Adds IDP term#21
Open
cabb99 wants to merge 38 commits into
Open
Conversation
…for partial inclusion, and consistent with info.dat for full inclusion
cabb99
commented
Jun 21, 2024
| group = atomGroup # atomGroup = [0, 1, 10, 12] means include residue 1, 2, 11, 13. | ||
| n = len(group) | ||
| normalization = n*n | ||
| rg_square = CustomBondForce(f"1.0/{normalization}*r^2") |
Owner
Author
There was a problem hiding this comment.
Review the units. OpenMM default units are in nanometers and the factors seem to be in Angstrom.
cabb99
commented
Jul 16, 2024
| structure_interactions.append(structure_interaction) | ||
| # print("Done reading") | ||
| # print(structure_interactions) | ||
| print(structure_interactions) |
| print(f"Including partial q value computation, start residue index: {startResidueIndex}, end residue index: {endResidueIndex}, residueIndexGroup: {residueIndexGroup}") | ||
| def partial_q_value(oa, reference_pdb_file, min_seq_sep=3, a=0.1, startResidueIndex=0, endResidueIndex=-1, residueIndexGroup=None, print_residues = False, forceGroup=4): | ||
| if print_residues: | ||
| print(f"Including partial q value computation, start residue index: {startResidueIndex}, end residue index: {endResidueIndex}, residueIndexGroup: {residueIndexGroup}") |
Owner
Author
There was a problem hiding this comment.
Remove the print statements
| qvalue.addPerBondParameter("r_ijN") | ||
| qvalue.addPerBondParameter("sigma_ij") | ||
| for structure_interaction in structure_interactions: | ||
| #print(structure_interaction) |
| unit = 10 | ||
| else: | ||
| unit = 1 | ||
| rg = CustomCVForce(f"{unit}*rg_square^0.5") |
Owner
Author
There was a problem hiding this comment.
Keep using the value_in_unit method for consistency
Taking updates 2025-01-02
… write (from append), but moved the file writing code before the for-chain loop (as opposed to within the for-chain loop)
cabb99
added a commit
that referenced
this pull request
Jan 22, 2025
close fixing of stand-alone burial term
2025-04-29 update
Direct/Mediated toggle addition and fixing constraints
Constraints update
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.