Scadnano

Release notes

Custom delimiters in exported DNA sequences
Added ability to control delimiter symbols in exported DNA sequence files, both delimiters between IDT fields (`;` in the example below) and between DNA sequences of different domains (`-` in the example below), e.g.,


Which exports this line to a file: `strand 1;/5Biosg/-AAAAAAAA-CCCC/ISp9/CCCC-GGGGGGGG;25nm;STD`.

Distinction between internal modifications that attach to a base, versus those between bases
Some internal modifications are attached to a base (e.g., internal biotin on a T: [`/iBiodT/`](https://www.idtdna.com/site/catalog/modifications/product/1105)) versus those that go in between bases (e.g., a spacer such as [`/ISp9/`](https://www.idtdna.com/site/catalog/modifications/product/1391)). Previously the web interface assumed all internal modifications are of the former type, and also assumed they could be attached to any base. Now in the web interface (as in the Python package), one can distinguish between these two types, and for modifications attached to a base, can specify a subset of bases that they can attach to (e.g., IDT's internal biotin may only be on a T base):



Commits
- d00fe82: bumped version (David Doty) [916](https://github.com/UC-Davis-molecular-computing/scadnano/pull/916)
- c219170: Update CONTRIBUTING.md (David Doty) [916](https://github.com/UC-Davis-molecular-computing/scadnano/pull/916)
- 0ef4f44: fixes 912: customize delimiter between domains in exported DNA sequences (David Doty) [914](https://github.com/UC-Davis-molecular-computing/scadnano/pull/914)
- c9698af: closes 913: handle internal modifications that go in between bases (David Doty) [915](https://github.com/UC-Davis-molecular-computing/scadnano/pull/915)
- eff3768: fixed edit mod dialog to account for base vs. linker (David Doty) [915](https://github.com/UC-Davis-molecular-computing/scadnano/pull/915)

Fixed (continuing) bug in helix roll relax algorithm to ignore intra-helix crossovers and inter-group crossovers.

Commits
- 0007983: bumped version (David Doty) [911](https://github.com/UC-Davis-molecular-computing/scadnano/pull/911)
- b82a8e9: fixes 906: fix warning about unique React keys (David Doty) [911](https://github.com/UC-Davis-molecular-computing/scadnano/pull/911)
- dd731bf: fixes null crash bug with showing newly created helix in newly created group (David Doty) [911](https://github.com/UC-Davis-molecular-computing/scadnano/pull/911)
- dbdf509: fixed null pointer bug in footer strand details (David Doty) [911](https://github.com/UC-Davis-molecular-computing/scadnano/pull/911)
- 663f28c: fixed helix roll relax algorithm to ignore intra-helix crossovers and inter-group crossovers (David Doty) [911](https://github.com/UC-Davis-molecular-computing/scadnano/pull/911)
- c940c72: formatting (David Doty) [911](https://github.com/UC-Davis-molecular-computing/scadnano/pull/911)

Bug fixes related to relaxing helix rolls.

Commits
- b1aca0e: bumped version (David Doty) [910](https://github.com/UC-Davis-molecular-computing/scadnano/pull/910)
- 2a8f685: Update menu.dart (David Doty) [910](https://github.com/UC-Davis-molecular-computing/scadnano/pull/910)
- 240c772: Update menu.dart (David Doty) [910](https://github.com/UC-Davis-molecular-computing/scadnano/pull/910)
- b85e234: added explanation of Ctrl+click for columns of insertions/deletions to tooltip text for those Edit Mode buttons (David Doty) [910](https://github.com/UC-Davis-molecular-computing/scadnano/pull/910)
- 98d9aec: fixed bug in relaxing helix rolls with intrahelix crossovers and added unit test for that case (David Doty) [910](https://github.com/UC-Davis-molecular-computing/scadnano/pull/910)
- 880194f: fixed relax helix rolls to ignore inter-group crossovers (David Doty) [910](https://github.com/UC-Davis-molecular-computing/scadnano/pull/910)

Fixed bugs in helix relax roll algorithm.

Commits
- 18bf88f: bumped version (David Doty) [909](https://github.com/UC-Davis-molecular-computing/scadnano/pull/909)
- fca783f: added (commented out) code for faster-rendering base pair lines, but that will not work when exporting selected strands to SVG (David Doty) [909](https://github.com/UC-Davis-molecular-computing/scadnano/pull/909)
- 30ffaca: fixed bug in relaxing helix rolls with loopouts (David Doty) [909](https://github.com/UC-Davis-molecular-computing/scadnano/pull/909)
- 4c65f2d: Update menu.dart (David Doty) [909](https://github.com/UC-Davis-molecular-computing/scadnano/pull/909)
- db57719: fixes 907: fix bug with relaxing helix rolls (David Doty) [908](https://github.com/UC-Davis-molecular-computing/scadnano/pull/908)

Release notes

Minor update re-arranging Edit menu.

Commits
- 060b609: bumped version (David Doty) [903](https://github.com/UC-Davis-molecular-computing/scadnano/pull/903)
- 3416b97: rearranged menu (David Doty) [903](https://github.com/UC-Davis-molecular-computing/scadnano/pull/903)
- e239f29: Update menu.dart (David Doty) [903](https://github.com/UC-Davis-molecular-computing/scadnano/pull/903)
- 6a5608c: Update menu.dart (David Doty) [903](https://github.com/UC-Davis-molecular-computing/scadnano/pull/903)

Release notes

automatically set Helix rolls based on crossover locations ("relax" the rolls)
In this design, the crossovers are well placed relative to each other, but the helix rolls need to be rotated. As the slice bar shows, with the default roll of 0, the crossovers do not point at the helices they connect to:



By selecting "Edit-->Helix rolls-->Set helix rolls to unstrain crossovers":


The helix rolls are set to minimize "strain" in the crossovers:



Formally, the strain is defined as the square of the angular distance between the "ideal" angle for the crossover (i.e., the relative angle of the other helix to which it is connecting) and the crossover's current angle. The roll is set so as to minimize this total strain across all crossovers in each helix.

The reason to minimize the sum of the squared angular distances is that, if we model each crossover as an angular spring exerting a rotational force on the helix proportional to its displacement from the "ideal" angle (pointing directly at the other helix), this minimizes the total energy stored in the springs.


Commits
- beb3335: Fixes 20, add shadow filter for domains (Benjamin Lee) [480](https://github.com/UC-Davis-molecular-computing/scadnano/pull/480)
- 8d0454d: Remove stopgap styling of domains on hover (Benjamin Lee) [480](https://github.com/UC-Davis-molecular-computing/scadnano/pull/480)
- e2d0d70: closes 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- fbe8e08: closes and fixes 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- 7435548: closes and fixes a typo in 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- 406b8bf: closes, updates, and fixes 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- 95e5a84: closes, updates, and fixes 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- 62160c5: closes additional changes in 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- f1c584f: closes and formats in 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- 5e0d8eb: closes again1 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- 7d28900: closes again2 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- 42d78d8: closes (finally) 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- 7c23d9c: closes (again) 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- 2dcee78: closes bug 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- f485b0d: closes the bug 849-give-more-useful-error-message-when-sc-file-format-is-incorrect (Pranav Gupta) [866](https://github.com/UC-Davis-molecular-computing/scadnano/pull/866)
- 77a4c54: bumped version (David Doty) [901](https://github.com/UC-Davis-molecular-computing/scadnano/pull/901)
- 87c3f10: added Helix.roll and backbond angles at slice bar position to side view Helix tooltip text (David Doty) [901](https://github.com/UC-Davis-molecular-computing/scadnano/pull/901)
- b4abdae: fixed setting helix roll saved response to be current value of roll (David Doty) [901](https://github.com/UC-Davis-molecular-computing/scadnano/pull/901)
- 4cdb3c4: changed modification Select Mode icon to have capital M instead of b (David Doty) [901](https://github.com/UC-Davis-molecular-computing/scadnano/pull/901)
- 68d7f50: implemented logic for relaxing helix rolls based on crossover locations (not in UI yet) (David Doty) [900](https://github.com/UC-Davis-molecular-computing/scadnano/pull/900)
- bb6db46: Update helix_relax_rolls_test.dart (David Doty) [900](https://github.com/UC-Davis-molecular-computing/scadnano/pull/900)
- 33a6702: more unit tests (David Doty) [900](https://github.com/UC-Davis-molecular-computing/scadnano/pull/900)
- e55eda9: closes 843: automatically set Helix rolls based on crossover locations ("relax" the rolls) (David Doty) [900](https://github.com/UC-Davis-molecular-computing/scadnano/pull/900)
- 6c15bb4: fixed bug with relaxing helix roll on helix with no crossovers and added unit test for that case (David Doty) [901](https://github.com/UC-Davis-molecular-computing/scadnano/pull/901)