Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fluorine fixes #1656

Merged
merged 3 commits into from Jul 18, 2019
Merged

Fluorine fixes #1656

Changes from 1 commit
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
2 changes: 1 addition & 1 deletion rmgpy/molecule/atomtype.py
View file
Open in desktop
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']
Copy link
Member

Choose a reason for hiding this comment

The 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 I as well?
BTW, if Ar is here, should we also consider He and Ne?

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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',]

Expand Down