Beta barrel parametrization#682
Open
everyday847 wants to merge 4 commits intoRosettaCommons:mainfrom
Open
Conversation
added 4 commits
April 30, 2026 20:46
Foundation for parametric beta-barrel backbone generation. Defines the BBPC_Parameters enum (r0, delta_omega0, delta_z0, delta_omega1 as perturbable; minor helix params from crick_params as invariant). BarrelParametrizationCalculator::build_strand() reuses the Crick equation infrastructure from helical_bundle/util, treating each barrel strand as a helix with omega0=0 on a cylindrical surface. BarrelParameters and BarrelParametersSet extend the core parametric containers with barrel-specific metadata (n_strands, shear_number, antiparallel topology, barrel_radius).
Completes the parametric beta-barrel system: - MakeBarrel/MakeBarrelStrand: builds a beta-barrel from parameters (n_strands, shear_number, r0, antiparallel topology) using Crick equations with beta_strand.crick_params - PerturbBarrel/PerturbBarrelStrand: MC perturbation of barrel parameters with per-strand or global perturbation settings - util: compute_strand_positions() derives per-strand azimuthal position, axial stagger, and inversion from barrel globals - Factory registration in init.MoverCreators/Registrators.ihh - Build system registration in protocols_a.6.src.settings - Unit tests for barrel construction and cylindrical geometry
Add omega0, delta_t, and epsilon to BBPC_Parameters enum: - omega0: superhelical twist per residue. Zero for closed barrels (strands parallel to axis); nonzero for solenoids/beta-helices (strands spiral around axis). Enables solenoid modeling. - delta_t: backbone offset in residues, matching helical bundle. - epsilon: lateral squash for non-circular cross-sections, relevant for TIM barrels and deformed barrels. build_strand() now reads these from the parameter values instead of hardcoding omega0=0 and epsilon=1. For TIM barrels, the strand elements use this calculator; alpha-helical elements between strands can be modeled with the existing helical bundle system.
Member
Member
Author
|
That's true. Really maybe the right approach is to think of this as a convenience thing: each more specialized class could ensure that the parameters being requested are generally in the range of helices/strands in their internal and collective parameters. What do you think? |
Member
|
Yes, makes sense. I'm not really doing any more Rosetta development, so
your call!
…On Fri, May 1, 2026 at 3:44 PM Andy Watkins ***@***.***> wrote:
*everyday847* left a comment (RosettaCommons/rosetta#682)
<#682 (comment)>
That's true. Really maybe the right approach is to think of this as a
convenience thing: each more specialized class could ensure that the
parameters being requested are generally in the range of helices/strands in
their internal and collective parameters. What do you think?
—
Reply to this email directly, view it on GitHub
<#682 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABACZUFZ76LXRFMRO3LOPJT4YT5CRAVCNFSM6AAAAACYNSKBEGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DGNRRGI3TGOBWGE>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
You are receiving this because you commented.Message ID:
***@***.***>
|
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
2 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.