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openforcefield / open-forcefield-data

Datasets for open forcefield parameterization and development
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Update smartsDepict.ipynb for SMARFF with angle energies #5

Closed davidlmobley closed 8 years ago

davidlmobley commented 8 years ago

Updated ipython notebook with angle energies from John Chodera, updated so it will still run when applied to non-angle terms.

Also made a minor fix to the README.txt for SMIRFF prototype at the same time.

jchodera commented 8 years ago

Weird---I don't see any energies in the output. Does this mean it is no longer working?

davidlmobley commented 8 years ago

Er, maybe I forgot and left it so it's set to display a torsion. Lemme check.

On Wed, May 11, 2016 at 2:09 PM, John Chodera notifications@github.com wrote:

Weird---I don't see any energies in the output. Does this mean it is no longer working?

— You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHub https://github.com/open-forcefield-group/open-forcefield-data/pull/5#issuecomment-218590974

David Mobley dmobley@gmail.com 949-385-2436

davidlmobley commented 8 years ago

Sorry about that. Just uncomment the one line and comment out the other:

Smarts = '[#6X4]-[#6X4]-[#8X2]' #Angle query

Smarts = '[#6X4]-[#6X4]-[#6X4]-[#6X4]' #Torsional query

davidlmobley commented 8 years ago

(Your code wouldn't run if one specified a torsion, so I fixed it so it would run - but not print any energies - until I can do #6 )

jchodera commented 8 years ago

Thanks!

Are we really sure this belongs in open-forcefield-data? What about open-forcefield-toymodels?

davidlmobley commented 8 years ago

I'm fine with putting it somewhere like that, yes.

On Wed, May 11, 2016 at 2:14 PM, John Chodera notifications@github.com wrote:

Thanks!

Are we really sure this belongs in open-forcefield-data? What about open-forcefield-toymodels?

— You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHub https://github.com/open-forcefield-group/open-forcefield-data/pull/5#issuecomment-218592379

David Mobley dmobley@gmail.com 949-385-2436