72 lack of solvents for packmol tool #73
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…d in the files/ directory
…d in the files/ directory
…kmol needs the pdb files in the same directory. files/pdb doesnt work. Corrected copy and pasting temporarily the pdb files from the path_registry and deleting after termination
…ame, id and description
SamCox822
reviewed
Jan 31, 2024
…le name instead of just the protein identifier making the name longer. 2. Adding some printing statements for clarity in case of errors for the user. 3. Fix registry of the path of packed structures. It mapped them originally when they where at the root directory and then moved the file to the files/pdb directory. Next calls of the file was failing because of this
SamCox822
approved these changes
Feb 7, 2024
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Basically what ive said in the issue #72. Added two solvents in files for future use.
Additionally, it improved the path_Registy initialization. As of now, it checks if there are already files downloaded.
Finally, I had to solve some Packmol bugs: Packmol needed the files in the root directory. My solution was to temporarily copy the registry files to the root directory. Once the tool is finished, it gets deleted.
To test the packmol tool (and nothing else), this was my prompt:
"Make a solvated box with protein 1A3N and 1000 water molecules using the packmol tool." You can reduce it to 100 or 10 to make it run faster (couple seconds)