Remove old score graph system and update tests (#238)

* working but flawed rework of modules tests

* move getting torsions into TorsionalEnergyNetwork

* rearrange score_support.py

* modify test_dof_space.py for removing score graph

* add ScoreSystem.intra_subscores for distinguishing poses and scoreterms

* un-comment-out test_score_graph (mistakenly commented out)

* remove some unused imports

* empty out score_module_support.py

* fix name of get_full_score_system_for parameter

* remove score imports from modules.py

* remove old graph from test_score_weights.py

* deletion of pieces of score graph and interatomic distance

* delete score_graph.py

* remove some score_graph imports from tests

* delete more remnants of score_graph

* restore delted dof minimization test

* delete some tests

* delete some score_graph imports in __init__.pys

* rename a member of cartesianenergynetwork

* move a single test from a deleted test file that we still want

* bad test_scoreterm_benchmarks.py

* first attempt at corrected score system intra total and benchmark test

* remove import

* modify test_total_gradcheck.py

* modify test_totalscore_benchmarks.py

* restore bonded path length (why was it deleted?)

* fix brackets in bonded_path_length

* fix some bonded atom imports

* remove score graph from ljlk test baseline

* update lk_ball/test_baseline.py

* update test_chemical_database.py imports

* update omega/test_baseline.py

* update rama/test_baseline.py

* fix import in test_dof_modules.py

* test_modules.py reflect intra_total namechange

* add todo notes for Tuesday

* change return value of score method intra forward

* fix ScoreSystem.intra_total

* update modules tests

* add helpers for term keywords

* modify more tests

* rename lk_ball terms

* update baseline tests

* update more tests

* fix lk_ball keys

* remove viewer

* delete intra_score_only

* delete intra_subscores

* delete old score_components.py

* delete old score_weights.py

* delete old factory_mixin.py

* delete old score_graph.py for each score method

* rename tests that used the word graph

* rename one more test parameter

* delete empty score_module_support.py

* use full word and move keyword to score_support for constraints

* update weights_keyword_to_score_method

* rename references to graph in tests

* refactor TorsionalEnergyNetwork and attempt to add mask

* rename dunbrack_one_two_three

* mask improvement and mask test

* remove unused import from test_dof_modules.py

* use specific default score weights

* Revert "remove unused import from test_dof_modules.py"

This reverts commit 8fd1562.

* masking for cartesian energy network

* change lr of LBFGS_Armijo back to 0.1 in test_modules.py

* update cartbonded/test_bench.py

* micro linting fixes

* corrections to micro linting

* remove unused variable

* add directive to ignore actually-used import

* shift noqa statement

* fix torch device in cartbonded/test_bench and ScoreSystem.intra_total

* use default torch device for minimization

* use designated device in test_scoreterm_benchmarks.py

Delete LICENSE.txt

Create module.