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Structure.copy() does not carry bond orders #1255

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Structure.copy() does not carry bond orders#1255
@sebastianmdick

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@sebastianmdick
sebastianmdick
opened on Jun 30, 2022

Copying a Structure causes all bond orders to be reset to 1.0.
This can be easily trace back to the lack of bond order specified in

ParmEd/parmed/structure.py

Lines 474 to 479 in b9f2955

for b in self.bonds:
c.bonds.append(
Bond(atoms[b.atom1.idx], atoms[b.atom2.idx],
b.type and c.bond_types[b.type.idx])
)
c.bonds[-1].funct = b.funct

so should be a straightforward fix.

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