Remove old scoring code

[fdimaio]

Some issues that have come up so far (will be updated as progress continues):

• There is no kinematic optimization module for new score system
• Much of the kinematic code testing used the old framework and was eliminated
• some other tests used old framework: hbond_identification, dunbrack_chi_sampler

With the latter two it is not clear if these tests are redundant or not. We can look at code coverage to see.

I will next focus on adding a kinematic optimization module

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 93.14%. Comparing base (ace29a8) to head (3dae8c3). Report is 11 commits behind head on master.

:exclamation: Current head 3dae8c3 differs from pull request most recent head dbdf026. Consider uploading reports for the commit dbdf026 to get more accurate results

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #282 +/- ## ========================================== - Coverage 94.93% 93.14% -1.80% ========================================== Files 374 297 -77 Lines 23883 19071 -4812 ========================================== - Hits 22673 17763 -4910 - Misses 1210 1308 +98 ``` | [Flag](https://app.codecov.io/gh/uw-ipd/tmol/pull/282/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | Coverage Δ | | |---|---|---| | [_shrug_Testing_CPU](https://app.codecov.io/gh/uw-ipd/tmol/pull/282/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `87.96% <100.00%> (-2.07%)` | :arrow_down: | | [_shrug_Testing_CPU_debug_w_o_jit](https://app.codecov.io/gh/uw-ipd/tmol/pull/282/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `90.37% <100.00%> (?)` | | | [_shrug_Testing_CPU_w_o_jit](https://app.codecov.io/gh/uw-ipd/tmol/pull/282/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `?` | | | [_shrug_Testing_CUDA](https://app.codecov.io/gh/uw-ipd/tmol/pull/282/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `90.71% <100.00%> (-1.67%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#carryforward-flags-in-the-pull-request-comment) to find out more.

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[jflat06]

You should be good to remove the old cartbonded database code:

https://github.com/uw-ipd/tmol/blob/0a705c3fa797b0d3ff1258539a3034e8691cff3a/tmol/database/scoring/cartbonded.py#L8-L68

https://github.com/uw-ipd/tmol/blob/0a705c3fa797b0d3ff1258539a3034e8691cff3a/tmol/database/scoring/__init__.py#L4

https://github.com/uw-ipd/tmol/blob/0a705c3fa797b0d3ff1258539a3034e8691cff3a/tmol/database/scoring/__init__.py#L19

https://github.com/uw-ipd/tmol/blob/0a705c3fa797b0d3ff1258539a3034e8691cff3a/tmol/database/scoring/__init__.py#L34-L36

[jflat06]

The DunbrackParamResolver:

https://github.com/uw-ipd/tmol/blob/0a705c3fa797b0d3ff1258539a3034e8691cff3a/tmol/score/dunbrack/params.py#L143

Is used by the new dunbrack code, but only a fairly small section of it.

You can see the scope of its usage by my new code here:

https://github.com/uw-ipd/tmol/blob/0a705c3fa797b0d3ff1258539a3034e8691cff3a/tmol/score/dunbrack/dunbrack_energy_term.py#L46-L51

It isn't immediately clear to me how to extricate the dead code from the ParamResolver, Since the new code calls from_database, which does a bunch of preprocessing of the database, it isn't as simple as removing unused functions. But I'm pretty sure most of this code is unnecessary now.

[jflat06]

Can we remove all of omega, now that it included in a sub-term of another term? Or is that in another PR? Maybe you have already done this, and I'm reading the diff wrong.

[jflat06]

This file

https://github.com/uw-ipd/tmol/blob/0a705c3fa797b0d3ff1258539a3034e8691cff3a/tmol/database/default/scoring/omega.yaml

and:

https://github.com/uw-ipd/tmol/blob/0a705c3fa797b0d3ff1258539a3034e8691cff3a/tmol/database/scoring/__init__.py#L47

Looks like they can be removed, since you added new versions for the BBdependent version.

[jflat06]

Can remove: https://github.com/uw-ipd/tmol/blob/0a705c3fa797b0d3ff1258539a3034e8691cff3a/tmol/database/default/scoring/cartbonded.old.yaml along with the other code from cartbonded above.

[jflat06]

No code removed from tmol/score/hbond/params.py - other terms seemed to either cut this entirely or partially.

[fdimaio]

Thanks! Will make these updates.

[fdimaio]

@jflat06 OK this should be ready for review

[aleaverfay]

This seems fine. It makes me think we ought to come up with some PoseStack-based initialization of the KinForest before we remove the PackedSystem code because we don't want to leave it untested or it will rot; so perhaps getting the PoseStack-based KinForest construction code is a higher priority than I first thought.

[jflat06]

I'll give my 'approval' on the parts of the code I am familiar with, but there is lots left that I don't feel confident in approving.

I don't know if we want to handle the trimming down of the DunbrackParamResolver, but it looks like that's still untouched.