Res-centric dunbrack

[jflat06]

A rework of dunbrack to the res-centric scheme.

This still uses the DunbrackParamResolver, though portions of it to annotate the block types.

In the C++, it compresses everything down into a single kernel launch per residue.

[jflat06]

I've cleaned up most of the code and added some of the requests from the cartbonded PR to this one as well.

... which actually let me find a bug on the jagged test in cuda:

E       RuntimeError: CUDA error: an illegal memory access was encountered
E       CUDA kernel errors might be asynchronously reported at some other API call,so the stacktrace below might be incorrect.
E       For debugging consider passing CUDA_LAUNCH_BLOCKING=1.

I'll be working on debugging this next. Hopefully something obvious.

Edit: Fixed now.

[codecov[bot]]

Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (b8940ef) 95.13% compared to head (353bcbe) 95.22%. Report is 1 commits behind head on master.

:exclamation: Current head 353bcbe differs from pull request most recent head 532fb08. Consider uploading reports for the commit 532fb08 to get more accurate results

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #270 +/- ## ========================================== + Coverage 95.13% 95.22% +0.09% ========================================== Files 340 340 Lines 21546 21334 -212 ========================================== - Hits 20497 20316 -181 + Misses 1049 1018 -31 ``` | [Flag](https://app.codecov.io/gh/uw-ipd/tmol/pull/270/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/270/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `90.03% <98.70%> (+0.04%)` | :arrow_up: | | [_shrug_Testing_CPU_w_o_jit](https://app.codecov.io/gh/uw-ipd/tmol/pull/270/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `91.88% <98.70%> (+0.06%)` | :arrow_up: | | [_shrug_Testing_CUDA](https://app.codecov.io/gh/uw-ipd/tmol/pull/270/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `92.54% <99.13%> (+0.07%)` | :arrow_up: | 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. | [Files](https://app.codecov.io/gh/uw-ipd/tmol/pull/270?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | Coverage Δ | | |---|---|---| | [tmol/score/dunbrack/dunbrack\_whole\_pose\_module.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/270?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zY29yZS9kdW5icmFjay9kdW5icmFja193aG9sZV9wb3NlX21vZHVsZS5weQ==) | `100.00% <100.00%> (ø)` | | | [tmol/score/dunbrack/potentials/compiled.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/270?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zY29yZS9kdW5icmFjay9wb3RlbnRpYWxzL2NvbXBpbGVkLnB5) | `100.00% <100.00%> (ø)` | | | [tmol/score/score\_types.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/270?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zY29yZS9zY29yZV90eXBlcy5weQ==) | `100.00% <100.00%> (ø)` | | | [tmol/score/terms/dunbrack\_creator.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/270?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zY29yZS90ZXJtcy9kdW5icmFja19jcmVhdG9yLnB5) | `100.00% <100.00%> (ø)` | | | [.../tests/score/dunbrack/test\_dunbrack\_energy\_term.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/270?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC90ZXN0cy9zY29yZS9kdW5icmFjay90ZXN0X2R1bmJyYWNrX2VuZXJneV90ZXJtLnB5) | `100.00% <100.00%> (ø)` | | | [tmol/tests/score/test\_score\_function\_benchmarks.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/270?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC90ZXN0cy9zY29yZS90ZXN0X3Njb3JlX2Z1bmN0aW9uX2JlbmNobWFya3MucHk=) | `86.31% <100.00%> (+0.14%)` | :arrow_up: | | [tmol/score/dunbrack/dunbrack\_energy\_term.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/270?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zY29yZS9kdW5icmFjay9kdW5icmFja19lbmVyZ3lfdGVybS5weQ==) | `98.31% <98.31%> (ø)` | | ... and [34 files with indirect coverage changes](https://app.codecov.io/gh/uw-ipd/tmol/pull/270/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd)

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