Re: [Open Babel] Batch minimization of ligands

2016-12-27 Thread Dimitri Maziuk 
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 obminimize, too, if one's willing to pay for that. Or
just "for i in *.mol ; do nohup obminimize ... & ; done"

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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu



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Re: [Open Babel] Batch minimization of ligands

2016-12-27 Thread David Hall 
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 prepared ligands in chemsketch, now I have to do energy minimization
> of the molecules before docking. I want this to be done in batch mode as
> there are hundreds of ligands. I have used obminimize -ff MMFF94 -sd
> input.mol > output.mol which does only for one molecule.
> Is it possible to do batch energy minimization in openbabel? Can anybody
> suggest me the correct command to do batch minimization?
>
> Thanks and Regards
> Ishan
>
>
>
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Re: [Open Babel] Batch minimization of ligands

2016-12-27 Thread Pranav 
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 if the code you
are trying to make parallel has no backward dependency, you can modify the
openbabel code and compile it all over again.

Thanks,
Pranav  



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Re: [Open Babel] Batch minimization of ligands

2016-12-26 Thread Dimitri Maziuk 
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 a large number of loosely-coupled tasks, while 
High Performance Computing systems tend to focus on tightly coupled 
parallel jobs, and as such they must execute within a particular site 
with low-latency interconnects.
'''

How tightly are your ligand minimizations coupled?

Dima


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Re: [Open Babel] Batch minimization of ligands

2016-12-26 Thread ishan 
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,
>
> You can use "GNU parallel" if you are using Linux/ Unix on a multi-core
> processor. You may have to use variables for filenames. Hope you find it
> helpful.
>
> Pranav
>
>
>
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> 
> .
> NAML
> 
>




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Re: [Open Babel] Batch minimization of ligands

2016-12-24 Thread Pranav 
Hey Ishan,

You can use "GNU parallel" if you are using Linux/ Unix on a multi-core
processor. You may have to use variables for filenames. Hope you find it
helpful.

Pranav





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[Open Babel] Batch minimization of ligands

2016-12-24 Thread ishan 
Dear All,

I have prepared ligands in chemsketch, now I have to do energy minimization
of the molecules before docking. I want this to be done in batch mode as
there are hundreds of ligands. I have used obminimize -ff MMFF94 -sd
input.mol > output.mol which does only for one molecule. 
Is it possible to do batch energy minimization in openbabel? Can anybody
suggest me the correct command to do batch minimization?

Thanks and Regards
Ishan



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