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Fluorine fixes #1656
Fluorine fixes #1656
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Original file line number | Diff line number | Diff line change |
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@@ -548,7 +548,7 @@ def getFeatures(self): | |
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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]) | ||
# examples for F1s: HF, [F], FO, CH3F, F2 | ||
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atomTypes['X' ].setActions(incrementBond=['X'], decrementBond=['X'], formBond=['X'], breakBond=['X'], incrementRadical=[], decrementRadical=[], incrementLonePair=[], decrementLonePair=[]) | ||
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@@ -665,7 +665,7 @@ def getFeatures(self): | |
atomTypes['F1s'].setActions(incrementBond=[], decrementBond=[], formBond=['F1s'], breakBond=['F1s'], incrementRadical=['F1s'], decrementRadical=['F1s'], incrementLonePair=[], decrementLonePair=[]) | ||
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#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'] | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. While at it, and although beyond the scope of the PR title, perhaps add There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Good point with |
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#list of elements that do not have more specific atomTypes | ||
nonSpecifics=['H', 'He', 'Ne', 'Ar',] | ||
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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.