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Verify features values of contact submodule for grids #342

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cbaakman opened this issue Feb 3, 2023 · 5 comments
Closed

Verify features values of contact submodule for grids #342

cbaakman opened this issue Feb 3, 2023 · 5 comments
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Query query module related issues stale issue not touched from too much time testing

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@cbaakman
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cbaakman commented Feb 3, 2023

We need to test and be sure that the deeprank-core grid data contains correct electrostatic as well as vanderwaals values, like in the original deeprank. Check that the values are the same.

@cbaakman cbaakman added the nice to have low priority issues label Feb 3, 2023
@cbaakman cbaakman closed this as completed Feb 3, 2023
@cbaakman cbaakman added priority Solve this first testing and removed nice to have low priority issues labels Feb 3, 2023
@cbaakman cbaakman self-assigned this Feb 3, 2023
@cbaakman cbaakman changed the title add documentation for grid datasets verify electrostatic values for grids Feb 3, 2023
@cbaakman cbaakman reopened this Feb 3, 2023
@cbaakman cbaakman changed the title verify electrostatic values for grids verify contact values for grids Feb 6, 2023
@gcroci2 gcroci2 changed the title verify contact values for grids Verify features values of contact submodule for grids Feb 6, 2023
@gcroci2 gcroci2 added the Query query module related issues label Feb 6, 2023
@cbaakman
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cbaakman commented Feb 8, 2023

It seems the cutoff (from the old deeprank) isn't applied to the deeprank core contact features. We must incorporate this also.

@cbaakman
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cbaakman commented Feb 8, 2023

The grid values are not the same. I presume this has many reasons, but one of them is that we don't use exactly the same set of atoms. Another reason is that we also consider contacts between atoms in the same chain, not just between two chains.

@gcroci2
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gcroci2 commented Mar 3, 2023

The grid values are not the same. I presume this has many reasons, but one of them is that we don't use exactly the same set of atoms. Another reason is that we also consider contacts between atoms in the same chain, not just between two chains.

Should this be further discussed or there is already a discussion going on (either on Slack or on GitHub)? @cbaakman

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cbaakman commented Mar 3, 2023

Should this be further discussed or there is already a discussion going on (either on Slack or on GitHub)? @cbaakman

It's being discussed in #357

@gcroci2 gcroci2 linked a pull request Mar 3, 2023 that will close this issue
@gcroci2 gcroci2 moved this from To Do to In progress in Generalization - Task 2 Mar 3, 2023
@gcroci2 gcroci2 removed the priority Solve this first label Mar 6, 2023
@gcroci2 gcroci2 linked a pull request Mar 7, 2023 that will close this issue
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github-actions bot commented Apr 7, 2023

This issue is stale because it has been open for 30 days with no activity.

@github-actions github-actions bot added the stale issue not touched from too much time label Apr 7, 2023
@gcroci2 gcroci2 closed this as completed Apr 26, 2023
Generalization - Task 2 automation moved this from In progress to Done Apr 26, 2023
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