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scripts/ReadMe.md

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@@ -48,7 +48,6 @@ This folder contains scripts submitted by users or CCDC scientists for anyone to
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- Calculates the surface charge for a given structure and surface terminations. Runs both from CMD and Mercury.
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## Tips
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A section for top tips in using the repository and GitHub.

scripts/surface_charge/ReadMe.md

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## Summary
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This tool returns the surface charge for a given structure and list of supplied hkl and offsets.
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The script provides a GUI that can be used from Mercury or from the command line.
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This tool returns the surface charge for a given structure and list of supplied hkl and offsets.
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The script provides a GUI that can be used from Mercury or from the command line.
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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.
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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.
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Charges are currently calculated using Gasteiger charges. Further development could be made to use user derived charges. Please let me know if that is something you'd like [amoldovan@ccdc.cam.ac.uk](amoldovan@ccdc.cam.ac.uk).
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Example Output:
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Example Output:
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![Example Output](assets/example_output.png)
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> **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.
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> **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.
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## Requirements
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- Requires a minimum of CSD 2022.2
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- Requires a minimum of CSD 2022.2
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## Licensing Requirements
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## Instructions on Running
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- To Run from command line:
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```commandline
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# With an activated environment
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> python surface_charge.py
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```
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- To run from mercury:
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- To run from mercury:
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Add the folder containing the script to your Python API menu. Mercury -> CSD Python API-> Options -> Add Location. Then just select the `surface_charge.py` script from the drop down menu
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![Adding_Locations](assets/adding_location.png)
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![Selecting Scripts](assets/selecting_script.png)
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Running either from the command line or Mercury you will get the same interface allowing you to select a refcode from the CSD or input a mol2 file directly.
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Example input :
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Example input :
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![Example Input](assets/example_input.png)
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## Author

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