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edp [2024/03/21 18:31] – editedp [2024/03/21 18:39] (current) – edit
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   - First edit the script **format.py**. Edit the LIPID_NAMES and LIPID_ABBRS lists. The script automatically changes the .cmp and.sim files, but this can be changed by editing the FILE_ENDINGS list. One side effect is that the comments at the start of the file will also be targeted by the regex, but this effect is minimal. The script will substitute all 'z's in atom names with a 26. If there is a different substitution you would prefer you can change that. You can also choose to either modify the original .sim files or create new formatted files. It is recommended to leave MODIFY_FILES to False to avoid having to regenerate the .sim and .cmp files if something goes wrong. Once you have edited the script, make sure you have loaded python with **module load python**. Then run the script with **python format.py**   - First edit the script **format.py**. Edit the LIPID_NAMES and LIPID_ABBRS lists. The script automatically changes the .cmp and.sim files, but this can be changed by editing the FILE_ENDINGS list. One side effect is that the comments at the start of the file will also be targeted by the regex, but this effect is minimal. The script will substitute all 'z's in atom names with a 26. If there is a different substitution you would prefer you can change that. You can also choose to either modify the original .sim files or create new formatted files. It is recommended to leave MODIFY_FILES to False to avoid having to regenerate the .sim and .cmp files if something goes wrong. Once you have edited the script, make sure you have loaded python with **module load python**. Then run the script with **python format.py**
-  - Next, edit the script **generate_excel_file.py**. Edit the LIPIDS list to add the lipid.sim files you want to compile. If in the previous step you generated new files, make sure to set USE_NEW_FILES to True. If this is the first time you have run this, you will need to install xlsxwriter for python. Do this with the following command: **pip install -/--user XlsxWriter**. Then, run the script with **python generate_excel_file.py**+  - Next, edit the script **generate_excel_file.py**. Edit the LIPIDS list to add the lipid.sim files you want to compile. If in the previous step you generated new files, make sure to set USE_NEW_FILES to True. If this is the first time you have run this, you will need to install xlsxwriter for python. Do this with the following command: **pip install %%--%%user XlsxWriter**. Then, run the script with **python generate_excel_file.py**
   - This will generate an excel file titled **sim_data.xlsx** along with .csv files for each lipid.   - This will generate an excel file titled **sim_data.xlsx** along with .csv files for each lipid.
 **Old method of renaming atoms and compiling in an excel file** **Old method of renaming atoms and compiling in an excel file**
edp.txt · Last modified: 2024/03/21 18:39 by edit