#957 InChI for senkirkine segfaults

[Steffen Neumann]

Hi,

OpenBabel seems to have an issue with Senkirkine.
http://www.chemspider.com/Chemical-Structure.10254880.html

The following will segfault, InChI comes from ChemSpider:

echo "InChI=1S/C19H27NO6/c1-5-13-10-12(2)19(3,24)18(23)25-11-14-6-8-20(4)9-7-15(16(14)21)26-17(13)22/h5-6,12,15,24H,7-11H2,1-4H3/b13-5-,14-6-/t12-,15-,19-/m1/s1" | obabel -i inchi - -xK -o inchi

The corresponding does not SEGV, but does not result in any conversion:

echo "C/C=C\1/CC@HC)(C)O)C" | obabel -i inchi - -xK -o inchi

Only the SDF/MOL get me an inchikey:

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6433332/record/SDF/?response_type=save&record_type=2d

and also

http://www.chemspider.com/FilesHandler.ashx?type=str&striph=yes&id=10254880

obabel -i sdf data.sdf -xK -o inchi HPDHKHMHQGCNPE-PYWIAZMFSA-N

It seems that also most depiction services choke on the InChI:

https://apps.ideaconsult.net/ambit2/depict?search=InChI%3D1S%2FC19H27NO6%2Fc1-5-13-10-12%282%2919%283%2C24%2918%2823%2925-11-14-6-8-20%284%299-7-15%2816%2814%2921%2926-17%2813%2922%2Fh5-6%2C12%2C15%2C24H%2C7-11H2%2C1-4H3%2Fb13-5%2B%2C14-6-%2Ft12-%2C15%3F%2C19-%2Fm1%2Fs1&smarts=

While the corresponding SMILES from ChemSpider seems to work in
several toolkits, including OpenBabel:

https://apps.ideaconsult.net/ambit2/depict?search=C%2FC%3DC\1%2FC[C%40H]%28[C%40%40]%28C%28%3DO%29OC%2FC%2F2%3DC%2FCN%28CC[C%40H]%28C2%3DO%29OC1%3DO%29C%29%28C%29O%29C&smarts=

I tried Open Babel 2.3.2 and today's Open Babel 2.3.90 -- Mar 4 2015 (a65a93bed157d66f8fd6b68e1d5e96ba77ffa744)

Anything else where I can help debug this ?

Yours,
Steffen

[Steffen Neumann]

The issue also occurs if the InChI is generated by obabel itself:

sneumann@acryl:~/Downloads$ obabel -i mol senkirkine.mol -o inchi - | obabel -i inchi - -xK -o inchi
1 molecule converted
Segmentation fault (core dumped)

[Steffen Neumann]

Sorry for the chatter, Open Babel 2.3.0 -- Dec 17 2011 -- 16:15:10
does work:

sneumann@balzer:~/Downloads $ /vol/local/bin/obabel -i mol senkirkine.mol -o inchi - | /vol/local/bin/obabel -i inchi - -xK -o inchi
1 molecule converted
HPDHKHMHQGCNPE-QLJRNOHWSA-N
1 molecule converted

Yours,
Steffen

[Noel O'Boyle]

Confirmed

[Noel O'Boyle]

Seems to work fine now with the latest code. Can you confirm?

[Steffen Neumann]

Unfortunately I can't check,
I get SEGV for many more cases,
even doing a fresh build and checkout,
possibly my setup is borked. If it is fixed for you,
I am happy to have this closed.
Yours, Steffen

[Noel O'Boyle]

Ah - seems to work on Windows but fail on Linux.

[Noel O'Boyle]

Forget my previous comment. It seems to be working fine for me on Linux too.

Your syntax is a bit wrong. No need for "-" when piping input into obabel.

[Christoph Helma]

I am running on Arch Linux with todays master branch from github and still get segfaults for this InChi or others like InChI=1S/C19H27NO7/c1-11-9-19(12(2)27-19)17(23)26-14-6-8-20(4)7-5-13(15(14)21)10-25-16(22)18(11,3)24/h5,11-12,14,24H,6-10H2,1-4H3/b13-5-/t11-,12-,14-,18-,19?/m1/s1

Best,
Christoph

[Christoph Helma]

I can confirm that the latest master branch (commit 7be9ee2fb614bfc5a2c0ffa97a14f94815ea5382) converts both InChis correctly on a fresh Debian 3.16.7 system. It is still unclear to me why the same branch segfaults on 4.1.4-1-ARCH.

Best regards,
Christoph