def check_connectivity(bond_set, filename):
""" Check if the connectivity in the molecule file is consistent with geometry
Using force balance Molecule.build_bonds() for this first draft
This can be improved by OpenEye or other methods
"""
fbmol = Molecule(filename)
fbmol.build_bonds()
new_bonds = set(fbmol.bonds)
return bond_set == new_bonds
def check_connectivity(filename):
""" Check if the connectivity in the molecule file is consistent with geometry
Using force balance Molecule.build_bonds() for this first draft
This can be improved by OpenEye or other methods
"""
fbmol = Molecule(filename)
orig_bonds = set(fbmol.bonds)
# for b1, b2 in fbmol.bonds:
# bond = (b1, b2) if b1 < b2 else (b2, b1)
# orig_bonds.add(bond)
fbmol.build_bonds()
new_bonds = set(fbmol.bonds)
# for b1, b2 in fbmol.bonds:
# bond = (b1, b2) if b1 < b2 else (b2, b1)
# new_bonds.add(bond)
return orig_bonds == new_bonds