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 wrote:
> Your structure is messed up (multiple
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
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
Any chance of a test case (an example SDF or SMILES that causes the problem)?
- Noel
On 20 February 2017 at 22:38, Tim Vandermeersch
wrote:
> Hi,
>
> Unfortunatly this is not possible out-of-the-box.
>
> The SMILES format uses the default timeout (5 seconds) for calculating the
> canonical code
Hi,
Unfortunatly this is not possible out-of-the-box.
The SMILES format uses the default timeout (5 seconds) for calculating the
canonical code (specified in include/openbabel/canon.h). Changing the call
in src/formats/smilesformat.cpp from
CanonicalLabels(&mol, symmetry_classes, canonical_order
