fix: allow direct scheme with XTC; add CSS alias to single_bead.yaml#3
Open
pinedaps wants to merge 1 commit into
Open
fix: allow direct scheme with XTC; add CSS alias to single_bead.yaml#3pinedaps wants to merge 1 commit into
pinedaps wants to merge 1 commit into
Conversation
…CSS alias - `--box` for `direct` is now optional (no default_value in clap); when omitted without an XTC the 200 Å fallback is applied in lib.rs, preserving existing single-frame behaviour - Removes the hard error that fired even when -b was not supplied, allowing trajectory-averaged SAXS via `direct` without specifying a box - Add CSS (disulfide-bonded cysteine) as an alias for CYS in single_bead.yaml Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
--boxfor thedirectsubcommand is nowOption<f64>with no clap default. When omitted without an XTC the 200 Å fallback is applied inlib.rs, preserving existing single-frame behaviour. Previously, the clap default of 200.0 was always passed asSome(...), causing a hard error whenever--boxwas not explicitly given alongside an XTC file.CSS(disulfide-bonded cysteine, used in Faunus/Calvados coarse-grained simulations) as an alias forCYSinassets/single_bead.yaml.Test plan
directwithout--boxand without--xtcfilestill runs (uses 200 Å default)directwith--box <L>and without--xtcfilestill runs (uses provided value)directwith--xtcfileand without--boxnow runs (box read from trajectory)directwith both--xtcfileand--boxstill errors as expectedsingle_bead.yaml🤖 Generated with Claude Code