Refactor protein-DNA forces into independent modules#28
Open
cabb99 wants to merge 53 commits into
Open
Conversation
…dds log of forces_setup.py into output sub-directory; fixes energy output log to output subdirectory; updates default steps to 1e7
Add new line to output after Caution message.
…lume parameters in protein_dna.py classes
… this maintains backward compatibility while allowing for future modification
…osition of the protein along the helical axis
Move the bias and collective-variable classes from dna.py, protein_dna.py to force/bias.py and force/collective_variables.py Only the core force-field terms exported by default. group_constraint_by_position -> bias.PositionRestraint measure_from_position -> collective_variables.DistanceFromPoint BiasElectrostaticsProteinDNA -> bias.ElectrostaticBias proteinBasePairGroupsHarmonicBias -> bias.BasePairProteinHarmonicBias proteinBasePairGroupsPosition -> collective_variables.BasePairProteinPosition StringProteinDNA (protein_dna) -> bias.StringProteinDNA Other changes: - PositionRestraint uses the geometric centroid (not the raw coordinate sum), k_new = k_old * mass - DistanceFromPoint reports the true centroid distance (not the squared deviation of a raw sum) - StringProteinDNA accepts one or many chains; its distance-only mode is now collective_variables.StringLength. - Bias/CV force-group defaults come from force_groups; readouts use MEASUREMENT.
![sourcery-ai[bot]](https://avatars.githubusercontent.com/in/48477?s=60&v=4){kind=small}
There was a problem hiding this comment.
Sorry @cabb99, your pull request is larger than the review limit of 150000 diff characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.