Rings new #12
Merged
Rings new #12
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
pckroon
requested changes
Jun 17, 2024
Comment on lines
-46
to
-47
| if keep_bonding: | ||
| hcount -= len(mol_graph.nodes[node]['bonding']) |
There was a problem hiding this comment.
This seems rather important, and it disappeared?
There was a problem hiding this comment.
because this is actually rather tricky thing. How do you deal with aromatic bonding connectors?
| if self.all_atom: | ||
| for edge_node in edge: | ||
| if self.molecule.nodes[edge_node]['element'] != 'H': | ||
| self.molecule.nodes[edge_node]['hcount'] -= 1 |
There was a problem hiding this comment.
Suggested change
| self.molecule.nodes[edge_node]['hcount'] -= 1 | |
| self.molecule.nodes[edge_node]['hcount'] -= order |
?
There was a problem hiding this comment.
this works is the short answer; having the order there does not presumably due to aromatic bond orders
|
Hmmn, about the aromatic bond orders. I'd say you round the aromatic bond order down (to 1), and after, if your atom is aromatic you subtract another hydrogen. Let me have a look at the code |
pckroon
requested changes
Jun 24, 2024
pckroon
approved these changes
Jul 8, 2024
This was referenced Jul 8, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
pending pysmiles 2.0