Surface Charge Script #67
Merged
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
Alex-AMC
requested review from
pmbulit,
siong-chin,
maloney-ccdc and
psacchi-ccdc
![github-actions[bot]](https://avatars.githubusercontent.com/in/15368?s=60&v=4){kind=small}
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
pmbulit
approved these changes
Aug 20, 2024
scripts/surface_charge/ReadMe.md
Outdated
| Example Output: | ||
|  | ||
|
|
||
| > **Note** - When comparing charges for structures out of the CSD and from mol2 files the values might be different as the bonding might not be the same. When importing a mol2 the bonding and charges have to be calculated on the fly. Whereas the CSD structures the bonding is pre-assigned. |
There was a problem hiding this comment.
Yes thank you! I got sidetracked whilst writing this note and it could probably do with re-writing anyway
| # HTML Table Footer | ||
| html += """ | ||
| </table> | ||
| <p><i> *-Surface charge is based on gasteiger partial charges <a href="https://www.sciencedirect.com/science/article/pii/S0040403901949779?via%3Dihub">10.1016/S0040-4039(01)94977-9</a></i> </p> |
There was a problem hiding this comment.
🚫 [flake8] <501> reported by reviewdog 🐶
line too long (205 > 200 characters)
| # HTML Table Footer | ||
| html += """ | ||
| </table> | ||
| <p><i> *-Surface charge is based on gasteiger partial charges <a href="https://www.sciencedirect.com/science/article/pii/S0040403901949779?via%3Dihub">10.1016/S0040-4039(01)94977-9</a></i> </p> |
There was a problem hiding this comment.
🚫 [flake8] <501> reported by reviewdog 🐶
line too long (205 > 200 characters)
|
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.
This tool returns the surface charge for a given structure and a list of supplied hkl and offsets.
The script provides a GUI that can be used from Mercury or from the command line.
The output is a HTML file with a table for all the all selected surfaces and their associated charge, projected surface areas and normalised surface charge.
GUI:
Output example: