Hi,
This patch [1] can be used to specify a timeout. The example molecule takes
60 seconds on my computer.
[1]
https://github.com/timvdm/openbabel/commit/117b2e510c3c174e08d4e5dee71314e69ba126ea
Tim
On Tue, Feb 21, 2017 at 3:33 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Your structure is messed up (multiple crystallographic models
> overlaid), but this is independent of the canonicalisation failure.
>
> When you say it "crashes" your program, what exactly do you mean? That
> you get the error message?
>
> - Noel
>
> On 21 February 2017 at 11:11, Jan-Joris Devogelaer
> <janjoris.devogel...@gmail.com> wrote:
> > Hi,
> >
> > By trail and error I found that the CSD entry AWETAZ 'crashes' my
> program.
> > The quite lenghty SMILES code derived from the CSD (not canonical) is:
> >
> > [CH]123456[H][CH2]789%101[N]1%11%12%13%142[CH2]2%15%165[CH2]
> 5%17%10%12[CH]%10%12%18%13([CH2]%139%11([CH2]961([C]16%11%
> 19%203[H][C]49([H]1)([H]6)([H]%11)([H]%19)[H]%20)[CH2]1%142%
> 10([C]23469%15[H][C]%161([H]2)([H]3)([H]4)([H]6)[H]9)[H]%18)
> [C]123467[H][C]8%13([H]1)([H]2)([H]3)([H]4)[H]6)[C]123465[
> H][C]%17%12([H]1)([H]2)([H]3)([H]4)[H]6.CCN1(CC)[CH2]23[CH2]
> 456([C]789%10%112[H]5[C]34([H]67)([H]8)([H]9)([H]%10)[H]%11)
> N([CH2]23[CH2]4561[H]1[C]789%1025[H]4[C]361([H]7)([H]8)([H]
> 9)[H]%10)(CC)CC.CCOC(=O)COc1c2Sc3cc(cc(c3O)Sc3cc(cc(
> Sc4c(c(Sc1cc(c2)C(C)(C)C)cc(c4)C(C)(C)C)O)c3[O-])C(C)(C)C)C(C)(C)C
> >
> > I also tried converted this SMILES code to a canonical SMILES code, again
> > resulting in a maximum time error.
> >
> > Thank you,
> >
> > Jan-Joris
> >
> >
> >
> >
> > --
> > View this message in context: http://forums.openbabel.org/
> Maximum-time-exceeded-tp4659742p4659745.html
> > Sent from the General discussion mailing list archive at Nabble.com.
> >
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