fix(data/mmcif/smiles): don't select bond partner as StereoAtom

[bbh-pharm]

…nt neighbors

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• Resolves seoklab/casp-pipe#7.

---

Covalent 리간드이면서 공유결합 부분 때문에 말단 이중결합이 생기면, 여기서 (Chem.AssignStereochemistry(mol, force=True)) 그냥 넘어가고, Chem.AssignCIPLabels(mol, chiral_atoms, configured_bonds) 에서 segfault 되는 것 같습니다.

gmol-base/src/gmol/base/data/mmcif/smiles.py

Lines 82 to 109 in 31dd926

	# This must be done here because hydrogens could be removed
	bond: Chem.Bond
	for bond in mol.GetBonds():
	if not bond.HasProp("absolute_config"):
	continue
	if bond.GetBondType() != Chem.BondType.DOUBLE:
	continue
	# Select any configuration and neighbors, will be corrected below
	bond.SetStereo(Chem.BondStereo.STEREOE)
	ni = bond.GetBeginAtom().GetNeighbors()[0].GetIdx()
	nj = bond.GetEndAtom().GetNeighbors()[0].GetIdx()
	# Required, set which neighbor is the "stereo atom".
	bond.SetStereoAtoms(ni, nj)
	# Required, if not specified, resulting smiles omits E/Z stereochemistry
	Chem.AssignStereochemistry(mol, force=True)
	chiral_atoms: list[int] = [
	atom.GetIdx()
	for atom in mol.GetAtoms()
	if atom.HasProp("absolute_config")
	]
	configured_bonds: list[int] = [
	bond.GetIdx()
	for bond in mol.GetBonds()
	if bond.HasProp("absolute_config")
	]
	Chem.AssignCIPLabels(mol, chiral_atoms, configured_bonds)

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[codecov]

Codecov Report

❌ Patch coverage is 70.00000% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 82.79%. Comparing base (31dd926) to head (46ad130).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
src/gmol/base/data/mmcif/smiles.py	70.00%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #14      +/-   ##
==========================================
- Coverage   82.91%   82.79%   -0.12%     
==========================================
  Files          14       14              
  Lines        1580     1587       +7     
  Branches      206      207       +1     
==========================================
+ Hits         1310     1314       +4     
- Misses        217      219       +2     
- Partials       53       54       +1     

Files with missing lines	Coverage Δ
src/gmol/base/data/mmcif/smiles.py	86.15% <70.00%> (-1.66%)	⬇️

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