lots of code to identity and flip TMCs to new symmetry groups

[jwtoney]

lots of code to identity and flip TMCs to new symmetry groups

[codecov]

Codecov Report

Attention: Patch coverage is 5.46448% with 173 lines in your changes missing coverage. Please review.

Project coverage is 37.11%. Comparing base (6efb628) to head (a44f4ce).
Report is 47 commits behind head on main.

Files with missing lines	Patch %	Lines
molSimplify/Classes/mol3D.py	5.46%	173 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #297      +/-   ##
==========================================
- Coverage   37.23%   37.11%   -0.13%     
==========================================
  Files          89       90       +1     
  Lines       29979    30374     +395     
==========================================
+ Hits        11163    11273     +110     
- Misses      18816    19101     +285     

Flag	Coverage Δ
unittests	37.11% <5.46%> (-0.13%)	⬇️

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[gianmarco-terrones]

Looks good! Can you add some brief comments around line 6376 indicating what that code does? It seems there is code there that is copy+pasted throughout the function, so it would be better to make a helper function and just call that. Also, adding a test for the new flip_symmetry function would also be good

Code that shows up a lot in the flip_symmetry function:

vec1 = np.array(tmc_mol.atoms[lig1_catoms[swap_idx_1]].coords()) - np.array(tmc_mol.atoms[metal_idx].coords())
vec3 = np.array(tmc_mol.atoms[lig3_catoms[swap_idx_3]].coords()) - np.array(tmc_mol.atoms[metal_idx].coords())
atoms_to_move_b = lig1_atoms[swap_idx_1] + lig3_atoms[swap_idx_3]

and

vec_reflect_b = vec1 / np.linalg.norm(vec1, 2) + vec3 / np.linalg.norm(vec3, 2)
vec_reflect_b = vec_reflect_b / np.linalg.norm(vec_reflect_b, 2)
for atom_idx in atoms_to_move_b:
    vec_atoms = np.array(tmc_mol.atoms[atom_idx].coords()) - np.array(tmc_mol.atoms[metal_idx].coords())
    vec_proj = np.dot(vec_atoms, vec_reflect_b) * vec_reflect_b
    reflected_coords = np.array(tmc_mol.atoms[metal_idx].coords()) + 2 * vec_proj - vec_atoms
    tmc_mol.atoms[atom_idx].setcoords(reflected_coords)

[gianmarco-terrones]

Looks good! Down the line, a pytest for flip_symmetry would be nice, but the changes you have made I think have improved the code.

[aarongarrison]

Looks good to me! A few small changes would be nice:

• In get_symmetry, if the user asks for details, but the structure does not have 2 or 3 unique ligands, you will run into an error. Adding in a check for this would be good.
• In reflect_coords, I believe that you edit the mol3D object passed in to the function. This may lead to unintended behavior, and I recommend using copymol3D instead. However, as long as you document it, this should be fine.