Quantcast

possibly a bug in smiles format

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
7 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

possibly a bug in smiles format

NakataMaho
Dear openbabel developers,
As I read:
https://open-babel.readthedocs.io/en/latest/FileFormats/Canonical_SMILES_format.html
"Do not include isotopic or chiral markings"

and I thought
$ obabel -:"[3H+].[F-]" -osmi -xi
should output  
[F-].[H-]
but
actually openbabel outputs
$ obabel -:"[3H+].[F-]" -osmi -xi
[F-]

Is is correct or intended?

BTW:I'm not sure why "-i" option trims all. I think these are separated options.

Best,
 Nakata Maho

------------------------------------------------------------------------------
_______________________________________________
OpenBabel-Devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Another bug: -oreport reports incorrect hydrogen number

NakataMaho
Dear openbabel developers,

I found another bug:

$ obabel -:"[BH-]" -h --gen3d -omol | obabel -imol -oreport | grep FO
1 molecule converted
1 molecule converted
FORMULA: BH2-   <----NG

$  obabel -:"[B].[F-]" -h --gen3d -oreport | grep FO
1 molecule converted
FORMULA: BFH3-  <--- NG

$ obabel -:"[C].[F-]" --addh --gen3d -omol

 OpenBabel09121613383D

  6  4  0  0  0  0  0  0  0  0999 V2000
    0.8573    0.1372   -0.4795 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5033   -0.9237    2.8746 F   0  5  0  0  0  0  0  0  0  0  0  0
    1.9457    0.2305   -0.4811 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4504    0.6368    0.4027 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5824   -0.9195   -0.4581 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4507    0.6013   -1.3802 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1  6  1  0  0  0  0
M  CHG  1   2  -1
M  END
1 molecule converted

<---- NG

thanks,
 Nakata Maho


------------------------------------------------------------------------------
_______________________________________________
OpenBabel-Devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

OBABEL crashes Re: Another bug: -oreport reports incorrect hydrogen number

NakataMaho
Dear openbabel developers,

I found another bug:

$ obabel -:"[HH].[Li]" -addh --gen3d -omol
Segmentation fault (core dumped)


$ obabel -:"[HH].[Li]" --gen3d -omol
Segmentation fault (core dumped)

Best,
 Nakata Maho

From: NakataMaho <[hidden email]>
Subject: Another bug: -oreport reports incorrect hydrogen number
Date: Mon, 12 Sep 2016 13:41:15 +0900 (JST)

> Dear openbabel developers,
>
> I found another bug:
>
> $ obabel -:"[BH-]" -h --gen3d -omol | obabel -imol -oreport | grep FO
> 1 molecule converted
> 1 molecule converted
> FORMULA: BH2-   <----NG
>
> $  obabel -:"[B].[F-]" -h --gen3d -oreport | grep FO
> 1 molecule converted
> FORMULA: BFH3-  <--- NG
>
> $ obabel -:"[C].[F-]" --addh --gen3d -omol
>
>  OpenBabel09121613383D
>
>   6  4  0  0  0  0  0  0  0  0999 V2000
>     0.8573    0.1372   -0.4795 C   0  0  0  0  0  0  0  0  0  0  0  0
>     2.5033   -0.9237    2.8746 F   0  5  0  0  0  0  0  0  0  0  0  0
>     1.9457    0.2305   -0.4811 H   0  0  0  0  0  0  0  0  0  0  0  0
>     0.4504    0.6368    0.4027 H   0  0  0  0  0  0  0  0  0  0  0  0
>     0.5824   -0.9195   -0.4581 H   0  0  0  0  0  0  0  0  0  0  0  0
>     0.4507    0.6013   -1.3802 H   0  0  0  0  0  0  0  0  0  0  0  0
>   1  3  1  0  0  0  0
>   1  4  1  0  0  0  0
>   1  5  1  0  0  0  0
>   1  6  1  0  0  0  0
> M  CHG  1   2  -1
> M  END
> 1 molecule converted
>
> <---- NG
>
> thanks,
>  Nakata Maho
>

------------------------------------------------------------------------------
_______________________________________________
OpenBabel-Devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: OBABEL crashes Re: Another bug: -oreport reports incorrect hydrogen number

Geoff Hutchison
> I found another bug:

While I appreciate the multiple bug reports, e-mail isn’t a good way to file bugs. My e-mail inbox is a mess.

The bug tracker is here:
https://github.com/openbabel/openbabel/issues

If you can take a minute to post them, we’d greatly appreciate it. Otherwise, it’s likely to get lost in the shuffle.

Thanks and best regards,
-Geoff
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
OpenBabel-Devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Another bug: -oreport reports incorrect hydrogen number

NakataMaho
In reply to this post by NakataMaho
Dear openbabel developers,

following issue has been raised as
https://github.com/openbabel/openbabel/issues/341
thanks,
 Nakata Maho

From: NakataMaho <[hidden email]>
Subject: Another bug: -oreport reports incorrect hydrogen number
Date: Mon, 12 Sep 2016 13:41:15 +0900 (JST)

> Dear openbabel developers,
>
> I found another bug:
>
> $ obabel -:"[BH-]" -h --gen3d -omol | obabel -imol -oreport | grep FO
> 1 molecule converted
> 1 molecule converted
> FORMULA: BH2-   <----NG
>
> $  obabel -:"[B].[F-]" -h --gen3d -oreport | grep FO
> 1 molecule converted
> FORMULA: BFH3-  <--- NG
>
> $ obabel -:"[C].[F-]" --addh --gen3d -omol
>
>  OpenBabel09121613383D
>
>   6  4  0  0  0  0  0  0  0  0999 V2000
>     0.8573    0.1372   -0.4795 C   0  0  0  0  0  0  0  0  0  0  0  0
>     2.5033   -0.9237    2.8746 F   0  5  0  0  0  0  0  0  0  0  0  0
>     1.9457    0.2305   -0.4811 H   0  0  0  0  0  0  0  0  0  0  0  0
>     0.4504    0.6368    0.4027 H   0  0  0  0  0  0  0  0  0  0  0  0
>     0.5824   -0.9195   -0.4581 H   0  0  0  0  0  0  0  0  0  0  0  0
>     0.4507    0.6013   -1.3802 H   0  0  0  0  0  0  0  0  0  0  0  0
>   1  3  1  0  0  0  0
>   1  4  1  0  0  0  0
>   1  5  1  0  0  0  0
>   1  6  1  0  0  0  0
> M  CHG  1   2  -1
> M  END
> 1 molecule converted
>
> <---- NG
>
> thanks,
>  Nakata Maho
>

------------------------------------------------------------------------------
_______________________________________________
OpenBabel-Devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: OBABEL crashes Re: Another bug: -oreport reports incorrect hydrogen number

NakataMaho
In reply to this post by NakataMaho
Dear openbabel developers,

Following issue has been raised as follows:
https://github.com/openbabel/openbabel/issues/342
Best,
 Nakata Maho

From: NakataMaho <[hidden email]>
Subject: OBABEL crashes Re: Another bug: -oreport reports incorrect hydrogen number
Date: Mon, 12 Sep 2016 14:41:27 +0900 (JST)

> Dear openbabel developers,
>
> I found another bug:
>
> $ obabel -:"[HH].[Li]" -addh --gen3d -omol
> Segmentation fault (core dumped)
>
>
> $ obabel -:"[HH].[Li]" --gen3d -omol
> Segmentation fault (core dumped)
>
> Best,
>  Nakata Maho
>
> From: NakataMaho <[hidden email]>
> Subject: Another bug: -oreport reports incorrect hydrogen number
> Date: Mon, 12 Sep 2016 13:41:15 +0900 (JST)
>
>> Dear openbabel developers,
>>
>> I found another bug:
>>
>> $ obabel -:"[BH-]" -h --gen3d -omol | obabel -imol -oreport | grep FO
>> 1 molecule converted
>> 1 molecule converted
>> FORMULA: BH2-   <----NG
>>
>> $  obabel -:"[B].[F-]" -h --gen3d -oreport | grep FO
>> 1 molecule converted
>> FORMULA: BFH3-  <--- NG
>>
>> $ obabel -:"[C].[F-]" --addh --gen3d -omol
>>
>>  OpenBabel09121613383D
>>
>>   6  4  0  0  0  0  0  0  0  0999 V2000
>>     0.8573    0.1372   -0.4795 C   0  0  0  0  0  0  0  0  0  0  0  0
>>     2.5033   -0.9237    2.8746 F   0  5  0  0  0  0  0  0  0  0  0  0
>>     1.9457    0.2305   -0.4811 H   0  0  0  0  0  0  0  0  0  0  0  0
>>     0.4504    0.6368    0.4027 H   0  0  0  0  0  0  0  0  0  0  0  0
>>     0.5824   -0.9195   -0.4581 H   0  0  0  0  0  0  0  0  0  0  0  0
>>     0.4507    0.6013   -1.3802 H   0  0  0  0  0  0  0  0  0  0  0  0
>>   1  3  1  0  0  0  0
>>   1  4  1  0  0  0  0
>>   1  5  1  0  0  0  0
>>   1  6  1  0  0  0  0
>> M  CHG  1   2  -1
>> M  END
>> 1 molecule converted
>>
>> <---- NG
>>
>> thanks,
>>  Nakata Maho
>>

------------------------------------------------------------------------------
_______________________________________________
OpenBabel-Devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: OBABEL crashes Re: Another bug: -oreport reports incorrect hydrogen number

NakataMaho
In reply to this post by Geoff Hutchison
Hi Geoffrey,

Thanks for your advice.
All found issues have been raised as github issues.

https://github.com/openbabel/openbabel/issues/340
https://github.com/openbabel/openbabel/issues/341
https://github.com/openbabel/openbabel/issues/342

Thanks,
 Nakata Maho

From: Geoffrey Hutchison <[hidden email]>
Subject: Re: [OpenBabel-Devel] OBABEL crashes Re: Another bug: -oreport reports incorrect hydrogen number
Date: Mon, 12 Sep 2016 13:13:28 -0400

>> I found another bug:
>
> While I appreciate the multiple bug reports, e-mail isn’t a good way to file bugs. My e-mail inbox is a mess.
>
> The bug tracker is here:
> https://github.com/openbabel/openbabel/issues
>
> If you can take a minute to post them, we’d greatly appreciate it. Otherwise, it’s likely to get lost in the shuffle.
>
> Thanks and best regards,
> -Geoff
------------------------------------------------------------------------------
_______________________________________________
OpenBabel-Devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Loading...