Solvation Free Energy

[katzberger]

Description

Changes needed to Calculate Solvation Free Energies

Status

• [ ] Ready to go

[katzberger]

Very nice PR. Could you also provide a JNB in the examples? @katzberger

Yes, I allready have on from the PyGromos day, one moment.

[codecov[bot]]

Codecov Report

Merging #206 (a6a7e6b) into release3 (4cb51b5) will increase coverage by 3.26%. The diff coverage is 53.67%.

@@             Coverage Diff              @@
##           release3     #206      +/-   ##
============================================
+ Coverage     50.32%   53.59%   +3.26%     
============================================
  Files            90       92       +2     
  Lines         11715    12450     +735     
============================================
+ Hits           5896     6672     +776     
+ Misses         5819     5778      -41     

Flag	Coverage Δ
unittests	53.59% <53.67%> (+3.26%)	:arrow_up:

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

Impacted Files	Coverage Δ
pygromos/files/blocks/coord_blocks.py	71.30% <0.00%> (+2.88%)	:arrow_up:
pygromos/files/blocks/topology_blocks.py	78.75% <39.03%> (-5.07%)	:arrow_down:
...n_free_energy_calculation/solvation_free_energy.py	54.51% <54.51%> (ø)
pygromos/analysis/error_estimate.py	100.00% <100.00%> (ø)
pygromos/files/blocks/imd_blocks.py	76.96% <100.00%> (+0.82%)	:arrow_up:
pygromos/files/trajectory/tre.py	43.92% <0.00%> (-7.89%)	:arrow_down:
pygromos/utils/utils.py	73.21% <0.00%> (-6.20%)	:arrow_down:
pygromos/analysis/coordinate_analysis.py	29.41% <0.00%> (-3.93%)	:arrow_down:
pygromos/files/qmmm/qmmm.py	90.00% <0.00%> (-1.84%)	:arrow_down:
pygromos/files/gromos_system/gromos_system.py	66.46% <0.00%> (-0.96%)	:arrow_down:
... and 22 more

---

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[MTLehner]

Oh, and could you please add some unit test? At least for the file classes, since we can't run simulations

[lgtm-com[bot]]

This pull request introduces 10 alerts when merging 78e210c00f87d63e2fb31fd0591a4e10ef079cc7 into 36cc2568ea2b4ab49ce19b80faff7a0611ff6f8c - view on LGTM.com

new alerts:

• 3 for Except block handles 'BaseException'
• 2 for `__eq__` not overridden when adding attributes
• 2 for Unused local variable
• 1 for Unreachable code
• 1 for Variable defined multiple times
• 1 for Wrong number of arguments in a call

[lgtm-com[bot]]

This pull request introduces 10 alerts when merging f4b9cc4a8077230b517abcf69f91e2aeef467a87 into 36cc2568ea2b4ab49ce19b80faff7a0611ff6f8c - view on LGTM.com

new alerts:

• 3 for Except block handles 'BaseException'
• 2 for `__eq__` not overridden when adding attributes
• 2 for Unused local variable
• 1 for Unreachable code
• 1 for Variable defined multiple times
• 1 for Wrong number of arguments in a call

[lgtm-com[bot]]

This pull request introduces 10 alerts when merging a6a7e6b80818337d1634f3f1cca2854666b157c2 into 36cc2568ea2b4ab49ce19b80faff7a0611ff6f8c - view on LGTM.com

new alerts:

• 3 for Except block handles 'BaseException'
• 2 for `__eq__` not overridden when adding attributes
• 2 for Unused local variable
• 1 for Unreachable code
• 1 for Variable defined multiple times
• 1 for Wrong number of arguments in a call

[katzberger]

Ok so from my side it would now be ready for merge. Any more suggestions?

[katzberger]

Nice! Thanks