An /inputs directory for typical inputs - pdbs, resfiles, fragsets, etc.
An /expected_outputs directory for all expected outputs - which can be used for the solution or for saving time in long-running steps.
An /outputs directory. This has a gitignore that will ignore ALL files. This is so that students get used to organizing their directories as should always be done. All dump pdb commands will dump them here. This also makes it easy for them to find what they did when they go through the notebooks.
All the notebooks have been updated to use this new organization.
This PR organizes all data into:
/inputsdirectory for typical inputs - pdbs, resfiles, fragsets, etc./expected_outputsdirectory for all expected outputs - which can be used for the solution or for saving time in long-running steps./outputsdirectory. This has a gitignore that will ignore ALL files. This is so that students get used to organizing their directories as should always be done. All dump pdb commands will dump them here. This also makes it easy for them to find what they did when they go through the notebooks.All the notebooks have been updated to use this new organization.