Trim coordinate_transform.py, new features for spin method

[daico007]

PR Summary:

Remove the removed methods from coordinate_transform.py. Add anchor option for Compound.spin(), so now the compound can choose an anchor to be any of its successors instead of just its center.

Pending unit tests.

PR Checklist

---

• Includes appropriate unit test(s)
• Appropriate docstring(s) are added/updated
• Code is (approximately) PEP8 compliant
• Issue(s) raised/addressed?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.56%. Comparing base (ba6fead) to head (9bf4c3b).
Report is 145 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1054      +/-   ##
==========================================
+ Coverage   90.53%   90.56%   +0.02%     
==========================================
  Files          60       60              
  Lines        8423     8406      -17     
==========================================
- Hits         7626     7613      -13     
+ Misses        797      793       -4     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[CalCraven]

Was testing out the PR on some more complicated stuff. Feel free to add these tests in!
This works:

mol = mb.load("CCCCCCO", smiles=True)
com = mol.center
for i in range(100):
    mol.spin(np.pi/2, [1,1,1], None)
    assert np.allclose(mol.center, com)

Which is to be expected because spinning by the center of mass shouldn't change the center of mass.
And this works

import mbuild as mb
import numpy as np

cpd = mb.Compound(name="center")
part = mb.Compound(name="C", pos=[0,0,0])
cpd.add(part)
mol = mb.load("CCCCCCO", smiles=True)
pos = [0,2,2]
mol.translate(pos)
com = mol.center
cpd.add(mol)

theta = np.pi/2
around = [0,0,1]
anchor = cpd.children[-1]

cpd.spin(theta, around, anchor)
assert np.allclose(cpd.children[0].pos, [2,2,0])
assert np.allclose(cpd.children[-1].center, com)

cpd.spin(theta, around, anchor)
assert np.allclose(cpd.children[0].pos, [0,4,0])
assert np.allclose(cpd.children[-1].center, com)

anchor = cpd.children[0] #set a new anchor
cpd.spin(theta, around, anchor)
assert np.allclose(cpd.children[0].pos, [0,4,0])
assert np.allclose(cpd.children[-1].center, com+np.array([2,2,0]))

[CalCraven]

If you pass it a compound, it should spin around the center of mass of that compound. This way you don't have to specify particle/compound, since it'll still use the center of mass of a single bead compound (the synonym for a particle in mbuild). Also, what does the "(self)" mean? I'm inferring that this means the value of None really will use self. Not sure if this is standard to put in the function definition, but maybe could add a bit of uncertainty?

[daico007]

so if None is provided for the anchor, the Compound will rotate around its own self.pos, which will be its center of mass, this option is for when you want rotate a compound but around one particular particle instead the center of mass (e.g., rotate a chain attached to a surface, but you want the particle attached to the surface to be fixed, or else that bond will be wonky)

[CalCraven]

This is smart.