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

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

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

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

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

[Open Babel] obminimize outputs only in pdb (multimolecule pdb)

Hi, obminimize outputs only in pdb format. I tried -osdf filename.sdf and it didn't work. How can I get it in sdf format? Or how can I convert multimolecule pdb file to an sdf file? Thanks, Sundar -- Check out the vibrant

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

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

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

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