Re: [Open Babel] gen3d doesn't convert all compounds

2017-10-26 Thread Sundar
Hi David and Geoff, I ran the calculation again to reproduce the problem and realized that it was my computer's memory that caused the program to abort not converting all the compounds. This time it converted all compounds. So no worries there. I still got several following warnings though. "*** O

Re: [Open Babel] gen3d doesn't convert all compounds

2017-10-25 Thread Geoffrey Hutchison
> Are you able to provide files that show this? Or reduce it to single > compounds that are being eliminated that can be shared? Even if it’s only a subset, that would be helpful. I’m working on a distance geometry method that should offer increased range. Either way, having examples is crucial

Re: [Open Babel] gen3d doesn't convert all compounds

2017-10-25 Thread David Hall
Are you able to provide files that show this? Or reduce it to single compounds that are being eliminated that can be shared? > On Oct 24, 2017, at 8:53 PM, Sundar wrote: > > Hi, > > I am refreshing this thread for an answer. > > obabel input.smi -h -r -b -c --unique --gen2d --partialcharge m

Re: [Open Babel] gen3d doesn't convert all compounds

2017-10-13 Thread Sundar Jubilant
Yes. Sundar Thangapandian > On Oct 13, 2017, at 3:08 PM, David Hall wrote: > > I assume your second command is actually using output2D.sdf as input? > > -David > >> On Oct 13, 2017, at 3:46 PM, Sundar wrote: >> >> Sure. >> Here it goes. >> >> obabel input.smi -h -r -b -c --unique --gen2d

Re: [Open Babel] gen3d doesn't convert all compounds

2017-10-13 Thread David Hall
I assume your second command is actually using output2D.sdf as input? -David > On Oct 13, 2017, at 3:46 PM, Sundar wrote: > > Sure. > Here it goes. > > obabel input.smi -h -r -b -c --unique --gen2d --partialcharge mmff94 -O > output2D.sdf > obabel output3D.sdf --gen3d -O output3D.sdf > > out

Re: [Open Babel] gen3d doesn't convert all compounds

2017-10-13 Thread Sundar
Sure. Here it goes. obabel input.smi -h -r -b -c --unique --gen2d --partialcharge mmff94 -O output2D.sdf obabel output3D.sdf --gen3d -O output3D.sdf output2D.sdf contains 7581 compounds exactly as in input.smi but output3D.sdf only has 881 compounds. Thanks, Sundar On Fri, Oct 13, 2017 at 2:18

Re: [Open Babel] gen3d doesn't convert all compounds

2017-10-13 Thread Noel O'Boyle
I'm a bit confused. Can you write out in full the commands you used? On 13 Oct 2017 6:53 p.m., "Sundar" wrote: > Hi Noel, > > No. I used --unique option to generate 2D coformations from smiles and got > ~7000 compounds. > While generating 3D from the 2D I only used --gen3d > > Thanks, > Jubilant

Re: [Open Babel] gen3d doesn't convert all compounds

2017-10-13 Thread Sundar
Hi Noel, No. I used --unique option to generate 2D coformations from smiles and got ~7000 compounds. While generating 3D from the 2D I only used --gen3d Thanks, Jubilant On Fri, Oct 13, 2017 at 11:28 AM, Noel O'Boyle wrote: > Hi there, > > The "--unique" option removes duplicates. My guess is

Re: [Open Babel] gen3d doesn't convert all compounds

2017-10-13 Thread Noel O'Boyle
Hi there, The "--unique" option removes duplicates. My guess is that you have only 800 unique compounds. Regards, - Noel On 13 October 2017 at 11:58, Sundar wrote: > Hi everyone, > > I am pretty new to OB. I am trying to convert a database of compounds > (~7000) from smiles to 3D. > I first co

[Open Babel] gen3d doesn't convert all compounds

2017-10-13 Thread Sundar
Hi everyone, I am pretty new to OB. I am trying to convert a database of compounds (~7000) from smiles to 3D. I first converted them into 2D using -h -r --unique -b -c --partialcharge mmff94 followed by --gen3d. It only converted ~800 compounds saying nothing about other conformers. Any idea it be