ff rework

[MTLehner]

Description

Rework of the forcefield structure in PyGromos

Introducing a generic_forcfield and all other forcefield have this class as super. This makes code more readable and unifies the structure.

[lgtm-com[bot]]

This pull request introduces 4 alerts and fixes 1 when merging 0f7c97d8565d77f0c75387639095d08ca2d14b74 into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 2 for Wrong name for an argument in a class instantiation
• 1 for Unused local variable
• 1 for `__init__` method calls overridden method

fixed alerts:

• 1 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 3 alerts and fixes 1 when merging 3cc90e0ae6e5cd8d7c12b9d2757fc75ba7692b2c into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Wrong name for an argument in a class instantiation
• 1 for `__init__` method calls overridden method

fixed alerts:

• 1 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 3 alerts and fixes 1 when merging 2968ee564ed3c1f2caae0a70df78b15bc5c82e20 into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Wrong name for an argument in a class instantiation
• 1 for `__init__` method calls overridden method

fixed alerts:

• 1 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 2 alerts and fixes 1 when merging 381623b8671f9774ad05f0bd045bc56691996771 into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for `__init__` method calls overridden method

fixed alerts:

• 1 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 2 alerts and fixes 1 when merging dd6c14554f96027508722e57569c6831495d333c into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for `__init__` method calls overridden method

fixed alerts:

• 1 for Unused local variable

[codecov[bot]]

Codecov Report

Merging #241 (3ca5a0e) into release3 (2453683) will decrease coverage by 0.96%. The diff coverage is 47.56%.

@@             Coverage Diff              @@
##           release3     #241      +/-   ##
============================================
- Coverage     54.60%   53.63%   -0.97%     
============================================
  Files            92       91       -1     
  Lines         14034    14026       -8     
============================================
- Hits           7663     7523     -140     
- Misses         6371     6503     +132     

Flag	Coverage Δ
unittests	53.63% <47.56%> (-0.97%)	:arrow_down:

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

Impacted Files	Coverage Δ
pygromos/files/forcefield/amber/amberff.py	0.00% <0.00%> (ø)
pygromos/files/forcefield/serenityff/serenityff.py	0.00% <0.00%> (ø)
.../forcefield/serenityff/serenityff_data/__init__.py	0.00% <ø> (ø)
...ns/approaches/hvap_calculation/hvap_calculation.py	0.00% <0.00%> (ø)
pygromos/files/forcefield/gromos/gromosff.py	69.23% <69.23%> (ø)
pygromos/files/forcefield/_generic_force_field.py	86.66% <86.66%> (ø)
pygromos/files/gromos_system/gromos_system.py	67.85% <87.50%> (+1.89%)	:arrow_up:
pygromos/files/forcefield/openff/openff.py	93.09% <88.57%> (ø)
pygromos/files/topology/ifp.py	100.00% <100.00%> (ø)
pygromos/files/topology/mtb.py	100.00% <100.00%> (ø)
... and 5 more

---

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Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 2453683...3ca5a0e. Read the comment docs.

[lgtm-com[bot]]

This pull request introduces 2 alerts and fixes 1 when merging f83d550a41b1e5db1737414d9a24904cae61e684 into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for `__init__` method calls overridden method

fixed alerts:

• 1 for Unused local variable

[SalomeRonja]

Hey @MTLehner I just added amber2gromos to the reworked ff structure, and updated the corresponding example notebook. I really like the changes you made, it's a lot cleaner now than before! :)

[lgtm-com[bot]]

This pull request introduces 1 alert and fixes 1 when merging 3ca5a0e9e2be64646b60f0206d45d2dca8ca5fab into 2453683ea340eacf610e1b00ae48e0df5b109532 - view on LGTM.com

new alerts:

• 1 for `__init__` method calls overridden method

fixed alerts:

• 1 for Unused local variable

[MTLehner]

Hey @MTLehner I just added amber2gromos to the reworked ff structure, and updated the corresponding example notebook. I really like the changes you made, it's a lot cleaner now than before! :)

Thank you! Also very nice from your side. Thank you for the quick rework