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Fluorine fixes #1656

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merged 3 commits into from Jul 18, 2019
Merged

Fluorine fixes #1656

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c4c190e
F atom type should have no quadruple bonds
rwest Jul 17, 2019
f681d9f
F needs to be in element list.
rwest Jul 17, 2019
6e8e4ac
Also consider I atoms when making sample molecules.
rwest Jul 18, 2019
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2 changes: 1 addition & 1 deletion rmgpy/molecule/atomtype.py
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Expand Up @@ -548,7 +548,7 @@ def getFeatures(self):

atomTypes['F' ] = AtomType('F', generic=['R','R!H','Val7'], specific=['F1s'])
atomTypes['F1s'] = AtomType('F1s', generic=['R','R!H','F','Val7'], specific=[],
single=[0,1], allDouble=[0], rDouble=[], oDouble=[], sDouble=[], triple=[0], benzene=[0], lonePairs=[3], charge=[0])
single=[0,1], allDouble=[0], rDouble=[], oDouble=[], sDouble=[], triple=[0], quadruple=[0], benzene=[0], lonePairs=[3], charge=[0])
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The default value for quadruple is an empty list. Shouldn't that be enough (I guess not from your experience with F, but I wonder why)?
Perhaps a quicker fix for all elements would be to change the default behaviour of AtomType.
I suggest editing line 118 to:
self.quadruple = quadruple or [0]
so zero quadruple bonds becomes the default.

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Actually, we don't know that the default was causing a problem, we just thought we'd make Fluorine the same as Chlorine. I think our actual problem was solved by the other change.

# examples for F1s: HF, [F], FO, CH3F, F2

atomTypes['X' ].setActions(incrementBond=['X'], decrementBond=['X'], formBond=['X'], breakBond=['X'], incrementRadical=[], decrementRadical=[], incrementLonePair=[], decrementLonePair=[])
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