On Mar 18, 2017, at 16:00, Jan Halborg Jensen <jhjen...@chem.ku.dk> 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
da...@dalkescientific.com
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