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

2019-03-06 Thread 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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Re: [Rdkit-discuss] Bug with Calculation of aromatic rings?

2019-03-06 Thread 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?

2019-03-06 Thread 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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 /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?

2019-03-06 Thread 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?

2019-03-06 Thread 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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*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?

2019-03-06 Thread 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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[Rdkit-discuss] Bug with Calculation of aromatic rings?

2019-03-05 Thread Colin Bournez 

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

-- 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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