Trajectory update trc

[katzberger]

Description

Update of TRC using mdtraj.

Todos

Notable points that this PR has either accomplished or will accomplish.

• [x] Write Tests - in progress
• [x] Include more mdtraj functionality
• [x] Create dummy topology
• [x] Refactoring
• [x] Example notebook visualization
• [x] Change Cnf to also use nglview
• [x] Make future promisable
• [x] Test with gromosSystem
• [x] Write TRC
• [x] Load h5 and hdf5

[lgtm-com[bot]]

This pull request introduces 9 alerts and fixes 4 when merging ff5e3af1240c15c27aa6be41eb80bba83abe982e into b70f1133e25994fdb055e05f853799d08ed8fb49 - view on LGTM.com

new alerts:

• 5 for Unused import
• 2 for Wrong name for an argument in a class instantiation
• 1 for Unnecessary pass
• 1 for NotImplemented is not an Exception

fixed alerts:

• 1 for Testing equality to None
• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Suspicious unused loop iteration variable

[codecov[bot]]

Codecov Report

Merging #226 (7ce5690) into release3 (d3a94d5) will increase coverage by 1.05%. The diff coverage is 81.79%.

:exclamation: Current head 7ce5690 differs from pull request most recent head 0947198. Consider uploading reports for the commit 0947198 to get more accurate results

@@             Coverage Diff              @@
##           release3     #226      +/-   ##
============================================
+ Coverage     53.67%   54.73%   +1.05%     
============================================
  Files            91       91              
  Lines         13997    14148     +151     
============================================
+ Hits           7513     7744     +231     
+ Misses         6484     6404      -80     

Flag	Coverage Δ
unittests	54.73% <81.79%> (+1.05%)	:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
...ng/workers/analysis_workers/simulation_analysis.py	11.94% <0.00%> (-0.19%)	:arrow_down:
.../simulations/modules/general_simulation_modules.py	68.00% <50.00%> (+0.78%)	:arrow_up:
pygromos/files/_basics/_general_gromos_file.py	75.49% <56.00%> (+0.66%)	:arrow_up:
...ygromos/visualization/coordinates_visualization.py	76.19% <75.00%> (+15.32%)	:arrow_up:
pygromos/files/gromos_system/gromos_system.py	68.25% <76.00%> (+0.39%)	:arrow_up:
pygromos/files/trajectory/trc.py	88.36% <87.76%> (+64.58%)	:arrow_up:
pygromos/files/coord/cnf.py	44.78% <95.45%> (+0.35%)	:arrow_up:
pygromos/utils/amino_acids.py	100.00% <100.00%> (ø)
...romos/files/trajectory/blocks/trajectory_blocks.py	63.35% <0.00%> (-12.22%)	:arrow_down:
pygromos/files/trajectory/_general_trajectory.py	67.56% <0.00%> (-4.33%)	:arrow_down:
... and 6 more

---

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[lgtm-com[bot]]

This pull request introduces 6 alerts and fixes 4 when merging f92cf2b44bbb3e129fa1580e70971e43530fa2b3 into b70f1133e25994fdb055e05f853799d08ed8fb49 - view on LGTM.com

new alerts:

• 4 for Unused import
• 1 for Unnecessary pass
• 1 for NotImplemented is not an Exception

fixed alerts:

• 1 for Testing equality to None
• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Suspicious unused loop iteration variable

[lgtm-com[bot]]

This pull request introduces 6 alerts and fixes 4 when merging 982ecfdd82ef47b5d227310313f1e75315af2427 into 017c7a038be8ab39d4375d87359e145658a695e2 - view on LGTM.com

new alerts:

• 4 for Unused import
• 1 for Unnecessary pass
• 1 for NotImplemented is not an Exception

fixed alerts:

• 1 for Testing equality to None
• 1 for Unused local variable
• 1 for Except block handles 'BaseException'
• 1 for Suspicious unused loop iteration variable

[lgtm-com[bot]]

This pull request introduces 2 alerts and fixes 1 when merging c1218b80c999a5704232b3ed0739b197f18c57c9 into 129a4199cdc1a17d7044159045c6c31bc29824a8 - view on LGTM.com

new alerts:

• 1 for Unnecessary pass
• 1 for Wrong number of arguments in a call

fixed alerts:

• 1 for Suspicious unused loop iteration variable

[lgtm-com[bot]]

This pull request introduces 2 alerts and fixes 1 when merging c7fa8ed527516a1f7194b68827b3355c560d97e4 into 129a4199cdc1a17d7044159045c6c31bc29824a8 - view on LGTM.com

new alerts:

• 1 for Unnecessary pass
• 1 for Wrong number of arguments in a call

fixed alerts:

• 1 for Suspicious unused loop iteration variable

[lgtm-com[bot]]

This pull request introduces 5 alerts and fixes 3 when merging 25f108be00c299ec9ee3ff80d2dc59718f791cba into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

• 1 for Unnecessary pass
• 1 for First parameter of a method is not named 'self'
• 1 for Unused import
• 1 for Variable defined multiple times
• 1 for Redundant assignment

fixed alerts:

• 1 for Unnecessary pass
• 1 for Non-callable called
• 1 for Wrong number of arguments in a call

[lgtm-com[bot]]

This pull request introduces 4 alerts and fixes 3 when merging c65ca48ab8777c4f8163a4df20de355ecff8c817 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

• 1 for First parameter of a method is not named 'self'
• 1 for Unused import
• 1 for Variable defined multiple times
• 1 for Redundant assignment

fixed alerts:

• 1 for Unnecessary pass
• 1 for Non-callable called
• 1 for Wrong number of arguments in a call

[RiesBen]

@katzberger @MTLehner now Trc should be compatible with all gromos_system functions / simulation functionality! :)

[lgtm-com[bot]]

This pull request introduces 6 alerts when merging c6d616fd06e07f881a4000301d9773439d06a88b into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 6 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 7 alerts when merging ffdc5e9a8f5ecbccb48fa53bccedf477190f9712 into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 6 for Unused local variable
• 1 for Unreachable code

[lgtm-com[bot]]

This pull request introduces 6 alerts when merging 773b0870a1e85d98ecb27da6df513e79360b528b into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 6 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 6 alerts when merging 1bf260898254b873204c65290767e2d07b4d5797 into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 6 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 1 alert when merging b59ddb43a6dc80b97d6537941471b85755253ae7 into 79a0bf514188a8260fae4b9e34c6857bf91eb395 - view on LGTM.com

new alerts:

• 1 for Unused import

[lgtm-com[bot]]

This pull request introduces 1 alert when merging 68c74cacc56de9e13a973c02eda40ae704dcadd2 into 5716477a689a9f6703e05cd7df36ed7d017d64bd - view on LGTM.com

new alerts:

• 1 for Unused import

[lgtm-com[bot]]

This pull request introduces 1 alert when merging 6c3ff10a2a5d7d288f336a4d187f8672b2e2ec15 into d3a94d5ef5c394dd17fc02f215ce673ac71e21bf - view on LGTM.com

new alerts:

• 1 for Unused local variable