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Allow creation of antisense chains in sequence mode #6252

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ljubica-milovic opened this issue Jan 10, 2025 · 0 comments
Open

Allow creation of antisense chains in sequence mode #6252

ljubica-milovic opened this issue Jan 10, 2025 · 0 comments
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Antisense Bucket: Antisense related issues Hydrogen bonds Bucket: Bugs related to Hydrogen bonds Sequence mode Bucket: Sequence mode related issues

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@ljubica-milovic
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ljubica-milovic commented Jan 10, 2025

Background

This ticket covers the creation of antisense chains in sequence mode.
Layout/representation of antisense chains in sequence mode is covered in the following ticket: #5942.

Requirements

  1. When appropriate monomers are selected right-clicking on the monomers should give a drop-down menu with the options of "Create RNA Antisense Strand" and "Create DNA Antisense Strand".

Appropriate selection described in ticket #5678.

1.1. When appropriate monomers are selected the "Create Antisense Strand" (issue: #5999) tool should be enabled.

1.2. If the selection of monomers in not appropriate the option in the drop-down menu, as well as the tool should be disabled.


  1. Options "Copy", "Paste" and "Delete" should be added to the r-click drop down menu:

2.1. When monomers are selected "Copy" will copy the selected monomers, "Paste" will replace them by the pasted monomers, and "Delete" will delete them.

2.2. R-clicking on a sequence when no monomers are selected "Copy", "Paste", and "Delete" should be disabled.

2.3. When r-clicking outside of the sequence "Copy" and "Delete" should be disabled, and "Paste" enabled.

Options "Establish Hydrogen Bonds" and "Delete Hydrogen Bonds" should also be added - covered in the scope of #6254 (requirements 1).


3.1. When "Create RNA/DNA Antisense Strand" is chosen from the drop-down menu or the "Create Antisense Strand" tool is used, the logic for creating the antisense chain in the same as for other modes, and already described in #5678 (requirements 2) for RNA and in #6383 for DNA.

3.2. Antisense and sense chains should be layouted following the logic described in #5942 (requirements 2 & 3).

3.3. If no other double-stranded sequences existed on the canvas before the creation of the new antisense chain, the sync icon should appear on the top bar and be enabled/toggled on by default #6254 (requirement 4).

UX

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@ljubica-milovic ljubica-milovic added feature request Sequence mode Bucket: Sequence mode related issues Hydrogen bonds Bucket: Bugs related to Hydrogen bonds labels Jan 10, 2025
@ljubica-milovic ljubica-milovic changed the title Allow creation of antisense chains in sequence mode Allow creation of antisense chains in sequence mode (1/2) Jan 10, 2025
@ljubica-milovic ljubica-milovic changed the title Allow creation of antisense chains in sequence mode (1/2) Allow creation of antisense chains in sequence mode Jan 10, 2025
@AlexeyGirin AlexeyGirin added the Antisense Bucket: Antisense related issues label Jan 24, 2025
@ljubica-milovic ljubica-milovic added this to the Ketcher 3.2.0-rc.1 milestone Jan 29, 2025
@NataliaLoginova NataliaLoginova self-assigned this Jan 30, 2025
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Labels
Antisense Bucket: Antisense related issues Hydrogen bonds Bucket: Bugs related to Hydrogen bonds Sequence mode Bucket: Sequence mode related issues
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