Add delete_atoms method and use bonding info for add_hatoms SO107 #178
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dormrod
commented
Nov 26, 2024
GiulioIlBen
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Nov 29, 2024
mol/molecule.py
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| @@ -3354,6 +3374,8 @@ def add_hatoms(self) -> "Molecule": | |||
| ) | |||
| p.communicate() | |||
| retmol = self.__class__(f_out.name) | |||
| if any(self.bonds): | |||
| retmol.guess_bonds() | |||
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I do not understand why we should guess bonds by default. I would remove this line.
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Previously the behaviour was that if you do add_hatoms to a molecule that already has bonds, the result will have no bonds at all, as it recreates a molecule from an xyz. This change means that if the previous molecule has bonds, it will guess them. But I can remove it if you think it is unexpected here.
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I have found a way to get the bonding information out of amsprep, so have used this instead of guess bonds
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Description
Two small changes to
Molecule:delete_atoms: add a method to delete multiple atoms in a single call. This uses "partial success" so that all passed atoms will attempted to be deleted, even if one of them fails.add_hatoms: use a.infile to amsprep instead of a.xyzso bonding information is respected when adding h-atoms. Also perform a guess bonds on the output, if there were bonds on the original molecule.