Scadnano

Release notes
Some bug fixes and issues below. The Python package had breaking changes, hence the change from 0.19.x to 0.20.0.

Keyboard shortcuts for selection modes
There are now keyboard shortcuts for selection modes. Hover the cursor over each button to see the keyboard shortcut:

<img width="354" alt="image" src="https://github.com/user-attachments/assets/ede19beb-ce28-4b4a-baa9-15becc4afba9" />


HelixGroups custom geometry
See also https://github.com/UC-Davis-molecular-computing/scadnano-python-package/issues/306#issuecomment-2365336899.

The Design has "geometry" parameters that can be set to control things such as rise per base pair, via Edit --> Set geometric parameters:


It is now possible to set custom geometric parameters for individual Helix groups:


For example, here are two helices in different groups, the top (helix 0) with the standard 10.5 base pairs per turn and the bottom (helix 1) with the 18 base pairs per turn of [PNA](https://en.wikipedia.org/wiki/Peptide_nucleic_acid), visualized here in the [oxView window](https://github.com/UC-Davis-molecular-computing/scadnano/releases/tag/v0.19.4):




Commits
- f6fe65e: bumped version (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 1fe7ed9: updated dart min sdk to 2.13 to turn on null safety for project and added `// dart=2.9` to all dart files to turn it off for now for individual files (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 3ae7e22: fixed null safety in two tests (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 70148c9: added some null safety to state/context_menu.dart but commented it out (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 8a88011: updated packages in prep for migration to null safety (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- f0fe1f4: fix String to Uri conversion errors (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 4375f75: added 2.9 constraint to some tests (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 9c34373: Update actions.dart (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- c9b03ff: first few null safety fixes (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 726b8c7: made actions.dart null-safe (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- c0ae8ef: migrated to null safety all middleware, actions, and files in root of lib/src; now need to handle reducers, state, and view (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- ce3a0f3: Update app_state.dart (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 69777a0: Update app_state.dart (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 8e93f21: Update menu.dart (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- b3fb06c: fixed pane width calculations (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 69d1e09: refactored some oxView code (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 0b1073a: fixedd bug with throttled actions where I was too aggressive in converting nullable ints to ints; need to be careful to check whether we actually allow some variables to be null on purpose (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- fba24cb: Update CONTRIBUTING.md (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 1f6ce3a: migrated util.dart and everything in state to null safety. Remaining is reducers and view (in that order) (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 84284ff: migrated all reducers to null safety, now "just" the view remains (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 0f9b157: removed unnecessary casts (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- fb1c7bb: Update app.dart (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 3e4eca3: migrated entire view directory to null-safety and scadnano.dart, so now whole scadnano package is null safe. only tests remain to migrate (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- fcf40e5: migrated tests to null safety... DONE! (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 82b415d: ws (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- a981249: closes 419: migrate to dart null safety mode (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 187dbb2: updated dart CI to use version 2.19.6 (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 15e1da1: Update dart_formatting.yml (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- b7809de: update github actions with dart pub instead of pub (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- dc0d18c: formatting (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 3410d3b: update CI tests action to use dart instead of pub (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 8f28436: Update dart.yml (David Doty) [989](https://github.com/UC-Davis-molecular-computing/scadnano/pull/989)
- 51f2a07: update gh-pages action dart version to 2.19.6 (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 358b234: Update gh-pages-dev.yml (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 235f81d: removed unnecessary middleware (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 635cb68: Update local_storage.dart (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 2453d53: Update app_state_reducer.dart (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- d9f5847: cleanup (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 602ece7: cleanup (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 0cca26c: cleanup (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- f8474e4: Update design_main_strand_dna_extension_end_moving.dart (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 666567c: Update menu_dropdown_right.dart (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 10cad76: cleanup (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 657f6c5: fixed bug in base pair calculation (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 6b77ed2: cleanup (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- e49014f: removed dependence on deprecated XmlSerializer (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- daab310: Update menu_form_file.dart (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- ece74bc: got rid of last Dart analyzer warnings (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- a375ee2: fixes 776 and 841 (actually earlier commits did that but I forgot to add this to the commit message) (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 42eaeba: removed codemirror dependency (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 870e7bf: updated CONTRIBUTING with instructions for installing Dart 2.19.6 (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 6c3735c: made some pre-emptive changes preparing for Dart 3 rules (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- aeec2f0: removed // dart=2.9 mistakenly left in web/main.dart, which was causing some null checks to be turned off when running the web server (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 18652f3: Update analysis_options.yaml (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- d5521d9: Update CONTRIBUTING.md (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- c51e9f1: Update design_main_strand.dart (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 995263b: added some tooltip help for assigning DNA sequences, and added two new custom scaffold sequences from Tilibit (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- bdbec35: closes 993 allow per-helix-group geometry (David Doty) [995](https://github.com/UC-Davis-molecular-computing/scadnano/pull/995)
- 828833b: removed unnecessary setting of group geometry in GroupChange reducer (David Doty) [995](https://github.com/UC-Davis-molecular-computing/scadnano/pull/995)
- 010be74: removed one helix.geometry ref (David Doty) [995](https://github.com/UC-Davis-molecular-computing/scadnano/pull/995)
- 945ff2c: fixes 992: adding keyboard shortcuts for select mode change (David Doty) [994](https://github.com/UC-Davis-molecular-computing/scadnano/pull/994)
- 4ab4bdf: removed Helix.geometry field to avoid errors introduced by new HelixGroup.geometry optional field (David Doty) [995](https://github.com/UC-Davis-molecular-computing/scadnano/pull/995)
- 588f0f9: fixed dna ends moving props geometry null bug (David Doty) [995](https://github.com/UC-Davis-molecular-computing/scadnano/pull/995)
- a57e905: fixed bug where context menu appears under oxView separator slider (David Doty) [995](https://github.com/UC-Davis-molecular-computing/scadnano/pull/995)
- db4de3e: formatting (David Doty) [995](https://github.com/UC-Davis-molecular-computing/scadnano/pull/995)
- 9b0a234: Update README.md (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 2eae2dd: Update README.md (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- a83de1a: fixes 996: display backbone angle correctly when `Geometry.base_pairs_per_turn` is not 10.5 (David Doty) [997](https://github.com/UC-Davis-molecular-computing/scadnano/pull/997)
- 796fc8d: fixed exception when cancelling dialog (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 6865786: fixed geometric parameters dialog that didn't let user type number (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- abd1c56: closes 985: fix React unique key bug in Edit menu (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 9f82fde: Update menu.dart (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- ba14bf0: fixed bug in oxView/oxDNA export when helix groups have non-zero rotation and translation (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 78f57e2: added warning if exporting strands without DNA assigned in oxView/oxDNA (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- b2adb08: Fixed 998 - Boolean Logic Error (William Orlopp) [1006](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1006)
- 50105ee: Fixed 999 - Right justified input fields in dialog (William Orlopp) [1007](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1007)
- 338a9ca: Fixed Layout for Dialogs with Inputs (William Orlopp) [1007](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1007)
- 38c4215: Added Arbitrary Gap of 10px to Dialog Input (William Orlopp) [1007](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1007)
- 5554be3: Made the Dialog Input Right-Justify Generalizable (William Orlopp) [1007](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1007)
- 23ad67e: Added Styles to Right-Justify Specific Fields (William Orlopp) [1007](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1007)
- d03a81b: Update export_cadnano_or_codenano_file.dart (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- f2e9db8: fixes bug in checking for legal cadnano export (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- af47af7: added ability to control whether base pair lines are exported for a selected strand when the other strand to which it is bound is not selected (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 35b9a9b: Updated Dependencies for Dart 3 Upgrade (William Orlopp) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- 90240ff: updated custom json serialization not to subclass JsonEncoder since it is final in Dart 3 (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- b350bab: fixed bug in paranemic crossover test case (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 8cf86d8: attempt to fix cadnano export bug (still not fixed) (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 157ef7b: Updated Dependencies to Dart 3 (William Orlopp) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- f61dadc: Reverted JSON Serializable to Dev Branch (William Orlopp) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- 63ad2b0: fixes 1004: import (previously exported) cadnano design with paranemic crossover (Dave Doty) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- 6621d14: Merge branch 'dev' into 990-upgrade-to-dart-3 (William) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- e9ecad8: Updated Dart CI for Dart v3 (William Orlopp) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- a0f2ca8: Updated Dart CI and Dart Formatting GitHub Actions (William Orlopp) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- 9af449a: Reverted to Old GitHub Workflow (William Orlopp) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- 6cb2eb4: Updated Dependencies (William Orlopp) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- 6072842: Changed Old Dart in Documentation (William Orlopp) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- 274418f: Formatted reducer_test.dart (William Orlopp) [1010](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1010)
- 92cd061: changed dart sdk lower bound to 3.5 so we can use syntactic features from that version (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 7f16b38: Update pubspec.lock (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 8f420ea: default extension location fixed (mongbean) [1014](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1014)
- 20be95d: added detail to error message to encourage bug reports to include necessary detail (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- dfebfda: changed type to modification_type and passes a boolean instead of a ModificationType (mongbean) [1014](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1014)
- d45b029: Update README.md (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)
- 95f05ca: bumped version (David Doty) [1021](https://github.com/UC-Davis-molecular-computing/scadnano/pull/1021)

Release notes
Embed oxView
You can now embed an [oxView](https://sulcgroup.github.io/oxdna-viewer/) window in scadnano that will show the current scadnano design. It exports the current design the same as clicking Export-->oxDNA and dragging the .dat and .top files it generates. (Soon we will support the oxView format directly being shown, which preserves colors and base pairs.)

Click on View-->Show oxView:


and a window will appear on the right side:


Things are a bit buggy right now, for instance if the focus is on the oxView part of the window, then keyboard shortcuts for scadnano will not be recognized (and may be interpreted by oxView instead, e.g., the delete key and undo keyboard shortcuts will be interpreted by oxView). Oddly, clicking on the design/main view, it will not restore the focus, but clicking on the gray background of the menu or slider bars will restore focus to scadnano.

In the future some more features may be added. Currently this is a read-only view; any edits to the structure in oxView are not updated in scadnano and will be lost when the scadnano design changes. One useful feature is to right click on a base and select "focus in oxview":


Which will zoom in on and select that base in oxView:


If you want to do more sophisticated things in oxView, click on the oxView
window and press `M`, and the full oxView menu will appear:


However, recall that any changes made in this way will be lost upon editing the scadnano design. To make permanent changes it is better to export to oxView via the Export menu and then load that design in a separate oxView page.



Commits
- ef386b1: bumped version (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- 94b387b: Update design_main_dna_sequence.dart (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- efab26b: removed .DS_Store and added to .gitignore (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- e073989: Update CONTRIBUTING.md (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- ac3b6f5: Update CONTRIBUTING.md (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- 18474aa: Update CONTRIBUTING.md (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- 1e25c86: added some hints for webdev errors (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- 39fba78: Update CONTRIBUTING.md (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- 6795ce7: replaced quadratic base-pair calculation in oxview export with linear-time search (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- 6e535d2: fixed bug in loading design with invalid JSON syntax (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- bb5097d: Update CONTRIBUTING.md (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- eeb65d1: Update main.dart (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- 3e75f1b: Create oxview_update_view.dart (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 1f47128: fixed middleware (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 2161d1b: added iframe to main page (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 5c82d20: using top and dat for now until we can fix the oxview iframe to accept .oxview files (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 561a762: fixed some styling of oxview and scadnano frames (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- accf6c0: fixed bad ref to oxview frame id (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- dbaec91: fixed slider separator for side pane and main pane; still can't get oxview and separator to display (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 05664b8: got oxview and separator to display; not loading design properly when show though (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 3e53221: cleaned up hover icon on separators after making them darker to distinguish from select modes (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 02aeef0: Update oxview.dart (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 58600d4: made oxview window full width in its container (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 35059e2: got hide/show oxview working almost (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- f523e9d: fixed oxview display when showing/hiding the pane. Still need to fix when design changes while pane is open, to replace instead of adding to what was there (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 3ccbe96: fixed bug where oxview displayed on startup even if show oxview is false (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- ad8e69b: added ability to focus on oxview base and fixed camera angles and reloading (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 5358919: formatted (David Doty) [978](https://github.com/UC-Davis-molecular-computing/scadnano/pull/978)
- 740d359: Update design_main_strand.dart (David Doty) [982](https://github.com/UC-Davis-molecular-computing/scadnano/pull/982)
- 2f0a36b: closes 980: remove smart_dialog package dependency (David Doty) [981](https://github.com/UC-Davis-molecular-computing/scadnano/pull/981)
- 132f191: formatting (David Doty) [981](https://github.com/UC-Davis-molecular-computing/scadnano/pull/981)

Bug fixes and one new feature: helices can be growth dynamically while moving/pasting strands: 579.



Commits
- 910189c: Closes 942 (RayBipse) [970](https://github.com/UC-Davis-molecular-computing/scadnano/pull/970)
- 75baf80: bumped version (David Doty) [976](https://github.com/UC-Davis-molecular-computing/scadnano/pull/976)
- d5ccc85: Update constants.dart (David Doty) [976](https://github.com/UC-Davis-molecular-computing/scadnano/pull/976)
- fc56866: updated some pub package versions (David Doty) [976](https://github.com/UC-Davis-molecular-computing/scadnano/pull/976)
- a7181b0: 579 grow helices dynamically as strands are drawn or pasted (967) (Abhishek Gokhale) [967](https://github.com/UC-Davis-molecular-computing/scadnano/pull/967)
- 9334aba: closes 974 (rayzhuca) [975](https://github.com/UC-Davis-molecular-computing/scadnano/pull/975)

Release notes

Several bug fixes and a few new features:

Export to oxView format
The scadnano web interface can now export to the [oxView format](https://github.com/sulcgroup/oxdna-viewer/blob/master/file-format.md), which (like oxDNA files) can be read the tool [oxView](https://sulcgroup.github.io/oxdna-viewer/).

It has been possible for a while to export to the oxDNA format, but this is nicer just for visualizing scadnano structures in oxView, because

1. The oxDNA format has two files, whereas oxView has only one.
2. The oxView format includes some extra data such as which bases are paired, and what color strands are. This information is populated with the relevant scadnano data. Have the strands be the same color in each tool makes it easier to figure out which strand is which.

For example, this scadnano design:


exports like this in oxView:


In particular, this provides an immediate visual cue that the view angle in oxView is reversed in both horizontal and vertical directions from that of scadnano, since the purple staple in the bottom right of scadnano appears in the top left of oxView. Rotating it 180 degrees around the *y* (up-down) axis, and then rotating 180 degree around the *z* (left-right) axis, then the oxView orientation matches scadnano's:


This can also be checked with the axis arrows of oxView and scadnano, which match colors:

 


Sequences of selected strands are *not* exported
There was already a feature where only sequences of selected strands could be exported. Now it is possible to declare that exactly the *unselected* strands should be exported:




Commits
- a071097: bumped version (David Doty) [972](https://github.com/UC-Davis-molecular-computing/scadnano/pull/972)
- 58cd26e: added css class for darker stroke on crossovers within the same helix (David Doty) [972](https://github.com/UC-Davis-molecular-computing/scadnano/pull/972)
- e487457: fixed batch remove label, remove name, set name (Raybipse) [954](https://github.com/UC-Davis-molecular-computing/scadnano/pull/954)
- abcecd2: fixes 953 (Raybipse) [954](https://github.com/UC-Davis-molecular-computing/scadnano/pull/954)
- 22ae227: Fixed batch remove/set for extensions and loopouts (Raybipse) [954](https://github.com/UC-Davis-molecular-computing/scadnano/pull/954)
- f72c32c: implemented logic for filtering connected base pairs (Raybipse) [955](https://github.com/UC-Davis-molecular-computing/scadnano/pull/955)
- 8657d04: Fixed typo in action name for remove strand name (Raybipse) [954](https://github.com/UC-Davis-molecular-computing/scadnano/pull/954)
- d291063: add menu option for retaining color on strand selection (Edwin Chang) [957](https://github.com/UC-Davis-molecular-computing/scadnano/pull/957)
- 1471f3f: implemented logic for filtering connected base pairs (Raybipse) [955](https://github.com/UC-Davis-molecular-computing/scadnano/pull/955)
- 17f944b: closes 895 selected base pair lines is exported (Raybipse) [955](https://github.com/UC-Davis-molecular-computing/scadnano/pull/955)
- 34ff35c: Rebased branch onto dev and fixed minor bug (Raybipse) [955](https://github.com/UC-Davis-molecular-computing/scadnano/pull/955)
- e438f97: Fixed copy image not displaying base lines (Raybipse) [955](https://github.com/UC-Davis-molecular-computing/scadnano/pull/955)
- b3dd9c7: Changed to letterSpacing (Raybipse) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- 146a350: closes 870: Feature request: selection preserves color (Edwin Chang) [957](https://github.com/UC-Davis-molecular-computing/scadnano/pull/957)
- d68babc: reformat code (Edwin Chang) [957](https://github.com/UC-Davis-molecular-computing/scadnano/pull/957)
- 94c0b0f: Refractored code for readability and consistency (RayBipse) [955](https://github.com/UC-Davis-molecular-computing/scadnano/pull/955)
- 1a66286: Setup separate export setting (RayBipse) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- 692e01d: moved set separate text menu (RayBipse) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- a0d3ac2: Added separate text support (RayBipse) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- 5d4cc56: Merge branch 'dev' of https://github.com/UC-Davis-molecular-computing/scadnano into dev (RayBipse) [#955](https://github.com/UC-Davis-molecular-computing/scadnano/pull/955)
- 760fb4a: fixes 959: display DNA sequence on extension in order 5' to 3' (David Doty) [960](https://github.com/UC-Davis-molecular-computing/scadnano/pull/960)
- 1840933: fixes bug with setting extension name when no extensions are selected (David Doty) [960](https://github.com/UC-Davis-molecular-computing/scadnano/pull/960)
- 35f4e9f: fixes bug with selecting strand "pieces" (domains/extensions/ends/etc) with new property `retain_strand_color_on_selection`, which was not being properly prop-drilled into those view components (David Doty) [960](https://github.com/UC-Davis-molecular-computing/scadnano/pull/960)
- da99847: fixed some variable/file names (David Doty) [972](https://github.com/UC-Davis-molecular-computing/scadnano/pull/972)
- c9c2894: fixed problem with non-unique React key when a strand has a 5' and a 3' extension adjacent to the same domain (David Doty) [972](https://github.com/UC-Davis-molecular-computing/scadnano/pull/972)
- 2cfac1f: Update README.md (David Doty) [972](https://github.com/UC-Davis-molecular-computing/scadnano/pull/972)
- 1e78e1e: Fixed the frequent "cannot read undefined" error in console (RayBipse) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- 63b66af: Fixes 941 (RayBipse) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- b307a48: Changed names to snakes case and fixed outline bug (RayBipse) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- bf718f2: Fixed bug export SVG main view doesn't contain a viewbox (RayBipse) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- d0adc28: Merge branch 'dev' into 941-dna-sequences-justified (Ray Zhu) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- 3ce8c86: Fixed wrong merge resolve (RayBipse) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- 3850c48: Fixed bug where selected strands were pink (RayBipse) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- a6b06ac: re-ordered export menu (David Doty) [963](https://github.com/UC-Davis-molecular-computing/scadnano/pull/963)
- 34ba098: added ability to exclude scaffolds from selection when using "select all with same..." (David Doty) [972](https://github.com/UC-Davis-molecular-computing/scadnano/pull/972)
- 33a5630: closes 964: exclude selected strands from export DNA sequences (Dave Doty) [965](https://github.com/UC-Davis-molecular-computing/scadnano/pull/965)
- 77e21ef: Added the button for base pair display (RayBipse) [966](https://github.com/UC-Davis-molecular-computing/scadnano/pull/966)
- 7c5645a: Closes 897 (RayBipse) [966](https://github.com/UC-Davis-molecular-computing/scadnano/pull/966)
- f842e25: Changed the layout for base pair display to checkboxes (RayBipse) [966](https://github.com/UC-Davis-molecular-computing/scadnano/pull/966)
- 4e75ec2: closes 588: export to oxView format (David Doty) [971](https://github.com/UC-Davis-molecular-computing/scadnano/pull/971)

Release notes

A few bug fixes.

Commits
- 3e752ec: bumped version (David Doty) [951](https://github.com/UC-Davis-molecular-computing/scadnano/pull/951)
- 7395f7f: changed "Select all with same..." trait named "IDT fields" to "Vendor fields" (David Doty) [951](https://github.com/UC-Davis-molecular-computing/scadnano/pull/951)
- 21b7287: fixes 904 large design should not hide strands on hover (Abhishek Gokhale) [949](https://github.com/UC-Davis-molecular-computing/scadnano/pull/949)
- 7da7a68: Formatting changes (Abhishek Gokhale) [949](https://github.com/UC-Davis-molecular-computing/scadnano/pull/949)
- 855fe21: Update README.md (David Doty) [951](https://github.com/UC-Davis-molecular-computing/scadnano/pull/951)
- ca85360: Update README.md (David Doty) [951](https://github.com/UC-Davis-molecular-computing/scadnano/pull/951)
- de91ace: Update README.md (David Doty) [951](https://github.com/UC-Davis-molecular-computing/scadnano/pull/951)
- 0f73968: fixes bug in reading .sc files with old modification keys (David Doty) [951](https://github.com/UC-Davis-molecular-computing/scadnano/pull/951)

Release notes

IDT fields renamed to Vendor fields
Previously, some fields had names specific to the DNA synthesis company IDT. Now, these have been renamed to the more generic "Vendor" fields:


Similarly, the field previously called "IDT text" for modifications has been renamed to "vendor code".


The vendor code is used, the same as IDT text was, when exporting DNA sequences to IDT file formats via the Export-->DNA sequences menu.

A similar change was made in the Python package: https://github.com/UC-Davis-molecular-computing/scadnano-python-package/releases/tag/v0.19.0

The change was breaking for the Python package since code using the old field names will have to be re-written. It is not a breaking change if you only use the web interface, since the code reading older `.sc` files is backwards compatible with the old field names.

Select all with same...
You can select a strand (or multiple strands) and pick Edit-->Copy/Paste/Select-->Select all with same... and select all strands that have the same "trait" as the currently selected strand.

A common case is to use Strand labels to generate "groups" of strands, where strands with the same label are considered in the same group. Then by selecting a strand with that label, and picking "Select all with same..." label:



all strands with the label are selected:




Option for selection box/rope to use intersection instead of containment
In some graphics programs, selecting many objects with a single box will select all objects *entirely contained* within the box. In others, it will select any object *intersecting* any part of the box. Scadnano's default behavior is the former, but now the latter can be done through Edit-->Copy/Paste/Select-->Selection box intersection:


Then draw a selection box:


Note that all strands touching the box are selected:


This also applies to rope select mode.

Note that, like with containment, the test for intersection is between the box (or rope-drawn polygon) and the *bounding box* containing the object (not the object itself). So for instance, although the selection box here does not appear to touch the strand, it does intersect the bounding box of the strand,


so the strand ends up selected:




Commits
- cb0d5a2: fixes 902: make menu dropdown wider for Edit-->Copy/Paste/Select (Edwin Chang) [905](https://github.com/UC-Davis-molecular-computing/scadnano/pull/905)
- 1117e88: bumped version (David Doty) [943](https://github.com/UC-Davis-molecular-computing/scadnano/pull/943)
- ff1b027: moved add modification code from design_main_strand.dart to design_main_strand_modification.dart to keep similar code together (David Doty) [943](https://github.com/UC-Davis-molecular-computing/scadnano/pull/943)
- 26bec37: fixed bug in regex for allowed bases on internal modification dialog (David Doty) [920](https://github.com/UC-Davis-molecular-computing/scadnano/pull/920)
- 3e09fab: fixes 919: display internal modifications un-attached to a base between bases (David Doty) [920](https://github.com/UC-Davis-molecular-computing/scadnano/pull/920)
- da641ab: closes 882: select all with same (David Doty) [922](https://github.com/UC-Davis-molecular-computing/scadnano/pull/922)
- ac3cb52: formatting (David Doty) [922](https://github.com/UC-Davis-molecular-computing/scadnano/pull/922)
- 4dece41: added helices as option for "Select all strands with same..." (David Doty) [943](https://github.com/UC-Davis-molecular-computing/scadnano/pull/943)
- b4fa336: closes 598: option for selection box and rope select to use intersection instead of containment (not yet implemented for rope select) (David Doty) [923](https://github.com/UC-Davis-molecular-computing/scadnano/pull/923)
- 8ff9225: formatting (David Doty) [923](https://github.com/UC-Davis-molecular-computing/scadnano/pull/923)
- b31c0dc: closes 924: option for rope select polygon to use intersection instead of containment (David Doty) [926](https://github.com/UC-Davis-molecular-computing/scadnano/pull/926)
- 7999921: Update menu.dart (David Doty) [926](https://github.com/UC-Davis-molecular-computing/scadnano/pull/926)
- 3365b50: fixed example, but problem with 921 still remains (David Doty) [928](https://github.com/UC-Davis-molecular-computing/scadnano/pull/928)
- beb614f: closes 929: rename IDTFields to VendorFields (David Doty) [930](https://github.com/UC-Davis-molecular-computing/scadnano/pull/930)
- 1b6066e: added more tooltips to modification dialogs (David Doty) [930](https://github.com/UC-Davis-molecular-computing/scadnano/pull/930)
- f325b61: bumped version (David Doty) [930](https://github.com/UC-Davis-molecular-computing/scadnano/pull/930)
- 20a2352: fixed unit test (David Doty) [930](https://github.com/UC-Davis-molecular-computing/scadnano/pull/930)
- 9abe176: Update design_footer.dart (David Doty) [943](https://github.com/UC-Davis-molecular-computing/scadnano/pull/943)
- 6208ca5: added keyboard shortcuts to Undo and Redo menus and optional `keyboard_shortcut' prop to all `MenuDropdownRight` components (David Doty) [943](https://github.com/UC-Davis-molecular-computing/scadnano/pull/943)
- da647f8: removed `display_connector` field from Modification JSON (David Doty) [932](https://github.com/UC-Davis-molecular-computing/scadnano/pull/932)
- 690c148: closes 931: remove field `Modification.id` (David Doty) [932](https://github.com/UC-Davis-molecular-computing/scadnano/pull/932)
- f82700a: Update menu.dart (David Doty) [943](https://github.com/UC-Davis-molecular-computing/scadnano/pull/943)
- 376956a: closes 934: deal with non-unique Modification vendor codes (David Doty) [935](https://github.com/UC-Davis-molecular-computing/scadnano/pull/935)
- 00cbd18: closes 917: change deploy action to use node16 (Edwin Chang) [936](https://github.com/UC-Davis-molecular-computing/scadnano/pull/936)
- d8107cb: update formatting and test actions to use latest `actions/checkout` (Edwin Chang) [936](https://github.com/UC-Davis-molecular-computing/scadnano/pull/936)
- 07a8de3: moved "Show helix coordinates in side view" to View-->Helices submenu and made helix dialogs for setting grid position and position not use saved responses (David Doty) [939](https://github.com/UC-Davis-molecular-computing/scadnano/pull/939)
- 33d2c56: closes 938: changing from grid to no grid removes major ticks (David Doty) [940](https://github.com/UC-Davis-molecular-computing/scadnano/pull/940)