Update solventcomponent to encompass all composition properties

[IAlibay]

Fixes #261

[pep8speaks]

Hello @IAlibay! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file gufe/components/solventcomponent.py:

Line 21:80: E501 line too long (80 > 79 characters)
Line 23:80: E501 line too long (106 > 79 characters)
Line 70:80: E501 line too long (80 > 79 characters)
Line 71:80: E501 line too long (81 > 79 characters)
Line 73:80: E501 line too long (93 > 79 characters)
Line 113:80: E501 line too long (133 > 79 characters)
Line 179:13: E129 visually indented line with same indent as next logical line
Line 198:17: E129 visually indented line with same indent as next logical line
Line 213:5: E129 visually indented line with same indent as next logical line
Line 213:80: E501 line too long (85 > 79 characters)

• In the file gufe/tests/test_chemicalsystem.py:

Line 122:80: E501 line too long (200 > 79 characters)

• In the file gufe/tests/test_solvents.py:

Line 215:80: E501 line too long (107 > 79 characters)

• In the file gufe/tests/test_transformation.py:

Line 35:80: E501 line too long (514 > 79 characters)
Line 130:80: E501 line too long (553 > 79 characters)

Comment last updated at 2023-12-27 23:52:45 UTC

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (ae96d30) 99.20% compared to head (02284dc) 99.23%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #262      +/-   ##
==========================================
+ Coverage   99.20%   99.23%   +0.02%     
==========================================
  Files          36       36              
  Lines        1898     1963      +65     
==========================================
+ Hits         1883     1948      +65     
  Misses         15       15              

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[IAlibay]

This is probably the wrong way to do this

[IAlibay]

missing box_size

[richardjgowers]

I'm not sure this is fitting the model we've got currently. ChemicalSystem is meant to capture things that can affect the free energy differences between different ChemicalSystems. This instead seems to be trying to capture a molecular simulation setup, which is different. The solvation additions here shouldn't be affecting the measured (D)DG; padding should be enough that isn't affecting (D)DG, box shape should also be unimportant.

I think the fields num_solvent / padding / vectors are implementation details and should be in a Settings object not here. E.g. if I ran ChemicalSystem(w/ LigA) -> ChemicalSystem(w/ LigB) using a triclinic box, and ChemicalSystem(w/ LigA) -> ChemicalSystem(w/ LigB) with a rectangular box, these two ChemicalSystem(w/ LigA) are identical.

[richardjgowers]

Once we get to storing boxes, I'm not sure it makes sense to store the box_shape independently of the vectors, the vectors can/should define the shape.

[IAlibay]

Not everyone can handle dealing with both - it's too much to ask users to provide box vectors a priori.

[richardjgowers]

this is probably worth including, as it does affect the reduced potential

[IAlibay]

I'm not sure what you mean here - density is a function of N and volume, everything here defines both of those things.

[richardjgowers]

Putting in box_vectors will be needed for explicit solvents, but I don't think we'll need to backport that field to this definition

[IAlibay]

@richardjgowers solvation, particularly the number of waters does affect both the dH (which we will want to be able to calculate), and the dG under certain circumstances.