Scadnano

This is a fairly hefty release with many features and bug fixes, including one breaking change related to oxDNA export.

Fix Pitch Angle on oxDNA Export

**Note:** This is a breaking change since it changes how oxDNA export is defined. If you were using oxDNA export before, you will have to change some helix angles (pitch and yaw) to create the same oxDNA output that was previously generated.

Previously, scadnano interpreted the pitch angle as a clockwise rotation in the Y-Z plane, following SVG convention. For example, the following design has a helix group (containing helix 1) with pitch=45 (clockwise, away from the single strand on helix 0):


Previously, exporting to oxDNA rotates the helix in the opposite direction (counter-clockwise, towards the single strand on helix 0). Now, exporting to oxDNA rotates the helix in the same direction as in scadnano:

| Old | New |
| ------------- | ------------- |
| <img src="https://user-images.githubusercontent.com/19274365/140661970-f1d2367a-7adb-4bd1-aa71-9cc290226dac.png" alt="drawing" width="400"/> | <img src="https://user-images.githubusercontent.com/31255679/145515095-ea0398b3-4e2a-41a8-8899-24b2c7ed5bee.png" alt="drawing" width="400"/> |
Move Selected Helices to Group

Users can now move selected helices to another helix group by right clicking on selected helices and clicking "set group."



Edit Strand IDT Fields

[IDT fields](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.IDTFields) of a strand enable one to specify options for ordering strands from the DNA synthesis company [IDT](https://www.idtdna.com/), which are used when doing Export&rarr;DNA sequences and selecting one of the IDT formats.

Previously, IDT fields could only be edited in the [Python scripting library](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Strand.idt) or manually in the `.sc` file. Now, scadnano provides an interface to enable users to edit IDT fields. Right click on any strand and click "edit idt fields" to open the edit IDT menu.


Display Axis Arrows in Main View and Side View

The main view and side view now displays the axis arrows, which makes it easier to keep track of the axis especially when "invert y axis" is selected.


The colors of the axis arrows match that of [oxView](https://sulcgroup.github.io/oxdna-viewer/), which helps when viewing a structure in both scadnano and oxView. Unfortunately the default orientation in oxView is reflected both horizontally and vertically compared to the main view of scadnano, but by rotating the view in oxView until the arrows match that displayed in the scadnano main view, the orientations can be made the same.

The axis arrow display can be toggled through the View menu.


New Edit Mode/Selection Mode UI

The Edit Mode and Selection Mode UI now features icons instead of text, which takes up less horizontal room on the screen.

| Old | New |
| ------------- | ------------- |
|  |  |

The previous text is still viewable by hovering over the icon.

In addition, to create more screen space for viewing a design, these menus can now be hidden by clicking on the toggle (bottom left of the screenshot).

Enable oxDNA Export for Only Selected Strands

Users now have the option to export only selected strands in oxDNA export. This is useful for exporting just a piece of a larger design, for instance a single design that contains many structures.


Commits
- 9b3f832: added reversed domain names (Cesar Alonso Guzman Avina) [631](https://github.com/UC-Davis-molecular-computing/scadnano/pull/631)
- 30bea3e: creating test file (rishabhmudradi) [631](https://github.com/UC-Davis-molecular-computing/scadnano/pull/631)
- 73473d3: updating test file (rishabhmudradi) [631](https://github.com/UC-Davis-molecular-computing/scadnano/pull/631)
- 42511e5: Update domain_label_move_test.dart (Cesar Alonso Guzman Avina) [631](https://github.com/UC-Davis-molecular-computing/scadnano/pull/631)
- 78a557e: Added AssertionError when view_order_of_helix is null (Cesar Alonso Guzman Avina) [631](https://github.com/UC-Davis-molecular-computing/scadnano/pull/631)
- 17713bc: moved assign/remove dna tests into assign_dna_unit_test, updated tests to use chain design methods, and added a test for assigning dna complement from bound strands (Cesar Alonso Guzman Avina) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- e9fb271: Added basic insertion unit test (Cesar Alonso Guzman Avina) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- 8d98555: added unit tests for insertions and deletions (Cesar Alonso Guzman Avina) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- 4a26915: ported tests from python library to dart for assigning dna (Cesar Alonso Guzman Avina) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- 1142361: closes 467: domain labels move when switching orientation of strand (Cesar Alonso Guzman Avina) [631](https://github.com/UC-Davis-molecular-computing/scadnano/pull/631)
- 8f332b0: porting more tests from python into dart (rishabhmudradi) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- 556abdd: ported more AssignDNA tests from python (Cesar Alonso Guzman Avina) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- 84b80d0: finish adding remaining test cases from scadnano python (sarahayu) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- 1f20980: fix mistakes on last commit (sarahayu) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- 5dc42c3: fix typo on ascii art (sarahayu) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- f8f184c: bumped version (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- e3eb58d: cleaned up menu (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- b708514: closes 608 (Cesar Alonso Guzman Avina) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- e9c4d5e: Fixing ASCII art to match python format (rishabhmudradi) [635](https://github.com/UC-Davis-molecular-computing/scadnano/pull/635)
- 8ea5202: added requested changes (Cesar Alonso Guzman Avina) [631](https://github.com/UC-Davis-molecular-computing/scadnano/pull/631)
- de5fa9f: fixed bug, and revised context menu item (Cesar Alonso Guzman Avina) [636](https://github.com/UC-Davis-molecular-computing/scadnano/pull/636)
- dd63e08: added unit tests for deleting helices (Cesar Alonso Guzman Avina) [636](https://github.com/UC-Davis-molecular-computing/scadnano/pull/636)
- e69dc4a: edit idt fields on a single strand (rishabhmudradi) [643](https://github.com/UC-Davis-molecular-computing/scadnano/pull/643)
- 16294ec: fix shift-clicking not working at times (sarahayu) [644](https://github.com/UC-Davis-molecular-computing/scadnano/pull/644)
- 0c14d40: closes 420 (sarahayu) [641](https://github.com/UC-Davis-molecular-computing/scadnano/pull/641)
- 5b638d1: disable hotkeys when adjusting or adding helix groups (sarahayu) [641](https://github.com/UC-Davis-molecular-computing/scadnano/pull/641)
- c85b7dc: Revert "628 deleting helices when using multiple groups of helixes causes the saved .sc file to be an illegal design when opened" (Cesar Alonso Guzman Avina) [637](https://github.com/UC-Davis-molecular-computing/scadnano/pull/637)
- 9749337: closes 628 (Cesar Alonso Guzman Avina) [639](https://github.com/UC-Davis-molecular-computing/scadnano/pull/639)
- 2d8bab5: closes 628: deleting helices when using multiple groups of helices (Cesar Alonso Guzman Avina) [639](https://github.com/UC-Davis-molecular-computing/scadnano/pull/639)
- 97ea21b: closes 561: add ability to edit IDT fields of a strand (rishabhmudradi) [643](https://github.com/UC-Davis-molecular-computing/scadnano/pull/643)
- 458b407: Revert "disable hotkeys when adjusting or adding helix groups" (sarahayu) [641](https://github.com/UC-Davis-molecular-computing/scadnano/pull/641)
- e75b8a2: fixes 640 (sarahayu) [642](https://github.com/UC-Davis-molecular-computing/scadnano/pull/642)
- 2af9487: added print warning if side helices are not in view; a good proxy for "the design didn't load but the view is trying to draw itself" (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- 4b80176: fixed bug where it was assumed Modificaiton.idt_text is non-null, but it is nullable. Also marked it nullable in each concrete subclass. (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- 696208c: Merge branch 'dev' into 628-Deleting-Helices-when-using-multiple-groups-of-helixes-causes-the-saved-.sc-file-to-be-an-Illegal-Design-when-opened (Cesar Alonso Guzman Avina) [639](https://github.com/UC-Davis-molecular-computing/scadnano/pull/639)
- 1175094: Readded previous commits that were removed (Cesar Alonso Guzman Avina) [639](https://github.com/UC-Davis-molecular-computing/scadnano/pull/639)
- 482a0d0: Update modification.dart (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- 1cc202e: Adding 4 submenue items to edit IDT fields (rishabhmudradi) [643](https://github.com/UC-Davis-molecular-computing/scadnano/pull/643)
- 72f9411: removing the original edit_idt_fields feature (rishabhmudradi) [643](https://github.com/UC-Davis-molecular-computing/scadnano/pull/643)
- ca01aa7: updating code for default fields (rishabhmudradi) [643](https://github.com/UC-Davis-molecular-computing/scadnano/pull/643)
- 7864065: fixing bug to add plate/well (rishabhmudradi) [643](https://github.com/UC-Davis-molecular-computing/scadnano/pull/643)
- 60c7ddf: Merge branch 'dev' into 561-add-ability-to-edit-IDT-fields-of-a-strand- (Rishabh Mudradi) [643](https://github.com/UC-Davis-molecular-computing/scadnano/pull/643)
- 0bdee9b: add svg elements and hook components (sarahayu) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- d30aace: Added x,y,z axis arrows for side and main view (Cesar Alonso Guzman Avina) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- 57e4078: fix tooltip and change svg pointer events (sarahayu) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- 05b2256: fixes 163 (sarahayu) [644](https://github.com/UC-Davis-molecular-computing/scadnano/pull/644)
- 26eb09e: added css for side eye and main view eye (Cesar Alonso Guzman Avina) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- e48f268: updatedt README to state that Edge is supported now that issue 127 seems to be solved (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- 74448a5: adding disable option for submenu (rishabhmudradi) [643](https://github.com/UC-Davis-molecular-computing/scadnano/pull/643)
- a1057fc: remove eye feature and change drawing order of axes (sarahayu) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- 0b6d706: move arrows closer to corner (sarahayu) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- 97bec94: added Show/Hide Axis Arrows as a View option (Cesar Alonso Guzman Avina) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- 7f2e872: closes 403 : add axis arrows to main view and side view (Cesar Alonso Guzman Avina) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- b46505f: Merge branch 'dev' into 403-add-axis-arrows-to-main-view-and-side-view (Cesar Alonso Guzman Avina) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- 2490794: added toggle edit mode feature (Cesar Alonso Guzman Avina) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- 9b241ed: add image file getters (sarahayu) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- 11a7b47: added images to buttons in edit mode menu (Cesar Alonso Guzman Avina) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- e3a30b8: add cleanup css and all_ends image link feature (sarahayu) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- e0c001b: added select mode images (Cesar Alonso Guzman Avina) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- b9f4710: rename axis arrow action (sarahayu) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- fa03809: fixes 645: crash on edit modification (rishabhmudradi) [649](https://github.com/UC-Davis-molecular-computing/scadnano/pull/649)
- 175c473: add axis labels (sarahayu) [646](https://github.com/UC-Davis-molecular-computing/scadnano/pull/646)
- 7493548: adding new images (rishabhmudradi) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- 4560662: closes 224: allow edit mode/selection mode to be hidable, and replace words with small icons (rishabhmudradi) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- 58ffee0: closes 437: add tooltips to edit and select mode buttons (rishabhmudradi) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- 9f144a4: Merge branch 'dev' into 224-allow-edit-mode/selection-mode-to-be-hidable-and-replace-words-with-small-icons (Rishabh Mudradi) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- 265719c: added citation request to landing page (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- cfb5405: added citation request to landing page (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- e54b139: fixed bibtex link (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- b6b1efc: Update error_message.dart (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- 2b8fec8: final icon modfications (rishabhmudradi) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- 38ca294: improved edit mode toggle button (rishabhmudradi) [651](https://github.com/UC-Davis-molecular-computing/scadnano/pull/651)
- d1c7de8: closes 654: domain name moves from 3' to 5' end when moving strand (rishabhmudradi) [656](https://github.com/UC-Davis-molecular-computing/scadnano/pull/656)
- f3dcc69: Update define_root_dir.sh (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- f82ddc7: Fixes 655; side menu not working in scadnano.org/dev (Benjamin Lee) [658](https://github.com/UC-Davis-molecular-computing/scadnano/pull/658)
- f628ee4: fixing bug (rishabhmudradi) [649](https://github.com/UC-Davis-molecular-computing/scadnano/pull/649)
- 293bde9: switched enum type to BuiltValue (rishabhmudradi) [649](https://github.com/UC-Davis-molecular-computing/scadnano/pull/649)
- 0983edc: fixes 664: allow oxDNA export when multiple helix groups are present (David Doty) [666](https://github.com/UC-Davis-molecular-computing/scadnano/pull/666)
- abe9913: closes 665: export oxDNA for only selected strands (David Doty) [669](https://github.com/UC-Davis-molecular-computing/scadnano/pull/669)
- 2dfb06e: Update oxdna_export.dart (David Doty) [669](https://github.com/UC-Davis-molecular-computing/scadnano/pull/669)
- eed9d94: added more explicit description of yaw, pitch, roll angles and linked to API documentation for details (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- e9bcc7a: added check for helices_view_order_inverse being well-defined (currently throws an exception, but more informative than the error it was causing previously) (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- d49cc9e: changed error message on trying to move DNA ends in different helix groups (previously said strands instead of DNA ends) (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- 452576a: creating modification_type (rishabhmudradi) [649](https://github.com/UC-Davis-molecular-computing/scadnano/pull/649)
- 3894fab: added roll_of_helix method to Design (to add group's roll to Helix.roll) (David Doty) [676](https://github.com/UC-Davis-molecular-computing/scadnano/pull/676)
- 1d88414: Merge branch 'dev' into crash-on-edit-modification-645 (David Doty) [649](https://github.com/UC-Davis-molecular-computing/scadnano/pull/649)
- 3e26e1f: added comments and changed mirrored_domain name (Cesar Alonso Guzman Avina) [656](https://github.com/UC-Davis-molecular-computing/scadnano/pull/656)
- 3936d7b: closes 671 (Cesar Alonso Guzman Avina) [672](https://github.com/UC-Davis-molecular-computing/scadnano/pull/672)
- 91bed90: closes 670 (Cesar Alonso Guzman Avina) [672](https://github.com/UC-Davis-molecular-computing/scadnano/pull/672)
- 8db70fb: some memoized getters in Strand were returning mutable lists; changed to BuiltList for safety (David Doty) [656](https://github.com/UC-Davis-molecular-computing/scadnano/pull/656)
- e3a1bd7: modified comments in move_strand function in strands_reducer (David Doty) [656](https://github.com/UC-Davis-molecular-computing/scadnano/pull/656)
- 0ccdc48: added assert statement about helices_view_order to help identify bug in 668 (David Doty) [656](https://github.com/UC-Davis-molecular-computing/scadnano/pull/656)
- 1b43ce6: Merge branch 'dev' into 654-domain-name-moves-from-3'-to-5'-end-when-moving-strand (David Doty) [656](https://github.com/UC-Davis-molecular-computing/scadnano/pull/656)
- eb8ab25: fixes 670: edit mode menu hidden on zoom in (sarahayu) [672](https://github.com/UC-Davis-molecular-computing/scadnano/pull/672)
- 2f98ac0: fixes 671: fix crash when loading for first time (sarahayu) [672](https://github.com/UC-Davis-molecular-computing/scadnano/pull/672)
- 32fac9a: undid the effect of 654, so that domain names now stay associated to the original domain when strands move to reverse orientation (David Doty) [656](https://github.com/UC-Davis-molecular-computing/scadnano/pull/656)
- 696ce81: changed type from Iterable<String> to BuiltList<String> (Cesar Alonso Guzman Avina) [675](https://github.com/UC-Davis-molecular-computing/scadnano/pull/675)
- 47c54fd: fixes 674: remove warning that appears in console on local host when adding modification (sarahayu) [675](https://github.com/UC-Davis-molecular-computing/scadnano/pull/675)
- 1391a5f: add comment with link referencing fix (sarahayu) [675](https://github.com/UC-Davis-molecular-computing/scadnano/pull/675)
- b34de1a: fixes 667: make scadnano pitch angle agree with oxDNA (David Doty) [676](https://github.com/UC-Davis-molecular-computing/scadnano/pull/676)
- 9ee4768: bumped version to 0.17.0 (breaking change in oxDNA export since rotation definitions were changed) (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- 3b35ac8: closes 679: move selected helices to group (David Doty) [687](https://github.com/UC-Davis-molecular-computing/scadnano/pull/687)
- 3669de3: added unit tests and fixed bug with one group (rishabhmudradi) [687](https://github.com/UC-Davis-molecular-computing/scadnano/pull/687)
- 34bd3c0: added more descriptive error messages (rishabhmudradi) [680](https://github.com/UC-Davis-molecular-computing/scadnano/pull/680)
- d2aaf2b: fixes 678: make more useful error message when helices view order input is invalid (sarahayu) [680](https://github.com/UC-Davis-molecular-computing/scadnano/pull/680)
- 4b58946: added more comments detailing how to handle moving helices from one group to another (David Doty) [687](https://github.com/UC-Davis-molecular-computing/scadnano/pull/687)
- 240c1ad: Implement cadnano import export in dart (653) (Benjamin Lee) [653](https://github.com/UC-Davis-molecular-computing/scadnano/pull/653)
- d884e37: update test cases for new domain name move behaviour (sarahayu) [656](https://github.com/UC-Davis-molecular-computing/scadnano/pull/656)
- 69b4d4f: fixes 684 (sarahayu) [688](https://github.com/UC-Davis-molecular-computing/scadnano/pull/688)
- dbb2f4b: Fixes 677; adjusting helices view order should update view (685) (Benjamin Lee) [685](https://github.com/UC-Davis-molecular-computing/scadnano/pull/685)
- 765e9b3: add requested changes (sarahayu) [688](https://github.com/UC-Davis-molecular-computing/scadnano/pull/688)
- c0af5e3: Add doc comments for reassign_svg_positions and helices_assign_svg (Benjamin Lee) [689](https://github.com/UC-Davis-molecular-computing/scadnano/pull/689)
- fb21b62: Update README.md (David Doty) [682](https://github.com/UC-Davis-molecular-computing/scadnano/pull/682)
- da0ff7e: closes 690: highlight helices in main view if selected (sarahayu) [695](https://github.com/UC-Davis-molecular-computing/scadnano/pull/695)
- 71926dc: closes 691: allow helices to be selected from main view (sarahayu) [695](https://github.com/UC-Davis-molecular-computing/scadnano/pull/695)
- 2960cc3: remove commented out lines (sarahayu) [695](https://github.com/UC-Davis-molecular-computing/scadnano/pull/695)
- dc1280a: gray out 'set group' instead of disabling if no other groups are available (sarahayu) [695](https://github.com/UC-Davis-molecular-computing/scadnano/pull/695)
- 5ad5d74: possible fix for move group assertion fail (sarahayu) [698](https://github.com/UC-Davis-molecular-computing/scadnano/pull/698)
- 4060489: fixes 696: Fix Assertion Failed Error When Attempting to Move Group (sarahayu) [698](https://github.com/UC-Davis-molecular-computing/scadnano/pull/698)
- 25b9657: Fixes 699; Fix release note workflow (Benjamin Lee) [700](https://github.com/UC-Davis-molecular-computing/scadnano/pull/700)

fixed bug in oxDNA export

We fixed a bug (633) in oxDNA export that made the helix roll go the opposite rotational direction from where it should have been.

submenus to reduce clutter

We've introduced submenus for the top-level menu and right-click context menus to reduce the amount of clutter and make it easier to fit the whole menu on the screen:


Microsoft Edge supported
The issues we previously saw with Microsoft Edge (e.g., 127 and some strangeness with mouse wheel/two-finger zoom) seem to be gone. We aren't sure why they are gone, but at any rate, scadnano now seems to work well with the [Edge](https://www.microsoft.com/en-us/edge) browser, so we're declaring it officially supported.

Commits
- [[e6c4e4c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e6c4e4c44211e1313b4ea4220db1d7db0c3e3b9a)]: add nested contextmenu and move main contextmenu when it doesn't fit (sarahayu) [#624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[43eeba4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/43eeba45337f8eb2509ee07c3a3dc73c08ce9c5b)]: align submenu based on if they fit within viewport (sarahayu) [#624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[aea6842](https://github.com/UC-Davis-molecular-computing/scadnano/commit/aea6842dac3d3e4688c19e869de63ab16bd89a9b)]: fix bug where submenus don't align correctly when directly clicking from one strand to another (sarahayu) [#624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[072a569](https://github.com/UC-Davis-molecular-computing/scadnano/commit/072a5691c7c261bcd6e98aec60e6a4251827dc8d)]: translate menu based on bottom/right edge of context menu (sarahayu) [#624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[abe9c89](https://github.com/UC-Davis-molecular-computing/scadnano/commit/abe9c89dff59c15e670b84f00d9f8b9268b97001)]: Added dropdown menus for Navbar (Cesar Alonso Guzman Avina) [#624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[d287bda](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d287bdaeed0dfc22dcb0e8d2b1e31d1c449b9c64)]: replace NavDropdown with MenuDropdownRight (sarahayu) [#624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[2866d62](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2866d62cc42dfbc89ed7c23883297f698fab6cbb)]: move assign domain name to edit names submenu (sarahayu) [#624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[62da977](https://github.com/UC-Davis-molecular-computing/scadnano/commit/62da977c2d76070f58c65725fb20134b9df00f87)]: closes #557 618 enable submenus in context menus and top level menu and move context menu position when it doesn't fit into window (sarahayu) [624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[f62cf4e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/f62cf4e58bfda1aae3a7a7979c987e2fce56d46c)]: Merge branch 'dev' into #557-618-enable-submenus-in-context-menus-and-top-level-menu-and-move-context-menu-position-when-it-doesn't-fit-into-window (sarahayu) [624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[68be43b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/68be43be1a7a141168f4949243874c9cadd11931)]: fix react key error for view_menu (sarahayu) [#624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[c5ebed3](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c5ebed309cf164656be8ec3c5f70ca5350579ab6)]: bumped version (David Doty) [#634](https://github.com/UC-Davis-molecular-computing/scadnano/pull/634)
- [[ad1cb2b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ad1cb2bbaeb15edb883299d54f037b7de983aa8a)]: add comments explaining how contextmenu positioning works (sarahayu) [#624](https://github.com/UC-Davis-molecular-computing/scadnano/pull/624)
- [[4338377](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4338377dc0ba3a567bea626cc863f2a0002977af)]: closes #629: add "bug report/feature request" link to Help menu, linking to scadnano GitHub issues page (David Doty) [632](https://github.com/UC-Davis-molecular-computing/scadnano/pull/632)
- [[83df613](https://github.com/UC-Davis-molecular-computing/scadnano/commit/83df613ba343d4219066008f050f1ac2ef990cc9)]: formatting (David Doty) [#634](https://github.com/UC-Davis-molecular-computing/scadnano/pull/634)
- [[4dbd62d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4dbd62d511c45a18110e1eeff66dac5da9afc267)]: fixes #633: fix Helix.roll translation to nucleotide positions in oxDNA export (David Doty) [634](https://github.com/UC-Davis-molecular-computing/scadnano/pull/634)

Fixes bugs in oxDNA export that would cause exported files not to be simulatable on oxDNA (due to non-cubic bounding box) and that, even with a cubic bounding box, would cause stable structures to melt.

Also fixes some other bugs described below related to 608 and 474.

Commits
- [[3b37848](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3b378485fe6757d2cf1f0b2728d736e83873ff07)]: Added memoized getters from address, app_state, domain, select_mode, and select_mode_state files (Cesar Alonso Guzman Avina) [#627](https://github.com/UC-Davis-molecular-computing/scadnano/pull/627)
- [[e9443d2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e9443d2a9df78ae943cf26ec8eb4a9ad23079f8b)]: replace all references of domains function to new getter (sarahayu) [#627](https://github.com/UC-Davis-molecular-computing/scadnano/pull/627)
- [[fa8b427](https://github.com/UC-Davis-molecular-computing/scadnano/commit/fa8b4277e9347385baa1340f6e16943263b1758e)]: Finished making memoized getters in strand.dart (Cesar Alonso Guzman Avina) [#627](https://github.com/UC-Davis-molecular-computing/scadnano/pull/627)
- [[7249bbc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7249bbc58101268dec1e6def2f04634cc15d42cd)]: rename domain name complement reducer and change Strand domains method to memoized getter (sarahayu) [#627](https://github.com/UC-Davis-molecular-computing/scadnano/pull/627)
- [[64656be](https://github.com/UC-Davis-molecular-computing/scadnano/commit/64656be95e514dc33522ed856200183fb8133a1e)]: Update oxdna_export.dart (Cesar Alonso Guzman Avina) [#627](https://github.com/UC-Davis-molecular-computing/scadnano/pull/627)
- [[b590c50](https://github.com/UC-Davis-molecular-computing/scadnano/commit/b590c502283e4eea13216800787aca1d7f541505)]: convert functions to memoized getters for grid and helix (sarahayu) [#627](https://github.com/UC-Davis-molecular-computing/scadnano/pull/627)
- [[de9381d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/de9381d5b080b6d0eda375f2508b7b7161eb67df)]: removed word "export" from options under Export menu (David Doty) [#630](https://github.com/UC-Davis-molecular-computing/scadnano/pull/630)
- [[e668743](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e6687433f38ea20b3ad286ea684cc2f343529bcc)]: closes #608: Fix crash bug on assigning DNA sequence (Cesar Alonso Guzman Avina) [623](https://github.com/UC-Davis-molecular-computing/scadnano/pull/623)
- [[452b79c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/452b79c9715ec278cdc975e5369d8d7962fba253)]: completed tutorial's incomplete sentence indiciating how to use autopaste and join selected ends by crossovers (David Doty) [#630](https://github.com/UC-Davis-molecular-computing/scadnano/pull/630)
- [[84b9f9f](https://github.com/UC-Davis-molecular-computing/scadnano/commit/84b9f9f29eddbeec7938d4ae86dcc0956a92c9cb)]: closes #474: prevent deletions and insertions from duplication when moving/copying strands (rishabhmudradi) [625](https://github.com/UC-Davis-molecular-computing/scadnano/pull/625)
- [[01113f2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/01113f2c835efa7a650fee13956b6a68f5689d44)]: closes #612 make memoized getters for zero argument methods in State BuiltValue classes (Cesar Alonso Guzman Avina) [627](https://github.com/UC-Davis-molecular-computing/scadnano/pull/627)
- [[46c729f](https://github.com/UC-Davis-molecular-computing/scadnano/commit/46c729f72ceb7eced765700ad6f1bd64460a195e)]: Merge branch 'dev' into #612-make-memoized-getters-for-zero-argument-methods-in-State-BuiltValue-classes (Cesar Alonso Guzman Avina) [627](https://github.com/UC-Davis-molecular-computing/scadnano/pull/627)
- [[bc29028](https://github.com/UC-Davis-molecular-computing/scadnano/commit/bc2902880647865b2edaf63610da4de37a72b2a6)]: adjusted domains_selectable to getter (Cesar Alonso Guzman Avina) [#627](https://github.com/UC-Davis-molecular-computing/scadnano/pull/627)
- [[45035c5](https://github.com/UC-Davis-molecular-computing/scadnano/commit/45035c55a0a066bfb9748c6580e396e74fe7ad89)]: fixed non-unique ID error with DialogRadio components (David Doty) [#630](https://github.com/UC-Davis-molecular-computing/scadnano/pull/630)
- [[3d038d6](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3d038d66e01c4fb91fae7e5b0ca3d66bcbb2709a)]: Delete xlsx.full.min.js (David Doty) [#630](https://github.com/UC-Davis-molecular-computing/scadnano/pull/630)
- [[6db5569](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6db5569a1f074b66b6819ad9eb715fed41816028)]: corrected bad forward vector in oxDNA export that caused DNA origami to melt upon relaxation in oxDNA (David Doty) [#630](https://github.com/UC-Davis-molecular-computing/scadnano/pull/630)
- [[74ef8bf](https://github.com/UC-Davis-molecular-computing/scadnano/commit/74ef8bf751f2348b63c54765ebad30608ef69772)]: updated oxDNA export to use cubic bounding box (taking all three sides to be max of computed bounding box) (David Doty) [#630](https://github.com/UC-Davis-molecular-computing/scadnano/pull/630)
- [[85bac1a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/85bac1ac8170c929afa53ec31324d687dca62938)]: bumped version (David Doty) [#630](https://github.com/UC-Davis-molecular-computing/scadnano/pull/630)

New features:

export to oxDNA
See 589. Exporting to the tool [oxDNA](https://oxdna.org/) and the web app [oxView](https://sulcgroup.github.io/oxdna-viewer/) is now supported via the Export menu:


[oxView](https://sulcgroup.github.io/oxdna-viewer/) can be used to visualize the intended 3D structure of the design, with base positions inferred based on Helix (x,y,z) position and roll angle, and HelixGroup (pitch, yaw, roll) orientation angles. [oxDNA](https://oxdna.org/) can be used to simulate physical stress and motion to predict an expected 3D structure.

Other export options, such as exporting to cadnano, have been moved from the File menu to the Export menu. (Importing from cadnano is still under the File menu.)

This is also supported in scripts via the [scadnano Python package](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/issues/139); see https://github.com/UC-Davis-molecular-computing/scadnano-python-package/releases/tag/v0.16.1

add "assign domain complement from bound strands"
See 592. You can right click on a strand/domain (or group of selected strands/domains) and assign their domain names to the "complement" name (adding/removing a `*` at the end of the name) of whatever domain(s) they are bound to. For example, if a strand is selected with domains `d1` and `d2`, which are bound to domains with names `ABC` and `XYZ*`, then afterward, domain `d1` will have name `ABC*` and domain `d2` will have name `XYZ`.

Domains are considered "bound" if they are on the same helix, in opposite directions, with the same `start` and `end` offsets.

For example, select a few strands bound to strands with domain names and right-click to select "assign domain name complement from bound strands":


Then new domain names are assigned:



zoom speed controllable
See 587. The Zoom speed is now controllable from the View menu. This helps with mice/trackpads that have different sensitivities.

add option to export DNA sequences for only selected strands
See 537. You can select a subset of strands and export DNA sequences for only those selected.



Commits
- [[518e1f3](https://github.com/UC-Davis-molecular-computing/scadnano/commit/518e1f396c7427b5e905b60cc956a1e66f836c21)]: CSS styles now show open hand cursor on SVG background, unless Shift or Ctrl is pressed to enable select box dragging, in which case cursor is crosshair; for some reason introduced a bug in Firefox where it crashes if the selection box is dragged too quickly (David Doty) [#620](https://github.com/UC-Davis-molecular-computing/scadnano/pull/620)
- [[6894c73](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6894c731df3ece3ec82cabfccdb9ce277621495f)]: Merge branch 'dev' into show-hand-grabbing-cursor-when-pointer-is-able-to-grab-for-click-and-drag-panning (David Doty) [#620](https://github.com/UC-Davis-molecular-computing/scadnano/pull/620)
- [[6146cd0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6146cd0a263edc8afd67ac11b8fb73835392d6cc)]: closes #603; add link to M13 variants in assign DNA sequence dialog; also gives displayed names of sequences more intuitive values (David Doty) [605](https://github.com/UC-Davis-molecular-computing/scadnano/pull/605)
- [[30f30c2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/30f30c298f1243caafce40ac75f1adba6245b77c)]: started implementing export of only selected strands; committing to we can merge changes from recent PR to dev (David Doty) [#606](https://github.com/UC-Davis-molecular-computing/scadnano/pull/606)
- [[98121fc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/98121fcdc4f8b3d316d15ff8b2dd7af00ffed0bd)]: Merge branch 'dev' into issue-537-add-option-to-export-DNA-sequences-for-only-selected-strands (David Doty) [#606](https://github.com/UC-Davis-molecular-computing/scadnano/pull/606)
- [[7ed5c4e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7ed5c4e6b1791764f53ba350dc92ca1f611e82c4)]: fixes #537; add option to export DNA sequences for only selected strands (David Doty) [606](https://github.com/UC-Davis-molecular-computing/scadnano/pull/606)
- [[4c7c7e5](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4c7c7e5b689a136067160e9d6442f1d8fb997131)]: Closes #592: add "assign domain complement from bound strands" option (Cesar Alonso Guzman Avina) [615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[ebb01ea](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ebb01ea00dab80625fd5a62782e9bb27e1773cb7)]: Fixed bug in with_domain_name and with_domain_label (Cesar Alonso Guzman Avina) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[d3179a1](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d3179a19d8ee24573d27d28174436f312eb633d0)]: Added unit tests for assigning domain name complements to linear strands (Cesar Alonso Guzman Avina) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[aa1b9b2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/aa1b9b23c48aa59ed67ba1788e8e1ab165614c24)]: updated CONTRIBUTING to mention non-coding steps in recipe for adding new features or fixing bugs (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[19cce66](https://github.com/UC-Davis-molecular-computing/scadnano/commit/19cce663178353730634147c7a56e20139b98994)]: closes #607 (actually last commit closed it but I forgot to tag it) (David Doty) [621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[6781c3d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6781c3d58bfb77d866b444777f8f08bb2d3dd9da)]: updated max Dart SDK version in preparation for possibly upgrading to Dart 2.13 (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[41b7b74](https://github.com/UC-Davis-molecular-computing/scadnano/commit/41b7b74a457033f6bf531469307210a84f2a5a6d)]: added notes to tutorial suggesting to use autopaste and auto-crossover-joining as suggested in issue #595, but did not yet re-write tutorial with new screenshots to show in detail how to use those features (David Doty) [621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[31a9a56](https://github.com/UC-Davis-molecular-computing/scadnano/commit/31a9a564d512ec9d19ebda41dd020be325770349)]: Update design.dart (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[7e45b28](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7e45b284ecf11799667d68ba88612c855e148e91)]: removed old requirement about AppUIStateStorableAction in CONTRIBUTING (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[fcb29a2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/fcb29a25be64525a368df118446ce6e045da8c1c)]: added sentence describing warning if `UndoableAction` not implemented by an action that changes the design (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[474660d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/474660d5904ae3d72e248dda011cb39f45612dc4)]: add test case for selected strands (sarahayu) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[b085c6b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/b085c6ba92d0d7bac8b1422428e1f436624ef7c5)]: closes #587; make zoom speed controllable (David Doty) [610](https://github.com/UC-Davis-molecular-computing/scadnano/pull/610)
- [[059a7d5](https://github.com/UC-Davis-molecular-computing/scadnano/commit/059a7d545d7d92fceb63b71738e7dfc2a92eb3ec)]: added note about zoom speed to README (David Doty) [#610](https://github.com/UC-Davis-molecular-computing/scadnano/pull/610)
- [[6f36523](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6f36523be0f50dbb81d7d295332c506f7c7b9ff8)]: Added more linear and circular strand unit tests for assigning domain name complements (Cesar Alonso Guzman Avina) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[dc496c4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/dc496c4c02ff5e25256d6979fd6516e192e5d5c0)]: Added circular unit tests and fixed domain name complement not assigning to circular strands bug (Cesar Alonso Guzman Avina) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[51be5bc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/51be5bcfff620fc23aff1360a2498e6806a3f137)]: fixed bug where zoom speed is not set initially based on stored value (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[33f1ec2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/33f1ec2f26b11cc40f9f223753c9bd5c4d456df3)]: added first unit test for oxDNA export and basic middleware function stub to make it compile, and updated files in test subdirectory with annotation to use Dart 2.9 so sound null safety is not checked (David Doty) [#611](https://github.com/UC-Davis-molecular-computing/scadnano/pull/611)
- [[cfa7681](https://github.com/UC-Davis-molecular-computing/scadnano/commit/cfa7681013d22c73d234e19bde6fdcd7d8ca153c)]: closes #589; export to oxDNA format (David Doty) [611](https://github.com/UC-Davis-molecular-computing/scadnano/pull/611)
- [[0d57cb7](https://github.com/UC-Davis-molecular-computing/scadnano/commit/0d57cb79a7b5a8e3da084e85a4dbcad76e974b49)]: Update oxdna_export_test.dart (David Doty) [#611](https://github.com/UC-Davis-molecular-computing/scadnano/pull/611)
- [[c5a6000](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c5a6000c6600826f3eabb56be53b9a6b1bfe51e7)]: Update oxdna_export.dart (David Doty) [#611](https://github.com/UC-Davis-molecular-computing/scadnano/pull/611)
- [[5e415d4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/5e415d4ebf2918eda61c29e94ce23dcad1c0980c)]: bumped version (David Doty) [#611](https://github.com/UC-Davis-molecular-computing/scadnano/pull/611)
- [[9df3ac2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9df3ac27670da21db9f2d78c4c4d8ccc9a2c9b7c)]: Finished adding oxDNA unit tests & implemented adding insertions and deletions to StrandMaker (rishabhmudradi) [#611](https://github.com/UC-Davis-molecular-computing/scadnano/pull/611)
- [[43bd771](https://github.com/UC-Davis-molecular-computing/scadnano/commit/43bd771a7f629f728c2fc94028d1970d52129c28)]: Update export_dna_format.dart (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[c400e62](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c400e62cb9c79408ffa8ed119cf84936dbfdd8f4)]: Update oxdna_export_test.dart (sarahayu) [#611](https://github.com/UC-Davis-molecular-computing/scadnano/pull/611)
- [[65f3d1e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/65f3d1ecccc42a4e9fad6a4899f9b7b3961a0e94)]: rename domain name complement reducer and change Strand domains method to memoized getter (sarahayu) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[8645131](https://github.com/UC-Davis-molecular-computing/scadnano/commit/86451312db32e3bd4d9e8c34e994c49d6ad5f862)]: replace all references of domains function to new getter (sarahayu) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[090d28c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/090d28ce0d7c917719936984bfe2d63307742e16)]: described oxDNA export in README (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[9a0b3e2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9a0b3e225a9404e286657e1ffdc68b2c25a6b2d4)]: suggested use of clean.sh script in CONTRIBUTING (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[4d8b588](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4d8b5884552412506768ac95d72e2e7d186ab96d)]: add both named unit tests (sarahayu) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[62b12b2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/62b12b24a3d661f744c471ec343bc30497e7212f)]: added unit tests for compute_domain_name_complements and fixed bug when working with named complementary strands (Cesar Alonso Guzman Avina) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[0772383](https://github.com/UC-Davis-molecular-computing/scadnano/commit/07723837205004aac7d192924ff483ad550ca571)]: Fixed bug for strand overlapping and added unit tests for it (Cesar Alonso Guzman Avina) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[e915d99](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e915d997e867736188f1e1af8cfca74ce0b444b7)]: Finished making memoized getters in strand.dart (Cesar Alonso Guzman Avina) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[c3b4b7d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c3b4b7d63622a34f83a5ccc76d8977cd5bef7a61)]: added Dart 2.9 bound to test files so they run under Dart >=2.12 with null safety off (David Doty) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[7b20fec](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7b20fecee11dd59edc24919173e8991e812bd803)]: moved reducer function to top of file (David Doty) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[8c4a36e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8c4a36e163ad6e524f22c8b74be11a2da6f49bfa)]: Update design_main_strand.dart (David Doty) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[a0f5866](https://github.com/UC-Davis-molecular-computing/scadnano/commit/a0f5866df9d85f4c9e86ea4aaed02d8b6d5eaf87)]: added action and serializer for AssignDomainNameComplementFromBoundDomains (Cesar Alonso Guzman Avina) [#616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[86554df](https://github.com/UC-Davis-molecular-computing/scadnano/commit/86554dfb2613549799fab3e9dfa1453f58d6ebb0)]: adding reducer code (rishabhmudradi) [#616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[7cd0d88](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7cd0d88a1b21e8ded30f8e9661244f89f29604dc)]: Added logic to assign domain name complement from bound domains reducer (Cesar Alonso Guzman Avina) [#616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[db06ed0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/db06ed0e3617213560c9bb89a596cc917a32471c)]: fixing bug (rishabhmudradi) [#616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[4b1ecf4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4b1ecf43583934c6f8732f75b7de3df4cbcb2c3f)]: finished adding test cases (rishabhmudradi) [#616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[58391c8](https://github.com/UC-Davis-molecular-computing/scadnano/commit/58391c82358f50cd02544118cf34b3b9a1d3b1ed)]: Merge branch 'dev' into #592-add-assign-domain-complement-from-bound-strands- (Rishabh Mudradi) [615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[5512162](https://github.com/UC-Davis-molecular-computing/scadnano/commit/55121625c9d725867cfd5e917af362d09e8b5c8f)]: Merge branch 'dev' into #614-add-assign-domaini-complement-from-bound-domains (Rishabh Mudradi) [616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[2a22962](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2a22962d43f94b0f6611a4d92056f930f02c4217)]: updating domain getter in oxdna_export (rishabhmudradi) [#615](https://github.com/UC-Davis-molecular-computing/scadnano/pull/615)
- [[ec0f03d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ec0f03dd2a0249fc6cf6c48946d668eaf24e56bf)]: update domain getter in oxdna_export (rishabhmudradi) [#616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[d913e63](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d913e6318f5a5647da2c0dc6362cf3ba6fd9ea20)]: Merge branch 'dev' into #614-add-assign-domaini-complement-from-bound-domains (Rishabh Mudradi) [616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[9ad91a7](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9ad91a78a14d2568e77821b5f3e931d2dc518e13)]: adding conditional property access when evaluating domain.name (rishabhmudradi) [#617](https://github.com/UC-Davis-molecular-computing/scadnano/pull/617)
- [[e3157da](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e3157da7c38efc0e312be34467f6f3b98c03150f)]: Combined domain name complement from bound domain and strand into one menu item (Cesar Alonso Guzman Avina) [#616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[209ad10](https://github.com/UC-Davis-molecular-computing/scadnano/commit/209ad106f0efb1824452a59d4569b98e989b8dd7)]: deleting assign_domain_name_complement_from_bound_domains from strand.dart (rishabhmudradi) [#616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[7bb1e73](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7bb1e73c6f90ec3ae14cbd8c1485a79b348c26c8)]: Merge branch 'dev' into show-hand-grabbing-cursor-when-pointer-is-able-to-grab-for-click-and-drag-panning (David Doty) [#620](https://github.com/UC-Davis-molecular-computing/scadnano/pull/620)
- [[ada56f3](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ada56f3e4869c50a045538cbb36c5b75d673af72)]: closes #55: show hand-grabbing cursor when pointer is able to grab for click-and-drag panning (David Doty) [620](https://github.com/UC-Davis-molecular-computing/scadnano/pull/620)
- [[0c9360b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/0c9360b9d2dacdcbb06d9982db3abc7b176d0aab)]: disable panning when in rope select mode and drawing a rope (David Doty) [#620](https://github.com/UC-Davis-molecular-computing/scadnano/pull/620)
- [[7e148a3](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7e148a3a49a113cc130e78330bb344f6e77732b6)]: changed tab icon to be more open on bottom "helix" (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[bd8cb5d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/bd8cb5d8e97a537ec73a6a3364fd0f570140a1a0)]: closes #614: assign domain complement from bound domains if domains are selected (instead of whole strand) (David Doty) [616](https://github.com/UC-Davis-molecular-computing/scadnano/pull/616)
- [[af7b67e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/af7b67e683b6473ca2ba0b9718b5110d877c0ac1)]: fixes #613: fix bug where right-click on DNAEnd raises exception; now context_menu_strand is always called with domain, address, and is_5p specified (David Doty) [617](https://github.com/UC-Davis-molecular-computing/scadnano/pull/617)
- [[f367ffd](https://github.com/UC-Davis-molecular-computing/scadnano/commit/f367ffd5b1e8a021a0d00d687ff8c0ef78a19051)]: fixed bug where helices_view_order not properly set after deleting selected helices (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[48922c3](https://github.com/UC-Davis-molecular-computing/scadnano/commit/48922c3444411657510c3b5816bf3c10c7d2e83f)]: fixed several linter warnings (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[b5d6a82](https://github.com/UC-Davis-molecular-computing/scadnano/commit/b5d6a82918d487f48877f575797737e4fdfcb0f5)]: fixed linter warning (David Doty) [#621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)
- [[8c7e37e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8c7e37e50a0ccbf2746569ff07a53eb362130a4e)]: fixed bug with right-click on DNA End (#613; forgot to uncomment lines that fix it in last PR) (David Doty) [621](https://github.com/UC-Davis-molecular-computing/scadnano/pull/621)

No major changes to the web interface, but we are bumping the version since there are breaking changes in the corresponding Python package release: https://github.com/UC-Davis-molecular-computing/scadnano-python-package/releases/tag/v0.16.0

Commits
- [[8a5734b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8a5734bc6d05a822728d9e2e48bf25b3827718b6)]: Correct coordinate description by swapping x and z (Benjamin Lee) [#601](https://github.com/UC-Davis-molecular-computing/scadnano/pull/601)
- [[76d3c2c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/76d3c2c3f0ced3c9a114ff8e9a7e10e901334058)]: Fixes #597; remove Helix.pitch and Helix.yaw (Benjamin Lee) [600](https://github.com/UC-Davis-molecular-computing/scadnano/pull/600)

There are several new features in this release.

Display strand names, Issue 576
If strands are assigned names, then can be optionally displayed in scadnano. They are displayed in the same location as the 5'-most domain name when domain names are displayed.

Copying strands to system clipboard, Issue 536
When strands are copied, this now puts some text on the system clipboard with details about the strands. This was originally done as a feature request (536) to make it easier to gather information about a few strands from a large design and paste them into a text file to visually inspect. However, it also allows us to copy and paste strands between different instances of scadnano; see next feature.

The next few features can make it faster to create designs.

Strands can be copied from one instance of scadnano and pasted into another, Issue 590
Previously, when strands were copied, it only affected internal memory of a scadnano instance. Several scadnano instances (for example, open in different browser tabs) would have their own internal representation of copied strands. The only way to copy strands from one instance of design to another was to copy the strands, then load the new designs in the same running instance of scadnano, then paste them. (issue 520)

Now that strands are copied to the system clipboard, it is possible to copy strands from one design and paste them into another already open instance of scadnano with a different design. The exact rules governing how this works are a bit esoteric, since the two designs may not have any helix indices in common, for example, but it is similar to pasting from one HelixGroup to another (issue 249).

The first time you attempt to paste, the browser will issue a warning, because it needs your permission to access the operating system clipboard to read the information stored there when the strands were copied. Give it permission to read the clipboard.

**Caution:** Whenever there are changes to the design or UI settings, scadnano writes these into your browser's local storage. If you use the same browser to open two different instances of scadnano, they will be writing to the same place. If you want two open instances of scadnano really to have no effect on each other, the best way is to use two different browsers. (Since currently scadnano only supports Chrome and Firefox, those are the only two that could both be used.)

Join many selected ends by vertical crossovers, Issue 581
This can speed up adding many crossovers to a design, especially scaffold crossovers in an DNA origami design. See 581 for details.

Autopaste, Issue 580
This idea was inspired by [ENSNano](http://www.ens-lyon.fr/ensnano/), which has a similar feature. If strands are copied and pasted, the translate "vector" is recorded (i.e., how many helices up or down were the pasted strands from the original, and how much did the offsets move, and did the forward/reverse orientation change). By pressing Ctrl+Shift+V, strands can be pasted again, with the new pasted positions automatically calculated to move along the same vector. This can speed up creating a large design from many repetitive strands. See #580 for details.


Commits
- [[474c087](https://github.com/UC-Davis-molecular-computing/scadnano/commit/474c087d2500bf63f7e0687b780a727c35c2ec44)]: added instructions for running scadnano offline to README and CONTRIBUTING (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[32db707](https://github.com/UC-Davis-molecular-computing/scadnano/commit/32db707aa2c2b6bfe67b00096b34a347021103b3)]: Deleted pyodide directory; takes up lots of room and we probably won't ever use it (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[03776aa](https://github.com/UC-Davis-molecular-computing/scadnano/commit/03776aa759980219438fb4a7aa8c3f55a764165b)]: Update CONTRIBUTING.md (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[2f6c855](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2f6c855d56eedbb350b3c8016e950523f51e2b8f)]: Update CONTRIBUTING.md (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[4f3db7c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4f3db7cffecc0b67b05818e89409547ba23c519f)]: Update CONTRIBUTING.md (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[6e12f2b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6e12f2b2a168868ced1e1e391206cf868954c693)]: Fixes #536; copy strand details to clipboard as human-readable text (578) (Benjamin Lee) [578](https://github.com/UC-Davis-molecular-computing/scadnano/pull/578)
- [[e74a78a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e74a78ae61c23b5750093c7b01bb6b00ec321941)]: Bump version to 0.15.3 (Benjamin Lee) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[03a5aec](https://github.com/UC-Davis-molecular-computing/scadnano/commit/03a5aecf38d58d83e46679f982749a6029119476)]: added tip about Chrome extension "Downloads Overwrite Already Existing Files" to tutorial (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[67214c4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/67214c4eb37646a87dfa1c0e521fa4f1f0a574ea)]: added table of contents to CONTRIBUTING (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[a51b8f3](https://github.com/UC-Davis-molecular-computing/scadnano/commit/a51b8f3e9cf0f5fbc0e795ea1f18ec84668470bc)]: closes #576: display strand names (David Doty) [582](https://github.com/UC-Davis-molecular-computing/scadnano/pull/582)
- [[79eba60](https://github.com/UC-Davis-molecular-computing/scadnano/commit/79eba608f126b5cbe7723091b981cbdd4fe4f2da)]: closes #581 ; add Edit menu item "Join selected ends by crossovers" (David Doty) [583](https://github.com/UC-Davis-molecular-computing/scadnano/pull/583)
- [[3706382](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3706382a6e2adeaf27eafadf2ef766424015184a)]: rearranged JoinStrandsByMultipleCrossovers action to have no information about ends to join, to push that complex logic from view code into the reducer (David Doty) [#583](https://github.com/UC-Davis-molecular-computing/scadnano/pull/583)
- [[2e9dd06](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2e9dd06861655c21bd4678e96bb1ad2351535f93)]: added basic (but incomplete) unit tests for JoinStrandsByMultipleCrossovers action (David Doty) [#583](https://github.com/UC-Davis-molecular-computing/scadnano/pull/583)
- [[c712bd9](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c712bd922b6644f24be9cedacbb64a8dacafe066)]: refactored response to Ctrl+C to use Actions (previously was doing hacky updates of member variable of view/Design class) (David Doty) [#593](https://github.com/UC-Davis-molecular-computing/scadnano/pull/593)
- [[6cc04b9](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6cc04b9a692dd07f1bf952f217012bd2cd86b1d1)]: closes #580; autopaste: paste strand with translation auto-calculated from last paste (David Doty) [593](https://github.com/UC-Davis-molecular-computing/scadnano/pull/593)
- [[da9cbd0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/da9cbd0eff9b33f83290811b3049c0942fb22d24)]: beefed up unit tests for autopaste to test that pasted strands are in correct positions (David Doty) [#593](https://github.com/UC-Davis-molecular-computing/scadnano/pull/593)
- [[1e59160](https://github.com/UC-Davis-molecular-computing/scadnano/commit/1e59160da82494d51b8af2a003a1fe2f6e394dd5)]: fixed bugs related to keeping strand color when autopasting, and a bad assertion when pasting that caused a crash if no copy was just done, and invalid behavior where copy buffer is unecessarily cleared when pressing Esc (David Doty) [#593](https://github.com/UC-Davis-molecular-computing/scadnano/pull/593)
- [[87e056a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/87e056a3a3102a5ccfb704b9586cf07b57038bc5)]: Update strands_copy_info_autopaste_reducer.dart (David Doty) [#593](https://github.com/UC-Davis-molecular-computing/scadnano/pull/593)
- [[972a7bc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/972a7bc440c903377f1a64e705b463e93a7397c4)]: fixed ability to paste strands from one HelixGroup into another (David Doty) [#593](https://github.com/UC-Davis-molecular-computing/scadnano/pull/593)
- [[3378553](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3378553c9ba038422676d50a64d5077b2b2efd7f)]: removed CopySelectedObjectTextToSystemClipboard action and just using CopySelectedStrands action now (David Doty) [#593](https://github.com/UC-Davis-molecular-computing/scadnano/pull/593)
- [[553dbe1](https://github.com/UC-Davis-molecular-computing/scadnano/commit/553dbe1c6d39649738d06a13d835e756fbeeaa74)]: fixed bug where strands could not be copied in rope select mode (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[4844b3a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4844b3a17669bda86d3c28f81643782047f1797a)]: Merge branch 'dev' into repeated-strand-paste-without-mouse-click (David Doty) [#593](https://github.com/UC-Davis-molecular-computing/scadnano/pull/593)
- [[2611e89](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2611e899846908ce76c0c345bb033e95920e669d)]: fixed bug where strand, domain, and loopout names altered with web interface were not being saved (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[25fa451](https://github.com/UC-Davis-molecular-computing/scadnano/commit/25fa4519069062c2d5d9cd34a91c3744485ef8a9)]: closes #590 ; paste strands from separate instance of scadnano (David Doty) [593](https://github.com/UC-Davis-molecular-computing/scadnano/pull/593)
- [[17d3a4f](https://github.com/UC-Davis-molecular-computing/scadnano/commit/17d3a4f8fe1ca6561129d4ad4abc18690b8bbedb)]: updated some comment docs in actions.dart (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)
- [[54951dd](https://github.com/UC-Davis-molecular-computing/scadnano/commit/54951dd971e44151be8166fb6707956d59d25bf8)]: fixed bug where DNA ends and HelixGroups could not be moved by dragging (David Doty) [#594](https://github.com/UC-Davis-molecular-computing/scadnano/pull/594)