Skip to content

Issues: UC-Davis-molecular-computing/nuad

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

36 Open 68 Closed
36 Open 68 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

remove strand groups invalid This doesn't seem right
#258 opened Apr 17, 2024 by dave-doty
@lia-n2
matplotlib histogram of nearest neighbor energies closed in dev enhancement New feature or request
#255 opened Apr 4, 2024 by dave-doty
@dave-doty
merge Result and Evaluation
#254 opened Mar 26, 2024 by dave-doty
@lia-n2
allow subdomains to have multiple parents enhancement New feature or request
#252 opened Dec 15, 2023 by dave-doty
@lia-n2
1
generalized dependent domains enhancement New feature or request
#251 opened Dec 15, 2023 by dave-doty
@dave-doty
mismatches enhancement New feature or request
#250 opened Dec 15, 2023 by dave-doty
@dave-doty
2
do not require length parameter to Domain constructor when Domain.dependent is True and subdomains are independent invalid This doesn't seem right
#249 opened Dec 13, 2023 by dave-doty
find/use/compare black box stochastic local search optimization software
#247 opened Nov 6, 2023 by dave-doty
RNAplex output missing lines with sufficiently long input bug Something isn't working
#244 opened Oct 8, 2023 by dave-doty
use _normalize_domains_pairs_disjoint_parameters and _normalize_strands_pairs_disjoint_parameters enhancement New feature or request
#241 opened Sep 19, 2023 by dave-doty
prevent two strands with the same name bug Something isn't working
#228 opened Sep 30, 2022 by dave-doty
@lia-n2
remove declaration of private properties in classes invalid This doesn't seem right
#210 opened Jul 21, 2022 by dave-doty
@dave-doty
store StrandPair instead of Tuple[Strand, Strand] in ConstraintWithStrandPairs and make _determine_strand_pairs_to_check more efficient enhancement New feature or request
#209 opened Jul 21, 2022 by dave-doty
@dave-doty
dependent domains whose independent source is fixed should be fixed high priority invalid This doesn't seem right
#208 opened Jul 20, 2022 by dave-doty
@dave-doty
Allow inclusion of other arguments in description for constraints. enhancement New feature or request
#195 opened Jul 4, 2022 by cgevans
3
simplify API of evaluate function in constraint high priority invalid This doesn't seem right
#148 opened Dec 1, 2021 by dave-doty
create tool that allows design to be specified and pre-packaged constraints to be picked without writing Python code enhancement New feature or request
#147 opened Nov 28, 2021 by dave-doty
add more unit tests invalid This doesn't seem right
#140 opened Oct 17, 2021 by dave-doty
profile parallelism to see if speedups can be obtained enhancement New feature or request
#132 opened Oct 12, 2021 by dave-doty
add RNA parameter to pfunc and pre-packaged constraints enhancement New feature or request
#126 opened Sep 14, 2021 by dave-doty
allow quit early optimization even when there is positive probability to keep a higher-scoring change enhancement New feature or request
#124 opened Sep 14, 2021 by dave-doty
1
add tutorial documentation Improvements or additions to documentation high priority
#120 opened Sep 13, 2021 by dave-doty
incorporate O(n^2) time vectorized RNAduplex replacement for sequence pairs enhancement New feature or request
#89 opened Aug 23, 2021 by dave-doty
make independent fields private for Design/Strand/Domain, so that derived fields can be consistently recomputed by setters bug Something isn't working high priority
#78 opened Aug 18, 2021 by dave-doty
Check complex base pair probability in relation to other strands not part of the complex enhancement New feature or request
#32 opened Apr 7, 2021 by UnHumbleBen
1
ProTip! Updated in the last three days: updated:>2024-10-29.