Fluorine fixes #1656
Fluorine fixes #1656
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rwest
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Status: Ready for Review
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@@ Coverage Diff @@
## master #1656 +/- ##
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- Coverage 41.68% 41.67% -0.02%
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Files 176 176
Lines 29374 29374
Branches 6059 6059
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- Hits 12246 12241 -5
- Misses 16259 16263 +4
- Partials 869 870 +1
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Otherwise when trying to make a sample molecule with an F groupAtom, it fails (and crashes with a segfault)
rmgpy/molecule/atomtype.py
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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'] | |||
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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.
| @@ -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]) | |||
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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.
This list should cover all elements used in atomTypes.
A couple of small atomType fixes for Fluorine, that were causing segfaults when testing the database ReactionMechanismGenerator/RMG-database#317