Helix groups to help display rotated and translated sets of helices
==
This release adds a major feature: helix groups with their own position and orientation.
Many origami designs have helices that are not all parallel, but in the great majority of those, there are a few *groups* of helices, where within a group, the helices are all parallel. scadnano now supports displaying these groups separately in the cross-section side view, and displaying them at different positions and rotations in the main view.
Although scadnano will never be ideal for visualizing 3D designs, this feature should help to directly visualize most 2D designs (where all DNA helices lie in a plane).
Briefly, the three angles to describe the orientation of any object in 3D space are pitch, roll, and yaw. In each helix, the roll is its forward domain backbone angle at offset 0, which is displayed in the side view when the [slice bar](https://github.com/UC-Davis-molecular-computing/scadnano/releases/tag/v0.15.0) is enabled. **Update:** helices have their pitch and yaw fields removed. See https://github.com/UC-Davis-molecular-computing/scadnano-python-package/releases/tag/v0.16.0, https://github.com/UC-Davis-molecular-computing/scadnano/releases/tag/v0.16.0, https://github.com/UC-Davis-molecular-computing/scadnano/issues/597. Now these are only settable through helix groups.
Yaw corresponds to rotating "out of the screen" in the main view, and it is ignored by the scadnano web interface (though remains a field that is stored for compatibility with 3D modeling tools).
Pitch corresponds to rotating in the plane of the main view. Helices can now be placed into different groups, and each group has its own pitch, roll, yaw, and 3D (x,y,z) position. The default is that all helices are in the same group, called "default_group", with all these values set to 0.
You can create new groups, and each helix will be translated by the *z*- and *y*- coordinates of the group's position (the main view is the *z*-*y* plane), and in the main view, each helix will be rotated clockwise by the pitch angle of the group (specified in degrees). For example, the following design (inspired by https://www.nature.com/articles/nnano.2016.256) has four groups, at pitch angles 0, 90, 180, and 270:
The "west" group, with pitch 0, is shown in the side view.
Each group also has its own grid (e.g., if you want you can use the square grid on one group, the honeycomb grid on another, and no grid on a third) and helices_view_order.
Selected strands cannot be copied or moved if they occupy more than one group. (Note that even a single strand can occupy many groups, e.g., the scaffold above.) However, a selected set of strands can be copied/moved from one group to another.
See the [README](https://github.com/UC-Davis-molecular-computing/scadnano/tree/latest#readme) for documentation. Helix groups are also supported in the [Python scripting package](https://github.com/UC-Davis-molecular-computing/scadnano-python-package#readme)
Move group edit mode
==
One can set the position, as well as any other property, of a helix group through the new side view menu. However, one can also set the position using the new "move group" edit mode. In this mode, one can still pan the main view by clicking and dragging the background.
However, if you press the Shift or Ctrl key (Cmd on Mac), then clicking and dragging will move the helix group currently displayed in the side view, i.e., it will change its *z* and *y* coordinates. The *x* coordinate of the helix group, like the *yaw* angle, is there for compatibility with 3D modeling tools, but is ignored by the scadnano web interface, although the *x* coordinate of a *helix* using the *none* grid is displayed in the side view.
[**Note:** At the time of this release, the *x* and *z* coordinates were swapped so that *x* was horizontal in the main view, but they have been changed since then and now *z* is horizontal in the main view (and *x* horizontal in the side view): 488]
Note that there's currently no way to use the pointer to change the pitch angle; these are set by manually typing an angle in the `pitch` field after selected Group→adjust current group.
Moving groups of domains
==
Domains are now selectable and movable. They can also be deleted by selecting and pressing delete (deleting a 5' or 3' deletes the domain as well). The same rules as strands apply: a set of domains can only be moved if they all are in the same helix group, but they can be moved to another helix group.
Commits
- [[442b5a5](https://github.com/UC-Davis-molecular-computing/scadnano/commit/442b5a57d395342acd642326ebd2fc3e13739589)]: added note to README about security restrictions preventing saving the file (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[c01e89a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c01e89aa889a7ee6638e8630a5e028e4cafd8d8e)]: fixed README link to issue for saving problems in Chrome (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[1b9e834](https://github.com/UC-Davis-molecular-computing/scadnano/commit/1b9e834119eedc5dc4d126dd2f231ef5fca05194)]: fixed README link to issue, again (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[86415d2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/86415d26a4f4f3ed64fc88f9f96e2bfdccfdfe38)]: Update README.md (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[f3f031e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/f3f031e2890e066d2dc7f67c4fe6a6c5cec9ebef)]: unselect strands when switching out of select mode; closes #389 (rishabhmudradi) [406](https://github.com/UC-Davis-molecular-computing/scadnano/pull/406)
- [[9f70130](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9f70130605c239454f2d336245d61b10403b8965)]: Updating onClick code to be inline (rishabhmudradi) [#406](https://github.com/UC-Davis-molecular-computing/scadnano/pull/406)
- [[d3df5a4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d3df5a4899e3346cd5dedf1bbcdad6529c07e68e)]: added link to dev version in help menu (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[38d51b0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/38d51b01ad2e72c9c7277750f4d0ebd0cbc09216)]: fixed reducer_test call to old function name app_state_from_dna_design (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[2eab946](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2eab9468ae81890bd7df9b3101b39aaa4dd445ee)]: addresses issue #36 but does not fix it totally; helix idxs can now be changed one at a time, and not with a recalculation of view order until 407 is addressed (David Doty) [439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[23468d5](https://github.com/UC-Davis-molecular-computing/scadnano/commit/23468d5cc5569e604b9673ccb4a04515537b962d)]: added geometry as prop to many view components so crossovers are drawn correctly based on main SVG distance between helices (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[d5f22a7](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d5f22a72d4c8c0baab034c730ae8128026eed1fb)]: cleaned up imports (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[234961d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/234961daffb4150c57bbe7e298fa444a223bb322)]: updated README to promote "easy to read file format" as a major feature, and added link to section with example (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[e29da26](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e29da26d6a5cc8a6b9e88d041da5518c5c779636)]: noted that screenshot is annotated (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[84e37dd](https://github.com/UC-Davis-molecular-computing/scadnano/commit/84e37dd3488dae9a838da4971b316d8bce8cac6d)]: removed debugging print statement (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[f6a58cc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/f6a58ccabe53257741f1492a6966d75d422b6ef7)]: added unit tests for Helix groups and added group type to state/group.dart and groups field to Design (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[2a40c8b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2a40c8b8eb72b2bd3c7d5d2a80ce9fac6e678b73)]: enabled visual display of helix groups with positions and pitch specified, and ability to move/copy strands and move DNA ends within and between the groups (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[239ba41](https://github.com/UC-Davis-molecular-computing/scadnano/commit/239ba410de3da5b40bb6d1939f7aea8d3690e83e)]: updated helix position set based on crossover to disable only if all group grids are not None, and to show a pop-up warning on any group with a non-none grid (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[4af349e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4af349e6f8ee50d606642e8f57915365dd7469fa)]: fixed bugs with updating helices_view_order within a group after helix is added or removed (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[3414d94](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3414d9407174fa1b1d7f5c744d5ef2f6bbbb9f10)]: fixed bugs in storing and restoring localStorage; changed so that we automatically detect on each Action whether Design or AppUIStateStorables changed instead of requiring explicit subtyping of correct Action type (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[a334411](https://github.com/UC-Davis-molecular-computing/scadnano/commit/a334411823c652419bc1ccb9cf99ec8cfdd39f7e)]: fixed calculation of selection box intersection with selectable elements to work with translated and rotated helix groups (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[ff3a279](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ff3a2793019e0b847fb97bebefe111c6bb08bdd5)]: fixed depicting of strand being creating when drawing a strand with pencil mode to properly transform for helix group (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[75cab27](https://github.com/UC-Davis-molecular-computing/scadnano/commit/75cab27dc182a532da7255fe2470f3325d509d6d)]: fixed bug where exception was thrown when moving strand(s) from one helix group to another (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[2a406b6](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2a406b6ad2b47c875b3b8115538c85d22a6f37e7)]: fixed drawing of movign strand so loopouts look like loopouts and not like crossovers (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[e46f294](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e46f294413b9b19dca9de1dee5db147faec8860f)]: selected helices are stored in localStorage so that a design can be refreshed without losing this information (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[2aa4033](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2aa4033f8bc64d3afbfef89143c7999d2c8a8222)]: ensured that non-visible helices (unselected when only_display_selected_helices is true) are not used to calculate closest helix address when moving strands (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[4a2b6b2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4a2b6b2f45a6a449894c6aa2b4b5a1c75c2e49bf)]: fixed some unit tests related to helices groups and JSON parsing (David Doty) [#418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[88d63f4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/88d63f4a21ccab7679df5c7d23f5c48f39d87074)]: fixes #416; make bound Domains selectable and moveable (David Doty) [418](https://github.com/UC-Davis-molecular-computing/scadnano/pull/418)
- [[9a8a2f0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9a8a2f056bb22917fcb92fd0cb394ed004b8ca74)]: fixed run-time type error with creating lists using List.of instead of List.from (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[75a3886](https://github.com/UC-Davis-molecular-computing/scadnano/commit/75a388636b06834e3312c173b70f36461cc8d49f)]: updated README to document new features (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[7383529](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7383529b9af56b0a4c9dbc0b54fbe8eea0756810)]: fixes #421; allow to delete a group with helices in it (David Doty) [439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[cbd8d6b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/cbd8d6bb453736057881fee582b7314d94d04228)]: fixeds #423; fix crash when changing between grids in a helix group (David Doty) [439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[fb243fc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/fb243fcf970d4d8d9a26b99df672e8bb43ccc675)]: Adding StrandMaker class and tests. (rishabhmudradi) [#424](https://github.com/UC-Davis-molecular-computing/scadnano/pull/424)
- [[df20f99](https://github.com/UC-Davis-molecular-computing/scadnano/commit/df20f9974ff487f79068c495fc7ab30cde33e91b)]: fixed check for helices_view_order in "adjust helix group" interactive dialog (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[d46e533](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d46e5333bfb69d03042c843f9c3e095a610bf2d3)]: removed ability to change grid in "adjust group" dialog; made textfield for helices_view_order wide enough to fit existing helix index (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[0744aae](https://github.com/UC-Davis-molecular-computing/scadnano/commit/0744aae9bdae79a7490aef38e242a174e7ec5b73)]: added ability to set helix min and max offsets based on exist domains; separate min and max offset settings for context menu options for helix to (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[9ad2815](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9ad2815e921a19d0aba44a697b0bad9967b78c37)]: Adding helices to the Design constructor (rishabhmudradi) [#424](https://github.com/UC-Davis-molecular-computing/scadnano/pull/424)
- [[10fc885](https://github.com/UC-Davis-molecular-computing/scadnano/commit/10fc885e1a4f5be506600658430c7516841ee2f5)]: fixes #429; deletions and insertions not being translated and rotated correctly in helix groups (David Doty) [439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[ea12916](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ea129166fd66d6438b48d8320a8e51af383d3f19)]: Changing Design constructor to accept an Iterable of helices (rishabhmudradi) [#424](https://github.com/UC-Davis-molecular-computing/scadnano/pull/424)
- [[6f1c767](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6f1c7678e9312ec66e455a62b512c146df3ff81f)]: fixes #323: add menu items to edit Geometry (David Doty) [439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[3f6cf2e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3f6cf2ee477650400c88fbfade47ddfa56642181)]: added README documentation for editing geometric parameters in menu (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[1b8a511](https://github.com/UC-Davis-molecular-computing/scadnano/commit/1b8a511eeeb848cd63875a8d994344b0193da575)]: fixed unit tests that assumed geometry.inter_helix_gap=0.5 and bug where helix default_position was ignoring geometry inter_helix_gap parameter (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[a69d19d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/a69d19db168cfafda21e3f1a97c84fb95a954908)]: Changing Iterable helices to a List (rishabhmudradi) [#424](https://github.com/UC-Davis-molecular-computing/scadnano/pull/424)
- [[49cadb0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/49cadb076e02a2cbdb3d90b266a85d0bfa1046e7)]: fixed bug where mouseover information in backbone mode was not being properly displayed when helix groups are translated and rotated (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[471adac](https://github.com/UC-Davis-molecular-computing/scadnano/commit/471adac79e4f87d55b50683509ee73e8ca7712fe)]: fixes #409; fix bug where crossover backbone information is shown for incorrect helix when hiding helices (David Doty) [439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[d38441a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d38441a14f9308e55152dadd20304a2a1251de7d)]: only rendering potential vertical crossovers between displayed helices (in case some are hidden) (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[64f42f7](https://github.com/UC-Davis-molecular-computing/scadnano/commit/64f42f7cc8f7305241bb50b8c98b9931ce5f8ab9)]: closes #400; (actually closed several commits ago but I forgot to mention it) (David Doty) [439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[d47564b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d47564b3d43cdcb56641e49e1d3fc7ebe26744ab)]: fixes #431; fix bug where, if some helices are selected with "show only selected helices" display option on, and scadnano is restarted, helices are drawn in incorrect positions in main view when scadnano first starts (David Doty) [439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[5f49e6d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/5f49e6dccba80ae246273c89cd7697c281a7d938)]: fixes #430; fix side view helix display positions, and make them depend properly on geometry parameters; This commit also removes constants.BASE_WIDTH_SVG and constants.BASE_HEIGHT_SVG, and replaces them with appropriate references to a Geometry object for customizing in different designs. But font sizes are still "hard-coded" for the current default values, so it doesn't look good right now to set them much differently from the defaults. (David Doty) [439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[1ea8aa2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/1ea8aa2bdbd76f38931d6986b12cd72963194800)]: fixed unit tests that were referencing removed constants (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[a3a24a3](https://github.com/UC-Davis-molecular-computing/scadnano/commit/a3a24a3eb7be4dba8775588f23a7d1a5365de72e)]: increased font size of helix index in side view (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[a4f30f4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/a4f30f43d063dcd3d096acdccbe1d7e1e0947d35)]: updated origami cross tile example (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[5402461](https://github.com/UC-Davis-molecular-computing/scadnano/commit/5402461927d3288d79c42c8910cba91097d7dbc5)]: added actions and reducers (but not yet edit mode) for ability to click and drag helix groups to change position (David Doty) [#435](https://github.com/UC-Davis-molecular-computing/scadnano/pull/435)
- [[1b4cc32](https://github.com/UC-Davis-molecular-computing/scadnano/commit/1b4cc32edc58e0d32355af81f542fc8f5f1ea76e)]: fixed bug where backbone mode information was not being displayed on mouse hover over helix (David Doty) [#434](https://github.com/UC-Davis-molecular-computing/scadnano/pull/434)
- [[75e4256](https://github.com/UC-Davis-molecular-computing/scadnano/commit/75e4256374fd6a77875992b5a962529140319269)]: fixed bug with setting helix rolls based on crossovers; added some unit tests for these actions (David Doty) [#434](https://github.com/UC-Davis-molecular-computing/scadnano/pull/434)
- [[23e293d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/23e293dfdc96320b16f636370cffb5dd046239ed)]: closes #422; allow helix group position to be changed "visually" by clicking and dragging (David Doty) [435](https://github.com/UC-Davis-molecular-computing/scadnano/pull/435)
- [[e4c7da0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e4c7da0feca1116a7980cd36c1a68be85c18b38c)]: fixed bug in displaying DNA sequences when some helix groups are rotated and/or translated (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[8a355c7](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8a355c7503991156b6db7f2442a71efa55969b09)]: fixed bug in displaying DNA base mismatches in helix groups that were translated or rotated (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[0f6dbfe](https://github.com/UC-Davis-molecular-computing/scadnano/commit/0f6dbfeffc47cccb6700c5cde24cf31d0f07390b)]: fixed error when exporting SVG (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[cc2377b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/cc2377b3085b4b4b722d800d4edfed86617db1fc)]: items such as strands no longer show shadow filter effect on mouseover unless Select mode is on (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[f60fcc0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/f60fcc0ea033f9bff167b7238e3d642c17641bd2)]: fixed visual display of strands moving while being dragged (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[7b0173c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7b0173ce8687f6ecf27f677369b95ca4c24067b7)]: removed print statements (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)
- [[2ce6885](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2ce6885e94da9fad5331efd40b2cab276f0d56a0)]: turned off React DevTools (David Doty) [#439](https://github.com/UC-Davis-molecular-computing/scadnano/pull/439)