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Pull Request Overview
This pull request introduces a new flag that controls the box size for solvent addition during protein preprocessing and updates the related function signatures and command line arguments.
- Modified the prepare_protein function to accept a new box_size parameter and adjusted solvent addition logic accordingly.
- Updated prepare_one and simulate_one signatures and the argparse configuration in batch_generate.py to pass the new box_size parameter.
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| scripts/module/preprocess.py | Added box_size parameter to prepare_protein and adjusted solvent logic. |
| scripts/batch_generate.py | Updated function signatures and argparse options to pass box_size. |
| # Add the water molecules if we're using explicit solvent | ||
| if not implicit_solvent: | ||
| modeller.addSolvent(forcefield, padding=1.0 * unit.nanometers, ionicStrength=0.15 * unit.molar) | ||
| # Attmpt to match box size |
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Correct the spelling error in the comment ('Attmpt' should be 'Attempt').
Suggested change
| # Attmpt to match box size | |
| # Attempt to match box size |
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| box_size(float): If 0.0 adds water solvent with padding = 1 Angstroms. If negative, attempts to match box size, defaulting back to padding = 1 Angstroms. If > 0, uses that value as a box size. | ||
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[nitpick] Clarify the expected units and behavior of the box_size parameter in the docstring. For example, specify that a positive value is expected in Angstroms (which is converted to nanometers inside the function) and that negative values fall back to using a padding of 1 nm.
Suggested change
| box_size(float): If 0.0 adds water solvent with padding = 1 Angstroms. If negative, attempts to match box size, defaulting back to padding = 1 Angstroms. If > 0, uses that value as a box size. | |
| box_size (float, optional): The size of the simulation box. Positive values are interpreted as the box size in Angstroms | |
| and are converted to nanometers internally. A value of 0.0 adds water solvent with a padding of 1 nm. Negative values | |
| fall back to using a default padding of 1 nm. Defaults to None. |
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added a flag for box size :D