Skip to content

created nupack wrapper and a way to plot the dot bracket notation for dna #78

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

Open
Katzi93 wants to merge 6 commits into
base: main
Choose a base branch
from
Open

created nupack wrapper and a way to plot the dot bracket notation for dna #78

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
1034af8
created nupack wrapper and a way to plot the dot bracket notation for…
Katzi93 Apr 22, 2026
310fe5e
added now module to pyproject.toml. added init file for new model. ad…
Katzi93 Apr 22, 2026
190336e
slight parameter adjustments for plotting
Katzi93 Apr 22, 2026
5e1e318
wrong file name .....
Katzi93 Apr 22, 2026
ab010c6
Re-formatted nupack wrapper to match repo spec and started regularizi…
mattaq31 Apr 23, 2026
b6b2eb4
remove spaces from input sequence automatically. script to analize ba…
Katzi93 Apr 23, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions crisscross_kit/pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,7 @@ packages = [
"orthoseq_generator.streamlit_app",
"orthoseq_generator.streamlit_app.tabs",
"eqcorr2d",
"sec_struc_pred",
]
include-package-data = true

Expand Down
1 change: 1 addition & 0 deletions crisscross_kit/sec_struc_pred/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@

16 changes: 16 additions & 0 deletions crisscross_kit/sec_struc_pred/default_configs/simple_binding_example.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
sequences = [
["GCGTATGC", 1000],
["GCATACGC", 1000],
["TTTTTTTT", 100]
]

material = "dna"
celsius = 37
sodium = 0.05
magnesium = 0.015
max_complex_size = 2
compute = ["pfunc", "mfe"]
tube_name = "simple_binding_example"
strand_prefix = "seq"

[options]
2 changes: 2 additions & 0 deletions crisscross_kit/sec_struc_pred/default_outputs/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
*
!.gitignore
Loading