Dimaio/bb dep omega

[fdimaio]

This code adds a backbone-dependent omega term to tmol. It matches the R3 implementation with 2 exceptions: 1) residues w/ undefined phi/psi are mapped to basic (non-bbdep) variant instead of setting undefined torsion to 0 2) preproline tables are not always used in R3 when they should be

The code replaces the rama and omega score terms with a single term, 'backbone_torsion,' that computes both in a single kernel.

[codecov[bot]]

Codecov Report

Patch coverage: 89.11% and project coverage change: -0.16% :warning:

Comparison is base (c25e66e) 95.19% compared to head (2a75671) 95.03%. Report is 3 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #269 +/- ## ========================================== - Coverage 95.19% 95.03% -0.16% ========================================== Files 331 330 -1 Lines 20508 20513 +5 ========================================== - Hits 19522 19494 -28 - Misses 986 1019 +33 ``` | [Flag](https://app.codecov.io/gh/uw-ipd/tmol/pull/269/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/269/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `89.64% <89.11%> (-0.16%)` | :arrow_down: | | [_shrug_Testing_CPU_w_o_jit](https://app.codecov.io/gh/uw-ipd/tmol/pull/269/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `91.56% <89.11%> (-0.16%)` | :arrow_down: | | [_shrug_Testing_CUDA](https://app.codecov.io/gh/uw-ipd/tmol/pull/269/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd) | `92.24% <89.11%> (-0.16%)` | :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. | [Files Changed](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?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/omega/potentials/compiled.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zY29yZS9vbWVnYS9wb3RlbnRpYWxzL2NvbXBpbGVkLnB5) | `100.00% <ø> (ø)` | | | [tmol/score/rama/potentials/compiled.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zY29yZS9yYW1hL3BvdGVudGlhbHMvY29tcGlsZWQucHk=) | `100.00% <ø> (ø)` | | | [tmol/support/scoring/rewrite\_rama\_binary.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zdXBwb3J0L3Njb3JpbmcvcmV3cml0ZV9yYW1hX2JpbmFyeS5weQ==) | `15.18% <0.00%> (ø)` | | | [...ts/optimization/test\_scorefunction\_minimization.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC90ZXN0cy9vcHRpbWl6YXRpb24vdGVzdF9zY29yZWZ1bmN0aW9uX21pbmltaXphdGlvbi5weQ==) | `100.00% <ø> (ø)` | | | [tmol/utility/cpp\_extension.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC91dGlsaXR5L2NwcF9leHRlbnNpb24ucHk=) | `98.07% <ø> (ø)` | | | [tmol/support/scoring/rewrite\_omega\_bbdep\_binary.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zdXBwb3J0L3Njb3JpbmcvcmV3cml0ZV9vbWVnYV9iYmRlcF9iaW5hcnkucHk=) | `21.95% <21.95%> (ø)` | | | [tmol/tests/support/test\_database\_converters.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC90ZXN0cy9zdXBwb3J0L3Rlc3RfZGF0YWJhc2VfY29udmVydGVycy5weQ==) | `25.35% <50.00%> (+2.27%)` | :arrow_up: | | [tmol/database/scoring/\_\_init\_\_.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9kYXRhYmFzZS9zY29yaW5nL19faW5pdF9fLnB5) | `100.00% <100.00%> (ø)` | | | [tmol/database/scoring/omega\_bbdep.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9kYXRhYmFzZS9zY29yaW5nL29tZWdhX2JiZGVwLnB5) | `100.00% <100.00%> (ø)` | | | [...l/score/backbone\_torsion/bb\_torsion\_energy\_term.py](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=uw-ipd#diff-dG1vbC9zY29yZS9iYWNrYm9uZV90b3JzaW9uL2JiX3RvcnNpb25fZW5lcmd5X3Rlcm0ucHk=) | `100.00% <100.00%> (ø)` | | | ... and [8 more](https://app.codecov.io/gh/uw-ipd/tmol/pull/269?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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[everyday847]

Question purely for documentation purposes -- what are the places in R3 where prepro isn't used where it should be? (Maybe this could inspire some improvements in R3.)