Re: [Rdkit-discuss] Bug with Calculation of aromatic rings?

[Greg Landrum]

Hi Colin,

The aromatic ring counting code identifies rings where every *bond* is
aromatic, so I guess one or more bonds in the rings of the first molecule
are not aromatic.
Could it be that you haven't sanitized the molecule before calculating
descriptors?

-greg



On Tue, Mar 5, 2019 at 6:00 PM Colin Bournez 
wrote:

> Dear all,
>
> I might have encountered a little problem concerning the function
> rdMolDescriptors.CalcNumAromaticRings().
> For this molecule shown with index:
>
> Here is what I do :
>
> So I have as expected my aromatic atoms but when I ask for aromatic Rings it 
> returns 0 instead of two.
> Anyone has an idea?
>
> For information if the molecule is in that form
> It returns 2 NAR as expected.
>
> Colin
>
>
> --
> *Bournez Colin *  
>  *Chemoinformatics PhD Student *
> * Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
>  Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759  45067
> Orléans Cedex 2 - France  +33 (0)2 38 49 45 77
> <+33%202%2038%2049%2045%2077>  SBC Tool Platform  - SBC
> Team   
>
> 
>  
>
> 
> ___
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>
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Re: [Rdkit-discuss] Bug with Calculation of aromatic rings?

[Colin Bournez]

Hi Greg,

Indeed it seems one bond is not tagged as aromatic.

Here are the aromatics bond (begin atom, end atom) :

0 1
1 19
19 16
11 14
14 12
12 7
7 20
11 0
20 16

We see that between the atom 11 and 16 it is not aromatic.
It is a single type:
16 11 SINGLE


The problem remains after sanitizing the molecule and both atoms are tagged as 
aromatic.
A bond between two aromatic atoms can be single?

On 06/03/19 10:49, Greg Landrum wrote:

Hi Colin,
The aromatic ring counting code identifies rings where every *bond* is 
aromatic, so I guess one or more bonds in the rings of the first 
molecule are not aromatic.
Could it be that you haven't sanitized the molecule before calculating 
descriptors?

-greg
On Tue, Mar 5, 2019 at 6:00 PM Colin Bournez 
mailto:colin.bour...@univ-orleans.fr>> 
wrote:


Dear all, I might have encountered a little problem concerning the
function rdMolDescriptors.CalcNumAromaticRings(). For this
molecule shown with index:

Here is what I do :


So I have as expected my aromatic atoms but when I ask for aromatic Rings 
it returns 0 instead of two.
Anyone has an idea?

For information if the molecule is in that form

It returns 2 NAR as expected.

Colin

-- 
*Bournez Colin *

 
 /Chemoinformatics PhD Student /
* Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
 Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759
 45067 Orléans Cedex 2 - France  +33 (0)2 38 49 45 77
 SBC Tool Platform
 - SBC Team 




 




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-- Signature
*Bournez Colin *  
  /Chemoinformatics PhD Student /
* Institute of Organic and Analytical Chemistry (ICOA UMR7311)* 
 Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759 
 45067 Orléans Cedex 2 - France  +33 (0)2 38 49 45 77 
 SBC Tool Platform 
 - SBC Team  	 

 


 
 



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Re: [Rdkit-discuss] Bug with Calculation of aromatic rings?

[Michal Krompiec]

It’s because the molecule with atom indices is a tautomer of the other one
(H at the other N), hence different Kekule structure and different
behaviour of the aromaticity perception code.
Best,
Michal

On Wed, 6 Mar 2019 at 10:04, Colin Bournez 
wrote:

> Hi Greg,
>
> Indeed it seems one bond is not tagged as aromatic.
>
> Here are the aromatics bond (begin atom, end atom) :
>
> 0 1
> 1 19
> 19 16
> 11 14
> 14 12
> 12 7
> 7 20
> 11 0
> 20 16
>
> We see that between the atom 11 and 16 it is not aromatic.
> It is a single type:
> 16 11 SINGLE
>
>
> The problem remains after sanitizing the molecule and both atoms are
> tagged as aromatic. A bond between two aromatic atoms can be single?
>
> On 06/03/19 10:49, Greg Landrum wrote:
>
> Hi Colin,
> The aromatic ring counting code identifies rings where every *bond* is
> aromatic, so I guess one or more bonds in the rings of the first molecule
> are not aromatic.
> Could it be that you haven't sanitized the molecule before calculating
> descriptors?
> -greg
>
> On Tue, Mar 5, 2019 at 6:00 PM Colin Bournez <
> colin.bour...@univ-orleans.fr> wrote:
>
>> Dear all, I might have encountered a little problem concerning the
>> function rdMolDescriptors.CalcNumAromaticRings(). For this molecule shown
>> with index:
>>
>> Here is what I do :
>>
>> So I have as expected my aromatic atoms but when I ask for aromatic Rings it 
>> returns 0 instead of two.
>> Anyone has an idea?
>>
>> For information if the molecule is in that form
>> It returns 2 NAR as expected.
>>
>> Colin
>>
>>
>> --
>> *Bournez Colin *  
>>  *Chemoinformatics PhD Student *
>> * Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
>>  Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759  45067
>> Orléans Cedex 2 - France  +33 (0)2 38 49 45 77
>> <+33%202%2038%2049%2045%2077>  SBC Tool Platform  - SBC
>> Team   
>>
>> 
>>  
>>
>> 
>> ___ Rdkit-discuss mailing
>> list Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
> --
> *Bournez Colin *  
>  *Chemoinformatics PhD Student *
> * Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
>  Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759  45067
> Orléans Cedex 2 - France  +33 (0)2 38 49 45 77
> <+33%202%2038%2049%2045%2077>  SBC Tool Platform  - SBC
> Team   
>
> 
>  
>
> 
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Re: [Rdkit-discuss] Bug with Calculation of aromatic rings?

[Colin Bournez]

Yes I know it's a tautomer, but I don't figure out how to handle it 
without returning to the other form.
If I transform the SINGLE bond to AROMATIC, it can't be sanitized still 
returns 0 NAR


Colin

On 06/03/19 11:11, Michal Krompiec wrote:
It’s because the molecule with atom indices is a tautomer of the other 
one (H at the other N), hence different Kekule structure and different 
behaviour of the aromaticity perception code.

Best,
Michal

On Wed, 6 Mar 2019 at 10:04, Colin Bournez 
mailto:colin.bour...@univ-orleans.fr>> 
wrote:


Hi Greg,

Indeed it seems one bond is not tagged as aromatic.

Here are the aromatics bond (begin atom, end atom) :

0 1
1 19
19 16
11 14
14 12
12 7
7 20
11 0
20 16

We see that between the atom 11 and 16 it is not aromatic.
It is a single type:
16 11 SINGLE


The problem remains after sanitizing the molecule and both atoms are tagged 
as aromatic.
A bond between two aromatic atoms can be single?

On 06/03/19 10:49, Greg Landrum wrote:

Hi Colin,
The aromatic ring counting code identifies rings where every
*bond* is aromatic, so I guess one or more bonds in the rings of
the first molecule are not aromatic.
Could it be that you haven't sanitized the molecule before
calculating descriptors?
-greg
On Tue, Mar 5, 2019 at 6:00 PM Colin Bournez
mailto:colin.bour...@univ-orleans.fr>> wrote:

Dear all, I might have encountered a little problem
concerning the function
rdMolDescriptors.CalcNumAromaticRings(). For this molecule
shown with index:

Here is what I do :


So I have as expected my aromatic atoms but when I ask for aromatic 
Rings it returns 0 instead of two.
Anyone has an idea?

For information if the molecule is in that form

It returns 2 NAR as expected.

Colin

-- 
*Bournez Colin *

 
 /Chemoinformatics PhD Student /
* Institute of Organic and Analytical Chemistry (ICOA
UMR7311)*  Université d'Orléans - Pôle de Chimie  Rue de
Chartres - BP 6759  45067 Orléans Cedex 2 - France  +33
(0)2 38 49 45 77  SBC Tool
Platform  - SBC Team
    



 




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-- 
*Bournez Colin *

 
 /Chemoinformatics PhD Student /
* Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
 Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759
 45067 Orléans Cedex 2 - France  +33 (0)2 38 49 45 77
 SBC Tool Platform
 - SBC Team 




 




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-- Signature
*Bournez Colin *  
  /Chemoinformatics PhD Student /
* Institute of Organic and Analytical Chemistry (ICOA UMR7311)* 
 Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759 
 45067 Orléans Cedex 2 - France  +33 (0)2 38 49 45 77 
 SBC Tool Platform 
 - SBC Team  	 

 


 
 



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Re: [Rdkit-discuss] RDKit Release 2018.09.2 available

[Markus Sitzmann]

Hi Greg,

in the meantime, I found a solution: I added a "conda update" as final step
when I build my base python/conda container. The RDKit container is build
on top of that and now it finds RDKit 2018.09.2 without telling conda the
version number explicitly.  Why this worked beforehand without this step
and why it is necessary although I start building the containers basically
from scratch and the newest version, I still don't know.

Best,
Markus

On Sat, Feb 23, 2019 at 12:29 AM Dimitri Maziuk via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:

> On 2/22/19 5:01 PM, Markus Sitzmann wrote:
>
> > It is odd, but one thing I learned from using conda is, sometimes it
> helps
> > to ignore problems and wait for a bit and they might go away ... well, I
> > have similar experiences with maven :-) ... but most likely I do
> something
> > stupid which I don't see right now :-)
>
> Simple test is to make a clean one and install only rdkit and nothing
> else and see what happens. It's pretty common for packagers to do
> something-that-may-or-may-not-be-stupid and have a dependency on an
> specific version of some other package that depends on a specific
> version of another package that depends on... turtles all the way down.
>
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
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[Rdkit-discuss] RDKIT Build Problems

[Markus Sitzmann]

Hi everybody,

Currently (the last couple of days) the build of one of my Docker images
stopped working:

https://github.com/chembience/chembience/blob/develop/context/build/rdkit-postgres-compile/Dockerfile

That occurred to me sporadically already over the last few years and
usually disappeared after a rebuild. Currently it is annoying enough to
write an email. The build ends with:

"""
== Using strict rotor definition
Downloading
http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar.
..
  % Total% Received % Xferd  Average Speed   TimeTime Time
Current
 Dload  Upload   Total   SpentLeft
Speed

100   178  100   1780 0   1181  0 --:--:-- --:--:-- --:--:--
1186
  0 00 00 0  0  0 --:--:-- --:--:-- --:--:--
 0
curl: (35) Unknown SSL protocol error in connection to sourceforge.net:443
*CMake Error at Code/cmake/Modules/RDKitUtils.cmake:215 (MESSAGE):*
*  The md5 checksum for*
*  /opt/rdkit/External/AvalonTools/AvalonToolkit_1.2.0.source.tar is*
*  incorrect; expected: 092a94f421873f038aa67d4a6cc8cb54, found:*
*  d41d8cd98f00b204e9800998ecf8427e*
*Call Stack (most recent call first):*
*  External/AvalonTools/CMakeLists.txt:29 (downloadAndCheckMD5)*


-- Configuring incomplete, errors occurred!
See also "/opt/rdkit/build/CMakeFiles/CMakeOutput.log".
See also "/opt/rdkit/build/CMakeFiles/CMakeError.log".
ERROR: Service 'rdkit-postgres-compile' failed to build: The command
'/bin/sh -c wget --quiet -O -
https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -  && echo
'deb http://apt.postgresql.org/pub/repos/apt/ stretch-pgdg main' >
/etc/apt/sources.list.d/pgdg.list  && apt-get update && apt-get install -y
--no-install-recommends  postgresql-server-dev-all
 postgresql-client postgresql-plpython-${PG_VERSION}
 postgresql-plpython3-${PG_VERSION} python-numpy python-dev
 sqlite3 libsqlite3-dev libboost-dev libboost-system-dev
 libboost-thread-dev libboost-serialization-dev
 libboost-python-dev libboost-regex-dev libeigen3-dev && git
clone -b $RDKIT_BRANCH --single-branch https://github.com/rdkit/rdkit.git
&& mkdir $RDBASE/build && cd $RDBASE/build && cmake
 -DRDK_BUILD_INCHI_SUPPORT=ON   -DRDK_BUILD_PGSQL=ON
 -DRDK_BUILD_AVALON_SUPPORT=ON
 -DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/${PG_VERSION}/server"
 -DPostgreSQL_ROOT="/usr/lib/postgresql/${PG_VERSION}" .. && make
-j `nproc` && make install' returned a non-zero code: 1
Exited with code 1
"""

Does someone maybe has the same problem? And an explanation whats going on
- the Avalon tools seemed to be unchanged since quite a while.

Thanks,
Markus
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Re: [Rdkit-discuss] Bug with Calculation of aromatic rings?

[David Cosgrove]

Sorry, I mistakenly replied to just Colin before, rather than the whole
list.

I think the answer is that the outer ring is aromatic, but the two inner
rings, the 5-ring and the 6-ring, aren’t. This would mean that the bond
between 11 and 16 isn’t aromatic.
It is certainly true that the bond between 2 aromatic atoms can be
non-aromatic.  The bond between the two benzene rings in bi-phenyl would be
the classic example.

Cheers,
Dave


On Wed, Mar 6, 2019 at 10:25 AM Colin Bournez 
wrote:

> Yes I know it's a tautomer, but I don't figure out how to handle it
> without returning to the other form.
> If I transform the SINGLE bond to AROMATIC, it can't be sanitized still
> returns 0 NAR
>
> Colin
>
> On 06/03/19 11:11, Michal Krompiec wrote:
>
> It’s because the molecule with atom indices is a tautomer of the other one
> (H at the other N), hence different Kekule structure and different
> behaviour of the aromaticity perception code.
> Best,
> Michal
>
> On Wed, 6 Mar 2019 at 10:04, Colin Bournez 
> wrote:
>
>> Hi Greg,
>>
>> Indeed it seems one bond is not tagged as aromatic.
>>
>> Here are the aromatics bond (begin atom, end atom) :
>>
>> 0 1
>> 1 19
>> 19 16
>> 11 14
>> 14 12
>> 12 7
>> 7 20
>> 11 0
>> 20 16
>>
>> We see that between the atom 11 and 16 it is not aromatic.
>> It is a single type:
>> 16 11 SINGLE
>>
>>
>> The problem remains after sanitizing the molecule and both atoms are tagged 
>> as aromatic.
>> A bond between two aromatic atoms can be single?
>>
>> On 06/03/19 10:49, Greg Landrum wrote:
>>
>> Hi Colin,
>> The aromatic ring counting code identifies rings where every *bond* is
>> aromatic, so I guess one or more bonds in the rings of the first molecule
>> are not aromatic.
>> Could it be that you haven't sanitized the molecule before calculating
>> descriptors?
>> -greg
>>
>> On Tue, Mar 5, 2019 at 6:00 PM Colin Bournez <
>> colin.bour...@univ-orleans.fr> wrote:
>>
>>> Dear all, I might have encountered a little problem concerning the
>>> function rdMolDescriptors.CalcNumAromaticRings(). For this molecule shown
>>> with index:
>>>
>>> Here is what I do :
>>>
>>> So I have as expected my aromatic atoms but when I ask for aromatic Rings 
>>> it returns 0 instead of two.
>>> Anyone has an idea?
>>>
>>> For information if the molecule is in that form
>>> It returns 2 NAR as expected.
>>>
>>> Colin
>>>
>>>
>>> --
>>> *Bournez Colin * 
>>>   *Chemoinformatics PhD Student *
>>> * Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
>>>  Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759  45067
>>> Orléans Cedex 2 - France  +33 (0)2 38 49 45 77
>>> <+33%202%2038%2049%2045%2077>  SBC Tool Platform 
>>> - SBC Team   
>>>
>>> 
>>>  
>>>
>>> 
>>> ___ Rdkit-discuss mailing
>>> list Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>> --
>> *Bournez Colin *  
>>  *Chemoinformatics PhD Student *
>> * Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
>>  Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759  45067
>> Orléans Cedex 2 - France  +33 (0)2 38 49 45 77
>> <+33%202%2038%2049%2045%2077>  SBC Tool Platform  - SBC
>> Team   
>>
>> 
>>  
>>
>> 
>> ___ Rdkit-discuss mailing
>> list Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
> --
> *Bournez Colin *  
>  *Chemoinformatics PhD Student *
> * Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
>  Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759  45067
> Orléans Cedex 2 - France  +33 (0)2 38 49 45 77
> <+33%202%2038%2049%2045%2077>  SBC Tool Platform  - SBC
> Team   
>
> 
>  
>
> 
> ___
> Rdkit-

Re: [Rdkit-discuss] Bug with Calculation of aromatic rings?

[Peter S. Shenkin]

Atom 20 appears to be an NH. Shouldn’t it be a pyridine N?

On Wed, Mar 6, 2019 at 5:04 AM Colin Bournez 
wrote:

> Hi Greg,
>
> Indeed it seems one bond is not tagged as aromatic.
>
> Here are the aromatics bond (begin atom, end atom) :
>
> 0 1
> 1 19
> 19 16
> 11 14
> 14 12
> 12 7
> 7 20
> 11 0
> 20 16
>
> We see that between the atom 11 and 16 it is not aromatic.
> It is a single type:
> 16 11 SINGLE
>
>
> The problem remains after sanitizing the molecule and both atoms are
> tagged as aromatic. A bond between two aromatic atoms can be single?
>
> On 06/03/19 10:49, Greg Landrum wrote:
>
> Hi Colin,
> The aromatic ring counting code identifies rings where every *bond* is
> aromatic, so I guess one or more bonds in the rings of the first molecule
> are not aromatic.
> Could it be that you haven't sanitized the molecule before calculating
> descriptors?
> -greg
>
> On Tue, Mar 5, 2019 at 6:00 PM Colin Bournez <
> colin.bour...@univ-orleans.fr> wrote:
>
>> Dear all, I might have encountered a little problem concerning the
>> function rdMolDescriptors.CalcNumAromaticRings(). For this molecule shown
>> with index:
>>
>> Here is what I do :
>>
>> So I have as expected my aromatic atoms but when I ask for aromatic Rings it 
>> returns 0 instead of two.
>> Anyone has an idea?
>>
>> For information if the molecule is in that form
>> It returns 2 NAR as expected.
>>
>> Colin
>>
>>
>> --
>> *Bournez Colin *  
>>  *Chemoinformatics PhD Student *
>> * Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
>>  Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759  45067
>> Orléans Cedex 2 - France  +33 (0)2 38 49 45 77
>> <+33%202%2038%2049%2045%2077>  SBC Tool Platform  - SBC
>> Team   
>>
>> 
>>  
>>
>> 
>> ___ Rdkit-discuss mailing
>> list Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
> --
> *Bournez Colin *  
>  *Chemoinformatics PhD Student *
> * Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
>  Université d'Orléans - Pôle de Chimie  Rue de Chartres - BP 6759  45067
> Orléans Cedex 2 - France  +33 (0)2 38 49 45 77
> <+33%202%2038%2049%2045%2077>  SBC Tool Platform  - SBC
> Team   
>
> 
>  
>
> 
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>
-- 
-P.
Sent from a cell phone. Pls forgive brvty and m1$tea@ks.
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Re: [Rdkit-discuss] RDKIT Build Problems

[Greg Landrum]

On Wed, Mar 6, 2019 at 1:15 PM Markus Sitzmann 
wrote:

>
> Does someone maybe has the same problem? And an explanation whats going on
> - the Avalon tools seemed to be unchanged since quite a while.
>

I've seen it a couple of times in the CI builds for the RDKit over the past
couple of days. It's caused by downloads failing since sourceforge is
unreliable.

-greg
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Re: [Rdkit-discuss] RDKIT Build Problems

[Markus Sitzmann]

Thanks Greg. 

I have the problem at CI, too. It was 100% failure rate the last two days. At 
home, occasionally. At least, it isn’t only me :-)

Markus


-
|  Markus Sitzmann
|  markus.sitzm...@gmail.com

> On 6. Mar 2019, at 17:25, Greg Landrum  wrote:
> 
> 
> 
>> On Wed, Mar 6, 2019 at 1:15 PM Markus Sitzmann  
>> wrote:
>> 
>> Does someone maybe has the same problem? And an explanation whats going on - 
>> the Avalon tools seemed to be unchanged since quite a while.
> 
> I've seen it a couple of times in the CI builds for the RDKit over the past 
> couple of days. It's caused by downloads failing since sourceforge is 
> unreliable.
> 
> -greg
> 
> 
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