Re: [Open Babel] Maximum time exceeded

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

Re: [Open Babel] Maximum time exceeded

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: >

[Open Babel] Installation issue on python 32bit

Hello! I'm writing because I'm having some issues installing the python bindings for Openbabel on Windows (python 32 bit). I followed the instructions on this website but I get the following error. [cid:image001.jpg@01D28B92.20148EF0] It's worth mentionin

Re: [Open Babel] Maximum time exceeded

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

Re: [Open Babel] Maximum time exceeded

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