>> $ mmpdb help-analysis
>> Traceback (most recent call last):
>>   File "C:/Users/---/Anaconda3/envs/my-rdkit-env/Scripts/mmpdb", line 8,
>> in 
>> signal.signal(signal.SIGPIPE, signal.SIG_DFL) # Allow the output pipe
>> to be closed
>> AttributeError: module 'signal' has no attribute 'SIGPIPE'
>>
>> Not sure what to do about it. Any input would be greatly appreciated.
>>
>> Cheers,
>> Markus
>>
>> 
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>
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Re: [Rdkit-discuss] mmpdb installation on windows using mingw

[Peter Gedeck]

Here is a relevant stackoverflow question.

https://stackoverflow.com/questions/1948862/is-the-python-3-x-signal-library-for-windows-incomplete

What happens if you comment out the code if you run on windows?

Best

Peter
On Fri, Sep 22, 2017 at 7:25 AM Markus Metz  wrote:

> Hello Christian:
>
> I am trying to install your program and get the following error message:
>
> $ mmpdb help-analysis
> Traceback (most recent call last):
>   File "C:/Users/---/Anaconda3/envs/my-rdkit-env/Scripts/mmpdb", line 8,
> in 
> signal.signal(signal.SIGPIPE, signal.SIG_DFL) # Allow the output pipe
> to be closed
> AttributeError: module 'signal' has no attribute 'SIGPIPE'
>
> Not sure what to do about it. Any input would be greatly appreciated.
>
> Cheers,
> Markus
>
>
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[Rdkit-discuss] mmpdb installation on windows using mingw

[Markus Metz]

Hello Christian:

I am trying to install your program and get the following error message:

$ mmpdb help-analysis
Traceback (most recent call last):
  File "C:/Users/---/Anaconda3/envs/my-rdkit-env/Scripts/mmpdb", line 8, in

signal.signal(signal.SIGPIPE, signal.SIG_DFL) # Allow the output pipe
to be closed
AttributeError: module 'signal' has no attribute 'SIGPIPE'

Not sure what to do about it. Any input would be greatly appreciated.

Cheers,
Markus
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