Re: [Open Babel] Batch minimization of ligands

On 12/27/2016 05:23 PM, David Hall wrote: > I would iterate over the molecules using pybel, calling localopt on each > molecule I would run obminimize under htcondor, but I do have 144-core pool here and access all the way to OSG if I need it. One could fire up hundreds of ec2 vms running

Re: [Open Babel] Batch minimization of ligands

I would iterate over the molecules using pybel, calling localopt on each molecule http://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html?highlight=pybel#pybel.Molecule.localopt On Wed, Dec 21, 2016 at 2:01 PM, ishan wrote: > Dear All, > > I have

Re: [Open Babel] Batch minimization of ligands

Hi Ishan, No, GNU parallel is not something you can use via an API. However, if you are looking forward to implement it "inherently", you should read more about parallel computing and multi threading. I have personally tried OpenMP and OpenACC with openbabel which didn't work out so well. Still

Re: [Open Babel] Batch minimization of ligands

On 2016-12-25 12:50, ishan wrote: > Hi Pranav, > > Thanks for the reply, that seems to be a nice trick, I will try it. But One > question still remains whether it is inherently possible in openbabel. ''' High Throughput Computing is a computing paradigm that focuses on the efficient execution of

Re: [Open Babel] Batch minimization of ligands

Hi Pranav, Thanks for the reply, that seems to be a nice trick, I will try it. But One question still remains whether it is inherently possible in openbabel. Regards, Ishan On Sun, Dec 25, 2016 at 12:32 AM, Pranav [via Open Babel] < ml-node+s957263n4659636...@n4.nabble.com> wrote: > Hey Ishan,