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wrong

Jan Halborg Jensen
Hi all

babel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF 

gives 

InChI=1/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3/p+1/fC9H12NO2/h10H/q+1 

but converting this InChI back to smiles gives CCOC(=O)c1ccc(cc1)[NH2+]

I use obabel -oinchi temp3.inchi -osmi

Any help appreciated

Best regards, Jan

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Re: wrong

Andrew Dalke
On Mar 18, 2017, at 16:00, Jan Halborg Jensen <[hidden email]> wrote:
> babel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF
>
> gives
>
> InChI=1/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3/p+1/fC9H12NO2/h10H/q+1
>
> but converting this InChI back to smiles gives CCOC(=O)c1ccc(cc1)[NH2+]
>
> I use obabel -oinchi temp3.inchi -osmi

When I do the first step (with "obabel", not "babel"), I get a warning message from obabel saying "Proton(s) added/removed".


% obabel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF
==============================
*** Open Babel Warning  in InChI code
  #1 :Proton(s) added/removed
InChI=1/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3/p+1/fC9H12NO2/h10H/q+1
1 molecule converted

This warning comes from InChI itself, not Open Babel.

I can verify this with the InChI binary. First, I'll convert the SMILES to SDF:

% obabel -:"CCOC(=O)c1ccc([NH3+])cc1" -osdf > test.sdf

Then use the pre-release version of InChI from early this year (I haven't yet upgraded to the final release)

% /Users/dalke/ftps/inchi-1.05pr2/INCHI-1-SRC/INCHI_EXE/bin/Linux/inchi-1 test.sdf -FixedH
InChI version 1, Software v. 1.05 (inchi-1 executable)
Linux Build of Jan  5 2017 00:51:46 *** pre-release, for evaluation only ***

Opened log file 'test.sdf.log'
Opened input file 'test.sdf'
Opened output file 'test.sdf.txt'
Opened problem file 'test.sdf.prb'
The command line used:
"/Users/dalke/ftps/inchi-1.05pr2/INCHI-1-SRC/INCHI_EXE/bin/Linux/inchi-1 test.sdf -FixedH"
Generating non-standard InChI with the options:
  Mobile H Perception OFF (include FixedH layer)
  Do not reconnect metals (omit RecMet layer)
  Absolute Stereo ON
  Omit undefined/unknown stereogenic centers and bonds
  Do not account for keto-enol tautomerism
  Do not account for 1,5-tautomerism
Input format: MOLfile
Output format: Plain text
Full Aux. info
Timeout per structure: 60 sec
Up to 1024 atoms per structure

Warning (Proton(s) added/removed) structure #1.
End of file detected after structure #1.
Finished processing 1 structure: 0 errors, processing time 0:00:00.00

% cat test.sdf.txt
* Input_File: "test.sdf"
Structure: 1
InChI=1/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3/p+1/fC9H12NO2/h10H/q+1
AuxInfo=1/1/N:1,2,7,15,8,14,6,9,4,10,5,3/E:(3,4)(5,6)/F:m/E:m/rA:15nCCOCOCCCCN+HHHCC/rB:s1;s2;s3;d4;s4;d6;s7;d8;s9;s10;s10;s10;s9;s6d14;/rC:;;;;;;;;;;;;;;;


You can see it gives the same InChI as you got from Open Babel, and it gives the same warning about "Proton(s) added/removed".

Cheers,

                                Andrew
                                [hidden email]



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Re: wrong

Noel O'Boyle
Administrator
In reply to this post by Jan Halborg Jensen
This is already fixed in my development code, where I have changed the
handling of implicit hydrogens throughout the library:

>obabel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF | obabel -iinchi -osmi
==============================
*** Open Babel Warning  in InChI code
  #1 :Proton(s) added/removed
1 molecule converted
CCOC(=O)c1ccc(cc1)[NH3+]
1 molecule converted

The problem is that the current code just gives the InChI a charged
nitrogen and tells it to guess the number of hydrogens (aka apply the
InChI implicit valence model). The new code gives it the number of
implicit hydrogens.

BTW, consider a less general subject line in future. :-)

Regards,
- Noel


On 18 March 2017 at 15:00, Jan Halborg Jensen <[hidden email]> wrote:

> Hi all
>
> babel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF
>
> gives
>
> InChI=1/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3/p+1/fC9H12NO2/h10H/q+1
>
> but converting this InChI back to smiles gives CCOC(=O)c1ccc(cc1)[NH2+]
>
> I use obabel -oinchi temp3.inchi -osmi
>
> Any help appreciated
>
> Best regards, Jan
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: wrong

Jan Halborg Jensen
Thanks Noel

When do you think this fix will get into the public version?  I found a not-soelegant workaround using the Cactus server, so no great hurry.

Sorry about the title :) I hit send before I was done typing

Best regards, Jan
 

> On 22 Mar 2017, at 21:24, Noel O'Boyle <[hidden email]> wrote:
>
> This is already fixed in my development code, where I have changed the
> handling of implicit hydrogens throughout the library:
>
>> obabel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF | obabel -iinchi -osmi
> ==============================
> *** Open Babel Warning  in InChI code
>  #1 :Proton(s) added/removed
> 1 molecule converted
> CCOC(=O)c1ccc(cc1)[NH3+]
> 1 molecule converted
>
> The problem is that the current code just gives the InChI a charged
> nitrogen and tells it to guess the number of hydrogens (aka apply the
> InChI implicit valence model). The new code gives it the number of
> implicit hydrogens.
>
> BTW, consider a less general subject line in future. :-)
>
> Regards,
> - Noel
>
>
> On 18 March 2017 at 15:00, Jan Halborg Jensen <[hidden email]> wrote:
>> Hi all
>>
>> babel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF
>>
>> gives
>>
>> InChI=1/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3/p+1/fC9H12NO2/h10H/q+1
>>
>> but converting this InChI back to smiles gives CCOC(=O)c1ccc(cc1)[NH2+]
>>
>> I use obabel -oinchi temp3.inchi -osmi
>>
>> Any help appreciated
>>
>> Best regards, Jan
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>


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Re: wrong

Noel O'Boyle
Administrator
I can't say anything regarding releases dates. But at some point, it
will reach sufficient quality that it will be merged into the
development codebase and you can download and compile it from there.
I'll try to remember to ping you at that point, but we're talking
timescales of a few months.

At the same time, if you are using the fixed hydrogen layer with
InChI, consider instead using canonical SMILES. I'm not sure what
extra you're getting from the InChI in this case.

- Noel

On 23 March 2017 at 09:04, Jan Halborg Jensen <[hidden email]> wrote:

> Thanks Noel
>
> When do you think this fix will get into the public version?  I found a not-soelegant workaround using the Cactus server, so no great hurry.
>
> Sorry about the title :) I hit send before I was done typing
>
> Best regards, Jan
>
>> On 22 Mar 2017, at 21:24, Noel O'Boyle <[hidden email]> wrote:
>>
>> This is already fixed in my development code, where I have changed the
>> handling of implicit hydrogens throughout the library:
>>
>>> obabel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF | obabel -iinchi -osmi
>> ==============================
>> *** Open Babel Warning  in InChI code
>>  #1 :Proton(s) added/removed
>> 1 molecule converted
>> CCOC(=O)c1ccc(cc1)[NH3+]
>> 1 molecule converted
>>
>> The problem is that the current code just gives the InChI a charged
>> nitrogen and tells it to guess the number of hydrogens (aka apply the
>> InChI implicit valence model). The new code gives it the number of
>> implicit hydrogens.
>>
>> BTW, consider a less general subject line in future. :-)
>>
>> Regards,
>> - Noel
>>
>>
>> On 18 March 2017 at 15:00, Jan Halborg Jensen <[hidden email]> wrote:
>>> Hi all
>>>
>>> babel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF
>>>
>>> gives
>>>
>>> InChI=1/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3/p+1/fC9H12NO2/h10H/q+1
>>>
>>> but converting this InChI back to smiles gives CCOC(=O)c1ccc(cc1)[NH2+]
>>>
>>> I use obabel -oinchi temp3.inchi -osmi
>>>
>>> Any help appreciated
>>>
>>> Best regards, Jan
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>

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wrong

taxiservices
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In reply to this post by Jan Halborg Jensen
wrong is a very good sentance in english and of them will not do good all the times.