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Fluorine fixes #1656

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merged 3 commits into from
Jul 18, 2019
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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 @@ -665,7 +665,7 @@ def getFeatures(self):
atomTypes['F1s'].setActions(incrementBond=[], decrementBond=[], formBond=['F1s'], breakBond=['F1s'], incrementRadical=['F1s'], decrementRadical=['F1s'], incrementLonePair=[], decrementLonePair=[])

#these are ordered on priority of picking if we encounter a more general atomType for make
allElements=['H', 'C', 'O', 'N', 'S', 'Si', 'Cl', 'Ne', 'Ar', 'He', 'X']
allElements=['H', 'C', 'O', 'N', 'S', 'Si', 'Cl', 'F', 'Ne', 'Ar', 'He', 'X']
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While at it, and although beyond the scope of the PR title, perhaps add I as well?
BTW, if Ar is here, should we also consider He and Ne?

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Good point with I. Added in subsequent commit.
He and Ne are already listed.

#list of elements that do not have more specific atomTypes
nonSpecifics=['H', 'He', 'Ne', 'Ar',]

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