[Open Babel] Segmentation fault in inchi conversion

2013-04-11 Thread Fredrik Wallner 
Hi,

I get a segmentation fault when running the following command:
obabel -iinchi 
-:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;" 
-osmi

I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3 (installed via 
homerbrew).
I have also tried it on an Ubuntu box (10.04.4) running ob 2.3.1 and here it's 
working without problem. Is there anyone else having problems with this, or is 
it just me?

Kind regards,
Fredrik
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Re: [Open Babel] Segmentation fault in inchi conversion

2013-04-11 Thread Fredrik Wallner 
Hi again,

Some more information…
The InChI "InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-2,7-8H,3-6H2/b2-1-,8-7-" gives 
the same problem.
I have now updated the ubuntu box to also run ob 2.3.2 and it segfaults now as 
well, so it seems it has something to do with differences between 2.3.1 and 
2.3.2.

Kind regards,
Fredrik

11 apr 2013 kl. 14:45 skrev Fredrik Wallner :

> Hi,
> 
> I get a segmentation fault when running the following command:
> obabel -iinchi 
> -:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;" 
> -osmi
> 
> I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3 (installed via 
> homerbrew).
> I have also tried it on an Ubuntu box (10.04.4) running ob 2.3.1 and here 
> it's working without problem. Is there anyone else having problems with this, 
> or is it just me?
> 
> Kind regards,
> Fredrik
> --
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
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> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss


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Re: [Open Babel] Segmentation fault in inchi conversion

2013-06-25 Thread Jon Fuller 
Hi Fredrik,

Did you find a solution to this problem? I found a similar example:
I pasted example code for pybel, but running the command below with both
inchis in the file inchi.txt:
babel -iinchi inchi.txt -osdf inchi.sdf
Will result in "Segmentation fault: 11"
Remove the second inchi and the command works.

mol1 = pybel.readstring("inchi",
"InChI=1S/C19H22N2O/c1-4-15-7-6-8-16(5-2)18(15)10-9-14-11-17(13-21-12-14)19(22)20-3/h6-13H,4-5H2,1-3H3,(H,20,22)/b10-9+")

print "molecule one works"


mol2smiles = pybel.readstring("smiles", "O=C(OC[C@H](\C3=C2/[C@@H](O[C@H
]1O[C@@H]([C@@H](O)[C@H](OC(=O)C)[C@H]1O)COC(\C=C)(C)C)[C@H](O)[C@H](C)[C@H
]4C(=C/[C@@]2(C)[C@@H](O)C3)\[C@@H](COC)CC4)C)C")

print "smiles works for molecule two!"

print mol2smiles



mol2inchichemspider = pybel.readstring("inchi",
"InChI=1S/C36H56O12/c1-10-35(6,7)45-17-26-30(41)33(46-21(5)38)31(42)34(47-26)48-32-28-24(18(2)15-44-20(4)37)13-27(39)36(28,8)14-25-22(16-43-9)11-12-23(25)19(3)29(32)40/h10,14,18-19,22-23,26-27,29-34,39-42H,1,11-13,15-17H2,2-9H3/b25-14-/t18-,19-,22-,23+,26-,27+,29-,30-,31-,32-,33+,34-,36+/m1/s1"
)

print "inchi does not work for molecule two"

print mol2inchichemspider


Best,

Jon


On 11 April 2013 16:21, Fredrik Wallner  wrote:

> Hi again,
>
> Some more information…
> The InChI "InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-2,7-8H,3-6H2/b2-1-,8-7-"
> gives the same problem.
> I have now updated the ubuntu box to also run ob 2.3.2 and it segfaults
> now as well, so it seems it has something to do with differences between
> 2.3.1 and 2.3.2.
>
> Kind regards,
> Fredrik
>
> 11 apr 2013 kl. 14:45 skrev Fredrik Wallner :
>
> > Hi,
> >
> > I get a segmentation fault when running the following command:
> > obabel -iinchi
> -:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;"
> -osmi
> >
> > I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3 (installed via
> homerbrew).
> > I have also tried it on an Ubuntu box (10.04.4) running ob 2.3.1 and
> here it's working without problem. Is there anyone else having problems
> with this, or is it just me?
> >
> > Kind regards,
> > Fredrik
> >
> --
> > Precog is a next-generation analytics platform capable of advanced
> > analytics on semi-structured data. The platform includes APIs for
> building
> > apps and a phenomenal toolset for data science. Developers can use
> > our toolset for easy data analysis & visualization. Get a free account!
> > http://www2.precog.com/precogplatform/slashdotnewsletter
> > ___
> > OpenBabel-discuss mailing list
> > OpenBabel-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
>
> --
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
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Re: [Open Babel] Segmentation fault in inchi conversion

2013-06-26 Thread Fredrik Wallner 
Hi,

No, I never found a solution to this. I managed a workaround for the specific 
problem (although I cannot remember for sure I believe I accepted some help 
from ChemDraw…) so my needs fainted…

Kind regards,
Fredrik

25 jun 2013 kl. 14:33 skrev Jon Fuller :

> Hi Fredrik,
> 
> Did you find a solution to this problem? I found a similar example:
> I pasted example code for pybel, but running the command below with both 
> inchis in the file inchi.txt:
> babel -iinchi inchi.txt -osdf inchi.sdf
> Will result in "Segmentation fault: 11"
> Remove the second inchi and the command works.
> mol1 = pybel.readstring("inchi", 
> "InChI=1S/C19H22N2O/c1-4-15-7-6-8-16(5-2)18(15)10-9-14-11-17(13-21-12-14)19(22)20-3/h6-13H,4-5H2,1-3H3,(H,20,22)/b10-9+")
> 
> print "molecule one works"
> 
> 
> 
> mol2smiles = pybel.readstring("smiles", 
> "O=C(OC[C@H](\C3=C2/[C@@H](O[C@H]1O[C@@H]([C@@H](O)[C@H](OC(=O)C)[C@H]1O)COC(\C=C)(C)C)[C@H](O)[C@H](C)[C@H]4C(=C/[C@@]2(C)[C@@H](O)C3)\[C@@H](COC)CC4)C)C")
> 
> print "smiles works for molecule two!"
> 
> print mol2smiles
> 
> 
> mol2inchichemspider = pybel.readstring("inchi", 
> "InChI=1S/C36H56O12/c1-10-35(6,7)45-17-26-30(41)33(46-21(5)38)31(42)34(47-26)48-32-28-24(18(2)15-44-20(4)37)13-27(39)36(28,8)14-25-22(16-43-9)11-12-23(25)19(3)29(32)40/h10,14,18-19,22-23,26-27,29-34,39-42H,1,11-13,15-17H2,2-9H3/b25-14-/t18-,19-,22-,23+,26-,27+,29-,30-,31-,32-,33+,34-,36+/m1/s1")
> 
> print "inchi does not work for molecule two"
> 
> print mol2inchichemspider
> 
> 
> 
> Best,
> 
> Jon
> 
> 
> 
> On 11 April 2013 16:21, Fredrik Wallner  wrote:
> Hi again,
> 
> Some more information…
> The InChI "InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-2,7-8H,3-6H2/b2-1-,8-7-" 
> gives the same problem.
> I have now updated the ubuntu box to also run ob 2.3.2 and it segfaults now 
> as well, so it seems it has something to do with differences between 2.3.1 
> and 2.3.2.
> 
> Kind regards,
> Fredrik
> 
> 11 apr 2013 kl. 14:45 skrev Fredrik Wallner :
> 
> > Hi,
> >
> > I get a segmentation fault when running the following command:
> > obabel -iinchi 
> > -:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;"
> >  -osmi
> >
> > I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3 (installed via 
> > homerbrew).
> > I have also tried it on an Ubuntu box (10.04.4) running ob 2.3.1 and here 
> > it's working without problem. Is there anyone else having problems with 
> > this, or is it just me?
> >
> > Kind regards,
> > Fredrik
> > --
> > Precog is a next-generation analytics platform capable of advanced
> > analytics on semi-structured data. The platform includes APIs for building
> > apps and a phenomenal toolset for data science. Developers can use
> > our toolset for easy data analysis & visualization. Get a free account!
> > http://www2.precog.com/precogplatform/slashdotnewsletter
> > ___
> > OpenBabel-discuss mailing list
> > OpenBabel-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> 
> 
> --
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
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Re: [Open Babel] Segmentation fault in inchi conversion

2013-06-26 Thread Chris Morley 
I think this is due to a bug in the stereo perception code which 
appeared in v2.3.2 . It has been mentioned before on this and the 
development list but a fix is not yet committed to the development code. 
Version 2.3.1 works ok for me.

Incidentally, prefer obabel to the older babel. obabel is safer with 
incorrect input and can handle commandline options with parameters much 
better than babel.

Chris

On 26/06/2013 11:57, Fredrik Wallner wrote:
> Hi,
>
> No, I never found a solution to this. I managed a workaround for the
> specific problem (although I cannot remember for sure I believe I
> accepted some help from ChemDraw…) so my needs fainted…
>
> Kind regards,
> Fredrik
>
> 25 jun 2013 kl. 14:33 skrev Jon Fuller  >:
>
>> Hi Fredrik,
>>
>> Did you find a solution to this problem? I found a similar example:
>> I pasted example code for pybel, but running the command below with
>> both inchis in the file inchi.txt:
>> babel -iinchi inchi.txt -osdf inchi.sdf
>> Will result in "Segmentation fault: 11"
>> Remove the second inchi and the command works.
>>
>> mol1 = pybel.readstring("inchi",
>> "InChI=1S/C19H22N2O/c1-4-15-7-6-8-16(5-2)18(15)10-9-14-11-17(13-21-12-14)19(22)20-3/h6-13H,4-5H2,1-3H3,(H,20,22)/b10-9+")
>>
>> print"molecule one works"
>>
>>
>> mol2smiles = pybel.readstring("smiles",
>> "O=C(OC[C@H](\C3=C2/[C@@H](O[C@H]1O[C@@H]([C@@H](O)[C@H](OC(=O)C)[C@H]1O)COC(\C=C)(C)C)[C@H](O)[C@H](C)[C@H]4C(=C/[C@@]2(C)[C@@H](O)C3)\[C@@H](COC)CC4)C)C")
>>
>> print"smiles works for molecule two!"
>>
>> print mol2smiles
>>
>>
>> mol2inchichemspider = pybel.readstring("inchi",
>> "InChI=1S/C36H56O12/c1-10-35(6,7)45-17-26-30(41)33(46-21(5)38)31(42)34(47-26)48-32-28-24(18(2)15-44-20(4)37)13-27(39)36(28,8)14-25-22(16-43-9)11-12-23(25)19(3)29(32)40/h10,14,18-19,22-23,26-27,29-34,39-42H,1,11-13,15-17H2,2-9H3/b25-14-/t18-,19-,22-,23+,26-,27+,29-,30-,31-,32-,33+,34-,36+/m1/s1")
>>
>> print"inchi does not work for molecule two"
>>
>> print mol2inchichemspider
>>
>>
>> Best,
>>
>> Jon
>>
>>
>>
>> On 11 April 2013 16:21, Fredrik Wallner > > wrote:
>>
>> Hi again,
>>
>> Some more information…
>> The InChI
>> "InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-2,7-8H,3-6H2/b2-1-,8-7-"
>> gives the same problem.
>> I have now updated the ubuntu box to also run ob 2.3.2 and it
>> segfaults now as well, so it seems it has something to do with
>> differences between 2.3.1 and 2.3.2.
>>
>> Kind regards,
>> Fredrik
>>
>> 11 apr 2013 kl. 14:45 skrev Fredrik Wallner > >:
>>
>> > Hi,
>> >
>> > I get a segmentation fault when running the following command:
>> > obabel -iinchi
>> 
>> -:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;"
>> -osmi
>> >
>> > I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3
>> (installed via homerbrew).
>> > I have also tried it on an Ubuntu box (10.04.4) running ob 2.3.1
>> and here it's working without problem. Is there anyone else having
>> problems with this, or is it just me?
>> >
>> > Kind regards,
>> > Fredrik
>> >
>> 
>> --
>> > Precog is a next-generation analytics platform capable of advanced
>> > analytics on semi-structured data. The platform includes APIs
>> for building
>> > apps and a phenomenal toolset for data science. Developers can use
>> > our toolset for easy data analysis & visualization. Get a free
>> account!
>> > http://www2.precog.com/precogplatform/slashdotnewsletter
>> > ___
>> > OpenBabel-discuss mailing list
>> > OpenBabel-discuss@lists.sourceforge.net
>> 
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>> 
>> --
>> Precog is a next-generation analytics platform capable of advanced
>> analytics on semi-structured data. The platform includes APIs for
>> building
>> apps and a phenomenal toolset for data science. Developers can use
>> our toolset for easy data analysis & visualization. Get a free
>> account!
>> http://www2.precog.com/precogplatform/slashdotnewsletter
>> ___
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> 
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>
>
>
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>
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Re: [Open Babel] Segmentation fault in inchi conversion

2013-06-26 Thread Jon Fuller 
Dear Chris and Fredrik,

Thanks for the information regarding this problem. The solution that I've
been using is to use an older version 2.3.0 to run my script.

Additional thanks for the information about the differences between obabel
and babel.

Best,

Jon


On 26 June 2013 15:01, Chris Morley  wrote:

> I think this is due to a bug in the stereo perception code which
> appeared in v2.3.2 . It has been mentioned before on this and the
> development list but a fix is not yet committed to the development code.
> Version 2.3.1 works ok for me.
>
> Incidentally, prefer obabel to the older babel. obabel is safer with
> incorrect input and can handle commandline options with parameters much
> better than babel.
>
> Chris
>
> On 26/06/2013 11:57, Fredrik Wallner wrote:
> > Hi,
> >
> > No, I never found a solution to this. I managed a workaround for the
> > specific problem (although I cannot remember for sure I believe I
> > accepted some help from ChemDraw…) so my needs fainted…
> >
> > Kind regards,
> > Fredrik
> >
> > 25 jun 2013 kl. 14:33 skrev Jon Fuller  > >:
> >
> >> Hi Fredrik,
> >>
> >> Did you find a solution to this problem? I found a similar example:
> >> I pasted example code for pybel, but running the command below with
> >> both inchis in the file inchi.txt:
> >> babel -iinchi inchi.txt -osdf inchi.sdf
> >> Will result in "Segmentation fault: 11"
> >> Remove the second inchi and the command works.
> >>
> >> mol1 = pybel.readstring("inchi",
> >>
> "InChI=1S/C19H22N2O/c1-4-15-7-6-8-16(5-2)18(15)10-9-14-11-17(13-21-12-14)19(22)20-3/h6-13H,4-5H2,1-3H3,(H,20,22)/b10-9+")
> >>
> >> print"molecule one works"
> >>
> >>
> >> mol2smiles = pybel.readstring("smiles",
> >> "O=C(OC[C@H](\C3=C2/[C@@H](O[C@H]1O[C@@H]([C@@H](O)[C@H](OC(=O)C)[C@H
> ]1O)COC(\C=C)(C)C)[C@H](O)[C@H](C)[C@H]4C(=C/[C@@]2(C)[C@@H](O)C3)\[C@
> @H](COC)CC4)C)C")
> >>
> >> print"smiles works for molecule two!"
> >>
> >> print mol2smiles
> >>
> >>
> >> mol2inchichemspider = pybel.readstring("inchi",
> >>
> "InChI=1S/C36H56O12/c1-10-35(6,7)45-17-26-30(41)33(46-21(5)38)31(42)34(47-26)48-32-28-24(18(2)15-44-20(4)37)13-27(39)36(28,8)14-25-22(16-43-9)11-12-23(25)19(3)29(32)40/h10,14,18-19,22-23,26-27,29-34,39-42H,1,11-13,15-17H2,2-9H3/b25-14-/t18-,19-,22-,23+,26-,27+,29-,30-,31-,32-,33+,34-,36+/m1/s1")
> >>
> >> print"inchi does not work for molecule two"
> >>
> >> print mol2inchichemspider
> >>
> >>
> >> Best,
> >>
> >> Jon
> >>
> >>
> >>
> >> On 11 April 2013 16:21, Fredrik Wallner  >> > wrote:
> >>
> >> Hi again,
> >>
> >> Some more information…
> >> The InChI
> >> "InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-2,7-8H,3-6H2/b2-1-,8-7-"
> >> gives the same problem.
> >> I have now updated the ubuntu box to also run ob 2.3.2 and it
> >> segfaults now as well, so it seems it has something to do with
> >> differences between 2.3.1 and 2.3.2.
> >>
> >> Kind regards,
> >> Fredrik
> >>
> >> 11 apr 2013 kl. 14:45 skrev Fredrik Wallner  >> >:
> >>
> >> > Hi,
> >> >
> >> > I get a segmentation fault when running the following command:
> >> > obabel -iinchi
> >>
> -:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;"
> >> -osmi
> >> >
> >> > I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3
> >> (installed via homerbrew).
> >> > I have also tried it on an Ubuntu box (10.04.4) running ob 2.3.1
> >> and here it's working without problem. Is there anyone else having
> >> problems with this, or is it just me?
> >> >
> >> > Kind regards,
> >> > Fredrik
> >> >
> >>
> --
> >> > Precog is a next-generation analytics platform capable of advanced
> >> > analytics on semi-structured data. The platform includes APIs
> >> for building
> >> > apps and a phenomenal toolset for data science. Developers can use
> >> > our toolset for easy data analysis & visualization. Get a free
> >> account!
> >> > http://www2.precog.com/precogplatform/slashdotnewsletter
> >> > ___
> >> > OpenBabel-discuss mailing list
> >> > OpenBabel-discuss@lists.sourceforge.net
> >> 
> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >>
> >>
> >>
> --
> >> Precog is a next-generation analytics platform capable of advanced
> >> analytics on semi-structured data. The platform includes APIs for
> >> building
> >> apps and a phenomenal toolset for data science. Developers can use
> >> our toolset for easy data analysis & visualization. Get a free
> >> account!
> >> http://www2.precog.com/precogplatform/slashdotnewsletter
> >> _

Re: [Open Babel] Segmentation fault in inchi conversion

2013-07-08 Thread Noel O'Boyle 
I've fixed this. It's a minor change so you could apply it locally if
you want. I just moved the call to DeleteHydrogens past the stereo
section when reading the InChI:

https://github.com/baoilleach/openbabel/commit/428ac8790d3b5307305912b892e9953c793b80dc

- Noel

On 26 June 2013 14:42, Jon Fuller  wrote:
> Dear Chris and Fredrik,
>
> Thanks for the information regarding this problem. The solution that I've
> been using is to use an older version 2.3.0 to run my script.
>
> Additional thanks for the information about the differences between obabel
> and babel.
>
> Best,
>
> Jon
>
>
> On 26 June 2013 15:01, Chris Morley  wrote:
>>
>> I think this is due to a bug in the stereo perception code which
>> appeared in v2.3.2 . It has been mentioned before on this and the
>> development list but a fix is not yet committed to the development code.
>> Version 2.3.1 works ok for me.
>>
>> Incidentally, prefer obabel to the older babel. obabel is safer with
>> incorrect input and can handle commandline options with parameters much
>> better than babel.
>>
>> Chris
>>
>> On 26/06/2013 11:57, Fredrik Wallner wrote:
>> > Hi,
>> >
>> > No, I never found a solution to this. I managed a workaround for the
>> > specific problem (although I cannot remember for sure I believe I
>> > accepted some help from ChemDraw…) so my needs fainted…
>> >
>> > Kind regards,
>> > Fredrik
>> >
>> > 25 jun 2013 kl. 14:33 skrev Jon Fuller > > >:
>> >
>> >> Hi Fredrik,
>> >>
>> >> Did you find a solution to this problem? I found a similar example:
>> >> I pasted example code for pybel, but running the command below with
>> >> both inchis in the file inchi.txt:
>> >> babel -iinchi inchi.txt -osdf inchi.sdf
>> >> Will result in "Segmentation fault: 11"
>> >> Remove the second inchi and the command works.
>> >>
>> >> mol1 = pybel.readstring("inchi",
>> >>
>> >> "InChI=1S/C19H22N2O/c1-4-15-7-6-8-16(5-2)18(15)10-9-14-11-17(13-21-12-14)19(22)20-3/h6-13H,4-5H2,1-3H3,(H,20,22)/b10-9+")
>> >>
>> >> print"molecule one works"
>> >>
>> >>
>> >> mol2smiles = pybel.readstring("smiles",
>> >>
>> >> "O=C(OC[C@H](\C3=C2/[C@@H](O[C@H]1O[C@@H]([C@@H](O)[C@H](OC(=O)C)[C@H]1O)COC(\C=C)(C)C)[C@H](O)[C@H](C)[C@H]4C(=C/[C@@]2(C)[C@@H](O)C3)\[C@@H](COC)CC4)C)C")
>> >>
>> >> print"smiles works for molecule two!"
>> >>
>> >> print mol2smiles
>> >>
>> >>
>> >> mol2inchichemspider = pybel.readstring("inchi",
>> >>
>> >> "InChI=1S/C36H56O12/c1-10-35(6,7)45-17-26-30(41)33(46-21(5)38)31(42)34(47-26)48-32-28-24(18(2)15-44-20(4)37)13-27(39)36(28,8)14-25-22(16-43-9)11-12-23(25)19(3)29(32)40/h10,14,18-19,22-23,26-27,29-34,39-42H,1,11-13,15-17H2,2-9H3/b25-14-/t18-,19-,22-,23+,26-,27+,29-,30-,31-,32-,33+,34-,36+/m1/s1")
>> >>
>> >> print"inchi does not work for molecule two"
>> >>
>> >> print mol2inchichemspider
>> >>
>> >>
>> >> Best,
>> >>
>> >> Jon
>> >>
>> >>
>> >>
>> >> On 11 April 2013 16:21, Fredrik Wallner > >> > wrote:
>> >>
>> >> Hi again,
>> >>
>> >> Some more information…
>> >> The InChI
>> >> "InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-2,7-8H,3-6H2/b2-1-,8-7-"
>> >> gives the same problem.
>> >> I have now updated the ubuntu box to also run ob 2.3.2 and it
>> >> segfaults now as well, so it seems it has something to do with
>> >> differences between 2.3.1 and 2.3.2.
>> >>
>> >> Kind regards,
>> >> Fredrik
>> >>
>> >> 11 apr 2013 kl. 14:45 skrev Fredrik Wallner > >> >:
>> >>
>> >> > Hi,
>> >> >
>> >> > I get a segmentation fault when running the following command:
>> >> > obabel -iinchi
>> >>
>> >> -:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;"
>> >> -osmi
>> >> >
>> >> > I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3
>> >> (installed via homerbrew).
>> >> > I have also tried it on an Ubuntu box (10.04.4) running ob 2.3.1
>> >> and here it's working without problem. Is there anyone else having
>> >> problems with this, or is it just me?
>> >> >
>> >> > Kind regards,
>> >> > Fredrik
>> >> >
>> >>
>> >> --
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>> >> > OpenBabel-discuss@lists.sourceforge.net
>> >> 
>> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >>
>> >>
>> >>
>> >> -